Starting phenix.real_space_refine on Sun Mar 10 23:22:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8v_13255/03_2024/7p8v_13255_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8v_13255/03_2024/7p8v_13255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8v_13255/03_2024/7p8v_13255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8v_13255/03_2024/7p8v_13255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8v_13255/03_2024/7p8v_13255_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8v_13255/03_2024/7p8v_13255_updated.pdb" } resolution = 3.6 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 41 5.49 5 Mg 2 5.21 5 S 16 5.16 5 C 3625 2.51 5 N 1108 2.21 5 O 1196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B ARG 264": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5988 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2601 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 13, 'TRANS': 317} Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2601 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 13, 'TRANS': 317} Chain: "C" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 458 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.91, per 1000 atoms: 0.65 Number of scatterers: 5988 At special positions: 0 Unit cell: (81.605, 73.015, 109.093, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 16 16.00 P 41 15.00 Mg 2 11.99 O 1196 8.00 N 1108 7.00 C 3625 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: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 4 sheets defined 35.6% alpha, 19.6% beta 12 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 8 through 19 removed outlier: 3.748A pdb=" N GLU A 18 " --> pdb=" O ILE A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 38 Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 97 through 104 Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.620A pdb=" N LYS A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 160' Processing helix chain 'A' and resid 164 through 181 Processing helix chain 'A' and resid 209 through 222 removed outlier: 7.471A pdb=" N THR A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N ALA A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 315 through 330 Processing helix chain 'B' and resid 8 through 19 removed outlier: 3.780A pdb=" N GLU B 18 " --> pdb=" O ILE B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 37 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 65 through 72 removed outlier: 4.151A pdb=" N ALA B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 164 through 181 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 315 through 330 Processing sheet with id= A, first strand: chain 'A' and resid 131 through 137 removed outlier: 3.726A pdb=" N ALA A 120 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 146 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR A 186 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE A 44 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASN A 188 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE A 46 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N SER A 190 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N HIS A 191 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE A 195 " --> pdb=" O HIS A 191 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 224 through 231 removed outlier: 3.671A pdb=" N GLY A 238 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 131 through 137 removed outlier: 3.644A pdb=" N ALA B 120 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA B 125 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU B 108 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR B 143 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG B 55 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR B 186 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE B 44 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN B 188 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE B 46 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N SER B 190 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 197 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N HIS B 191 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE B 195 " --> pdb=" O HIS B 191 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 224 through 230 removed outlier: 3.714A pdb=" N GLY B 238 " --> pdb=" O ILE B 227 " (cutoff:3.500A) 225 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 951 1.31 - 1.44: 1701 1.44 - 1.56: 3415 1.56 - 1.69: 78 1.69 - 1.82: 24 Bond restraints: 6169 Sorted by residual: bond pdb=" N3B ANP A 701 " pdb=" PG ANP A 701 " ideal model delta sigma weight residual 1.795 1.620 0.175 2.00e-02 2.50e+03 7.66e+01 bond pdb=" N3B ANP B 702 " pdb=" PG ANP B 702 " ideal model delta sigma weight residual 1.795 1.620 0.175 2.00e-02 2.50e+03 7.64e+01 bond pdb=" O3A ANP B 702 " pdb=" PB ANP B 702 " ideal model delta sigma weight residual 1.700 1.579 0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" O3A ANP A 701 " pdb=" PB ANP A 701 " ideal model delta sigma weight residual 1.700 1.589 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" O3G ANP A 701 " pdb=" PG ANP A 701 " ideal model delta sigma weight residual 1.528 1.424 0.104 2.00e-02 2.50e+03 2.73e+01 ... (remaining 6164 not shown) Histogram of bond angle deviations from ideal: 97.54 - 104.91: 228 104.91 - 112.29: 2956 112.29 - 119.67: 2949 119.67 - 127.04: 2243 127.04 - 134.42: 149 Bond angle restraints: 8525 Sorted by residual: angle pdb=" CA GLY B 127 " pdb=" C GLY B 127 " pdb=" O GLY B 127 " ideal model delta sigma weight residual 122.52 117.40 5.12 7.90e-01 1.60e+00 4.19e+01 angle pdb=" C GLN A 117 " pdb=" CA GLN A 117 " pdb=" CB GLN A 117 " ideal model delta sigma weight residual 109.54 120.67 -11.13 1.84e+00 2.95e-01 3.66e+01 angle pdb=" CA GLY A 127 " pdb=" C GLY A 127 " pdb=" O GLY A 127 " ideal model delta sigma weight residual 122.52 118.13 4.39 7.90e-01 1.60e+00 3.09e+01 angle pdb=" CA GLY A 217 " pdb=" C GLY A 217 " pdb=" O GLY A 217 " ideal model delta sigma weight residual 122.39 117.41 4.98 9.30e-01 1.16e+00 2.87e+01 angle pdb=" CA PRO A 7 " pdb=" C PRO A 7 " pdb=" O PRO A 7 " ideal model delta sigma weight residual 120.90 117.14 3.76 7.20e-01 1.93e+00 2.73e+01 ... (remaining 8520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.54: 3336 29.54 - 59.07: 312 59.07 - 88.60: 19 88.60 - 118.14: 1 118.14 - 147.67: 2 Dihedral angle restraints: 3670 sinusoidal: 1752 harmonic: 1918 Sorted by residual: dihedral pdb=" C GLN A 117 " pdb=" N GLN A 117 " pdb=" CA GLN A 117 " pdb=" CB GLN A 117 " ideal model delta harmonic sigma weight residual -122.60 -134.60 12.00 0 2.50e+00 1.60e-01 2.30e+01 dihedral pdb=" O1B ANP A 701 " pdb=" N3B ANP A 701 " pdb=" PB ANP A 701 " pdb=" PG ANP A 701 " ideal model delta sinusoidal sigma weight residual 35.15 -177.18 -147.67 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" O1A ANP B 702 " pdb=" O3A ANP B 702 " pdb=" PA ANP B 702 " pdb=" PB ANP B 702 " ideal model delta sinusoidal sigma weight residual 83.11 -46.03 129.14 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 3667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 354 0.061 - 0.121: 368 0.121 - 0.182: 186 0.182 - 0.242: 52 0.242 - 0.303: 6 Chirality restraints: 966 Sorted by residual: chirality pdb=" CA GLN A 117 " pdb=" N GLN A 117 " pdb=" C GLN A 117 " pdb=" CB GLN A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA LEU B 234 " pdb=" N LEU B 234 " pdb=" C LEU B 234 " pdb=" CB LEU B 234 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C3' ANP A 701 " pdb=" C2' ANP A 701 " pdb=" C4' ANP A 701 " pdb=" O3' ANP A 701 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 963 not shown) Planarity restraints: 983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 208 " -0.019 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C LYS A 208 " 0.068 2.00e-02 2.50e+03 pdb=" O LYS A 208 " -0.025 2.00e-02 2.50e+03 pdb=" N GLU A 209 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 163 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C THR A 163 " 0.055 2.00e-02 2.50e+03 pdb=" O THR A 163 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 164 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 185 " 0.014 2.00e-02 2.50e+03 2.93e-02 8.56e+00 pdb=" C VAL B 185 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL B 185 " 0.019 2.00e-02 2.50e+03 pdb=" N THR B 186 " 0.018 2.00e-02 2.50e+03 ... (remaining 980 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 834 2.81 - 3.33: 5843 3.33 - 3.85: 9536 3.85 - 4.38: 12683 4.38 - 4.90: 19297 Nonbonded interactions: 48193 Sorted by model distance: nonbonded pdb=" OD1 ASN A 33 " pdb="MG MG A 702 " model vdw 2.287 2.170 nonbonded pdb="MG MG B 701 " pdb=" O2B ANP B 702 " model vdw 2.320 2.170 nonbonded pdb=" OD1 ASN B 33 " pdb="MG MG B 701 " model vdw 2.337 2.170 nonbonded pdb=" O3G ANP A 701 " pdb="MG MG A 702 " model vdw 2.341 2.170 nonbonded pdb=" O1A ANP A 701 " pdb="MG MG A 702 " model vdw 2.374 2.170 ... (remaining 48188 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 1 through 331) selection = (chain 'B' and resid 1 through 331) } 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.670 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.940 Find NCS groups from input model: 0.360 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 : 0.013 0.175 6169 Z= 0.877 Angle : 1.812 12.797 8525 Z= 1.349 Chirality : 0.102 0.303 966 Planarity : 0.009 0.040 983 Dihedral : 20.306 147.672 2426 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.36 % Allowed : 7.85 % Favored : 91.79 % Cbeta Deviations : 0.16 % 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: -0.42 (0.31), residues: 658 helix: 1.02 (0.32), residues: 250 sheet: -0.83 (0.39), residues: 150 loop : -1.15 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP A 229 HIS 0.011 0.003 HIS B 170 PHE 0.031 0.005 PHE A 168 TYR 0.017 0.004 TYR A 257 ARG 0.013 0.002 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 143 THR cc_start: 0.9100 (m) cc_final: 0.8816 (p) REVERT: A 169 ASN cc_start: 0.8237 (m110) cc_final: 0.7878 (m110) REVERT: A 173 GLU cc_start: 0.7886 (tp30) cc_final: 0.7613 (tp30) REVERT: A 229 TRP cc_start: 0.8208 (t-100) cc_final: 0.7829 (t-100) REVERT: A 231 HIS cc_start: 0.6665 (t70) cc_final: 0.6349 (t70) REVERT: B 22 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7729 (mtm-85) REVERT: B 274 GLN cc_start: 0.7801 (mt0) cc_final: 0.7304 (tt0) outliers start: 2 outliers final: 0 residues processed: 78 average time/residue: 0.2086 time to fit residues: 20.9831 Evaluate side-chains 51 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6169 Z= 0.193 Angle : 0.567 7.529 8525 Z= 0.310 Chirality : 0.041 0.155 966 Planarity : 0.005 0.060 983 Dihedral : 21.036 138.460 1176 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.82 % Allowed : 14.05 % Favored : 84.12 % 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: 0.28 (0.33), residues: 658 helix: 1.56 (0.33), residues: 242 sheet: -0.49 (0.39), residues: 172 loop : -0.60 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 229 HIS 0.004 0.001 HIS B 308 PHE 0.015 0.002 PHE A 168 TYR 0.011 0.002 TYR B 124 ARG 0.006 0.001 ARG A 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.674 Fit side-chains REVERT: A 293 GLU cc_start: 0.7772 (tp30) cc_final: 0.7315 (tt0) outliers start: 10 outliers final: 7 residues processed: 66 average time/residue: 0.1839 time to fit residues: 16.3976 Evaluate side-chains 49 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 94 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6169 Z= 0.183 Angle : 0.511 6.573 8525 Z= 0.279 Chirality : 0.040 0.148 966 Planarity : 0.004 0.050 983 Dihedral : 20.630 129.870 1172 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.82 % Allowed : 17.88 % Favored : 80.29 % 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: 0.16 (0.34), residues: 658 helix: 1.52 (0.34), residues: 254 sheet: -0.59 (0.39), residues: 178 loop : -0.84 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 229 HIS 0.005 0.001 HIS B 308 PHE 0.015 0.002 PHE B 168 TYR 0.008 0.001 TYR B 291 ARG 0.008 0.000 ARG A 162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.690 Fit side-chains REVERT: A 45 ASP cc_start: 0.7821 (t0) cc_final: 0.7614 (t0) REVERT: A 167 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8199 (mt-10) REVERT: A 173 GLU cc_start: 0.8086 (tp30) cc_final: 0.7808 (tp30) REVERT: A 293 GLU cc_start: 0.7672 (tp30) cc_final: 0.7347 (tt0) outliers start: 10 outliers final: 7 residues processed: 61 average time/residue: 0.1759 time to fit residues: 14.7713 Evaluate side-chains 50 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 59 optimal weight: 0.0970 chunk 17 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6169 Z= 0.241 Angle : 0.513 6.700 8525 Z= 0.278 Chirality : 0.041 0.142 966 Planarity : 0.004 0.052 983 Dihedral : 20.573 133.868 1172 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.38 % Allowed : 16.42 % Favored : 79.20 % 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: 0.09 (0.34), residues: 658 helix: 1.46 (0.34), residues: 254 sheet: -0.67 (0.39), residues: 180 loop : -0.83 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 229 HIS 0.004 0.001 HIS B 308 PHE 0.021 0.002 PHE A 168 TYR 0.009 0.001 TYR B 291 ARG 0.003 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 48 time to evaluate : 0.615 Fit side-chains REVERT: A 173 GLU cc_start: 0.8096 (tp30) cc_final: 0.7810 (tp30) REVERT: A 293 GLU cc_start: 0.7693 (tp30) cc_final: 0.7321 (tt0) REVERT: B 128 ARG cc_start: 0.8425 (tpm170) cc_final: 0.8170 (tpm170) outliers start: 24 outliers final: 16 residues processed: 66 average time/residue: 0.2030 time to fit residues: 18.1944 Evaluate side-chains 60 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 6169 Z= 0.361 Angle : 0.591 6.370 8525 Z= 0.318 Chirality : 0.043 0.147 966 Planarity : 0.005 0.060 983 Dihedral : 20.708 142.544 1172 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 5.11 % Allowed : 16.61 % Favored : 78.28 % 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: -0.21 (0.34), residues: 658 helix: 1.22 (0.34), residues: 254 sheet: -0.81 (0.38), residues: 180 loop : -1.02 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 229 HIS 0.006 0.001 HIS B 170 PHE 0.027 0.003 PHE A 168 TYR 0.015 0.002 TYR B 291 ARG 0.006 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 43 time to evaluate : 0.708 Fit side-chains REVERT: A 293 GLU cc_start: 0.7775 (tp30) cc_final: 0.7348 (tt0) REVERT: B 128 ARG cc_start: 0.8521 (tpm170) cc_final: 0.8243 (tpm170) outliers start: 28 outliers final: 22 residues processed: 66 average time/residue: 0.1736 time to fit residues: 15.6945 Evaluate side-chains 63 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 41 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 55 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 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 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 ASN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6169 Z= 0.219 Angle : 0.498 6.342 8525 Z= 0.270 Chirality : 0.040 0.142 966 Planarity : 0.004 0.056 983 Dihedral : 20.364 134.758 1172 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.83 % Allowed : 17.88 % Favored : 78.28 % 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: -0.09 (0.34), residues: 658 helix: 1.24 (0.34), residues: 256 sheet: -0.65 (0.39), residues: 180 loop : -0.94 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 229 HIS 0.003 0.001 HIS B 308 PHE 0.015 0.002 PHE A 168 TYR 0.008 0.001 TYR B 124 ARG 0.003 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 47 time to evaluate : 0.603 Fit side-chains REVERT: A 173 GLU cc_start: 0.7988 (tp30) cc_final: 0.7623 (tp30) REVERT: A 293 GLU cc_start: 0.7733 (tp30) cc_final: 0.7339 (tt0) REVERT: B 128 ARG cc_start: 0.8522 (tpm170) cc_final: 0.8277 (tpm170) outliers start: 21 outliers final: 17 residues processed: 63 average time/residue: 0.1712 time to fit residues: 14.6104 Evaluate side-chains 61 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 44 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 26 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 0.0670 chunk 13 optimal weight: 20.0000 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN B 153 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6169 Z= 0.152 Angle : 0.469 7.618 8525 Z= 0.253 Chirality : 0.039 0.143 966 Planarity : 0.004 0.052 983 Dihedral : 20.022 127.875 1172 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.47 % Allowed : 18.98 % Favored : 77.55 % 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: 0.05 (0.34), residues: 658 helix: 1.29 (0.34), residues: 256 sheet: -0.46 (0.39), residues: 180 loop : -0.90 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 229 HIS 0.003 0.001 HIS B 308 PHE 0.019 0.002 PHE A 160 TYR 0.005 0.001 TYR B 124 ARG 0.005 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 53 time to evaluate : 0.606 Fit side-chains REVERT: A 167 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7923 (mt-10) REVERT: A 173 GLU cc_start: 0.7877 (tp30) cc_final: 0.7546 (tp30) REVERT: A 293 GLU cc_start: 0.7646 (tp30) cc_final: 0.7287 (tt0) REVERT: B 45 ASP cc_start: 0.7487 (m-30) cc_final: 0.6902 (t0) REVERT: B 128 ARG cc_start: 0.8543 (tpm170) cc_final: 0.8293 (tpm170) outliers start: 19 outliers final: 15 residues processed: 66 average time/residue: 0.1737 time to fit residues: 15.4494 Evaluate side-chains 62 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 47 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 0.6980 chunk 42 optimal weight: 0.0570 chunk 45 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6169 Z= 0.162 Angle : 0.467 7.548 8525 Z= 0.253 Chirality : 0.039 0.142 966 Planarity : 0.004 0.051 983 Dihedral : 19.990 128.647 1172 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.28 % Allowed : 20.62 % Favored : 76.09 % 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: 0.13 (0.34), residues: 658 helix: 1.34 (0.34), residues: 256 sheet: -0.39 (0.40), residues: 180 loop : -0.87 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.004 0.001 HIS B 308 PHE 0.011 0.001 PHE B 168 TYR 0.006 0.001 TYR B 124 ARG 0.007 0.000 ARG A 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 48 time to evaluate : 0.681 Fit side-chains REVERT: A 173 GLU cc_start: 0.7896 (tp30) cc_final: 0.7674 (tp30) REVERT: A 293 GLU cc_start: 0.7590 (tp30) cc_final: 0.7241 (tt0) REVERT: B 128 ARG cc_start: 0.8553 (tpm170) cc_final: 0.8258 (tpm170) REVERT: B 273 ARG cc_start: 0.8546 (mmt90) cc_final: 0.8281 (tpp-160) outliers start: 18 outliers final: 16 residues processed: 60 average time/residue: 0.2066 time to fit residues: 16.3957 Evaluate side-chains 62 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6169 Z= 0.192 Angle : 0.468 6.104 8525 Z= 0.255 Chirality : 0.039 0.138 966 Planarity : 0.004 0.051 983 Dihedral : 19.982 130.549 1172 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.47 % Allowed : 20.26 % Favored : 76.28 % 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: 0.15 (0.34), residues: 658 helix: 1.35 (0.34), residues: 256 sheet: -0.39 (0.40), residues: 180 loop : -0.84 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 229 HIS 0.003 0.001 HIS B 304 PHE 0.015 0.002 PHE A 168 TYR 0.006 0.001 TYR B 291 ARG 0.004 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 48 time to evaluate : 0.695 Fit side-chains REVERT: A 173 GLU cc_start: 0.7914 (tp30) cc_final: 0.7694 (tp30) REVERT: A 293 GLU cc_start: 0.7606 (tp30) cc_final: 0.7257 (tt0) REVERT: B 128 ARG cc_start: 0.8552 (tpm170) cc_final: 0.8248 (tpm170) REVERT: B 273 ARG cc_start: 0.8554 (mmt90) cc_final: 0.8290 (tpp-160) outliers start: 19 outliers final: 16 residues processed: 62 average time/residue: 0.1969 time to fit residues: 16.1932 Evaluate side-chains 61 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 0.0020 chunk 16 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6169 Z= 0.168 Angle : 0.474 6.821 8525 Z= 0.257 Chirality : 0.039 0.139 966 Planarity : 0.004 0.051 983 Dihedral : 19.899 128.734 1172 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.47 % Allowed : 20.62 % Favored : 75.91 % 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: 0.18 (0.34), residues: 658 helix: 1.37 (0.34), residues: 256 sheet: -0.35 (0.40), residues: 180 loop : -0.83 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 229 HIS 0.003 0.001 HIS A 308 PHE 0.011 0.001 PHE B 168 TYR 0.006 0.001 TYR B 124 ARG 0.005 0.000 ARG A 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 43 time to evaluate : 0.709 Fit side-chains REVERT: A 167 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7799 (mt-10) REVERT: A 173 GLU cc_start: 0.7880 (tp30) cc_final: 0.7658 (tp30) REVERT: A 293 GLU cc_start: 0.7582 (tp30) cc_final: 0.7248 (tt0) REVERT: B 128 ARG cc_start: 0.8562 (tpm170) cc_final: 0.8265 (tpm170) REVERT: B 273 ARG cc_start: 0.8540 (mmt90) cc_final: 0.8281 (tpp-160) outliers start: 19 outliers final: 17 residues processed: 57 average time/residue: 0.2092 time to fit residues: 15.7933 Evaluate side-chains 59 residues out of total 548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 42 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 256 CYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 323 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 0.1980 chunk 36 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.122103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.091733 restraints weight = 10102.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.094939 restraints weight = 5465.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.097058 restraints weight = 3675.421| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6169 Z= 0.198 Angle : 0.484 9.419 8525 Z= 0.262 Chirality : 0.039 0.138 966 Planarity : 0.005 0.124 983 Dihedral : 19.908 129.813 1172 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.47 % Allowed : 20.99 % Favored : 75.55 % 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: -0.02 (0.34), residues: 658 helix: 1.03 (0.34), residues: 270 sheet: -0.30 (0.41), residues: 168 loop : -0.97 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 229 HIS 0.003 0.001 HIS B 170 PHE 0.014 0.002 PHE A 168 TYR 0.008 0.001 TYR B 124 ARG 0.014 0.000 ARG A 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1477.34 seconds wall clock time: 27 minutes 38.70 seconds (1658.70 seconds total)