Starting phenix.real_space_refine on Wed Mar 4 09:06:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zms_11300/03_2026/6zms_11300.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zms_11300/03_2026/6zms_11300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zms_11300/03_2026/6zms_11300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zms_11300/03_2026/6zms_11300.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zms_11300/03_2026/6zms_11300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zms_11300/03_2026/6zms_11300.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 51 5.16 5 C 4031 2.51 5 N 1087 2.21 5 O 1228 1.98 5 H 6173 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12570 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 4236 Classifications: {'peptide': 271} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "B" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 3782 Classifications: {'peptide': 252} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 238} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3661 Classifications: {'peptide': 238} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 223} Chain: "D" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 891 Inner-chain residues flagged as termini: ['pdbres="GLY D 10 "', 'pdbres="ALA D 11 "'] Classifications: {'peptide': 57} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain breaks: 2 Time building chain proxies: 2.29, per 1000 atoms: 0.18 Number of scatterers: 12570 At special positions: 0 Unit cell: (90.52, 71.92, 107.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 O 1228 8.00 N 1087 7.00 C 4031 6.00 H 6173 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 397.1 milliseconds 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 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: 9 helices and 13 sheets defined 5.9% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 54 through 59 removed outlier: 3.604A pdb=" N LEU A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 99 removed outlier: 3.549A pdb=" N LYS A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.526A pdb=" N TRP A 153 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 155 " --> pdb=" O VAL A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 178 through 182 removed outlier: 3.550A pdb=" N LEU B 182 " --> pdb=" O VAL B 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 69 removed outlier: 3.546A pdb=" N TYR C 68 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG C 69 " --> pdb=" O GLU C 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 65 through 69' Processing helix chain 'C' and resid 144 through 149 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 removed outlier: 4.796A pdb=" N CYS C 212 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 23 Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 71 removed outlier: 5.654A pdb=" N CYS A 64 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N PHE A 231 " --> pdb=" O CYS A 64 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE A 66 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 184 removed outlier: 7.309A pdb=" N VAL A 240 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE A 104 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA A 238 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA A 238 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 164 Processing sheet with id=AA6, first strand: chain 'B' and resid 14 through 18 Processing sheet with id=AA7, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.537A pdb=" N VAL B 32 " --> pdb=" O VAL B 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.537A pdb=" N VAL B 32 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE B 239 " --> pdb=" O TRP B 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 82 removed outlier: 3.783A pdb=" N PHE B 219 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS B 121 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLN B 119 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 99 through 105 removed outlier: 4.676A pdb=" N HIS B 99 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY B 254 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU B 101 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR B 252 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ARG B 103 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 250 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 81 through 86 removed outlier: 7.492A pdb=" N GLN C 81 " --> pdb=" O TYR C 194 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TYR C 194 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE C 83 " --> pdb=" O CYS C 192 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 107 through 111 removed outlier: 6.208A pdb=" N TYR C 107 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU C 225 " --> pdb=" O TYR C 107 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 6 141 hydrogen bonds defined for protein. 348 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 6154 1.13 - 1.31: 1052 1.31 - 1.48: 2756 1.48 - 1.65: 2685 1.65 - 1.83: 83 Bond restraints: 12730 Sorted by residual: bond pdb=" N ILE D 23 " pdb=" H ILE D 23 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.11e+01 bond pdb=" CE1 HIS A 117 " pdb=" HE1 HIS A 117 " ideal model delta sigma weight residual 0.930 1.089 -0.159 2.00e-02 2.50e+03 6.34e+01 bond pdb=" CE1 HIS B 118 " pdb=" HE1 HIS B 118 " ideal model delta sigma weight residual 0.930 1.089 -0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" CE1 HIS B 99 " pdb=" HE1 HIS B 99 " ideal model delta sigma weight residual 0.930 1.089 -0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" CE1 HIS A 43 " pdb=" HE1 HIS A 43 " ideal model delta sigma weight residual 0.930 1.089 -0.159 2.00e-02 2.50e+03 6.33e+01 ... (remaining 12725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 20212 2.85 - 5.71: 2508 5.71 - 8.56: 140 8.56 - 11.41: 4 11.41 - 14.27: 19 Bond angle restraints: 22883 Sorted by residual: angle pdb=" N ILE C 103 " pdb=" CA ILE C 103 " pdb=" C ILE C 103 " ideal model delta sigma weight residual 113.20 104.17 9.03 9.60e-01 1.09e+00 8.86e+01 angle pdb=" N PHE D 52 " pdb=" CA PHE D 52 " pdb=" C PHE D 52 " ideal model delta sigma weight residual 114.31 105.72 8.59 1.29e+00 6.01e-01 4.43e+01 angle pdb=" CA PRO A 139 " pdb=" C PRO A 139 " pdb=" O PRO A 139 " ideal model delta sigma weight residual 120.90 116.18 4.72 7.20e-01 1.93e+00 4.29e+01 angle pdb=" N GLU A 26 " pdb=" CA GLU A 26 " pdb=" C GLU A 26 " ideal model delta sigma weight residual 112.94 103.92 9.02 1.41e+00 5.03e-01 4.09e+01 angle pdb=" CA PHE C 118 " pdb=" CB PHE C 118 " pdb=" CG PHE C 118 " ideal model delta sigma weight residual 113.80 107.51 6.29 1.00e+00 1.00e+00 3.96e+01 ... (remaining 22878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5680 17.95 - 35.90: 208 35.90 - 53.85: 90 53.85 - 71.81: 132 71.81 - 89.76: 10 Dihedral angle restraints: 6120 sinusoidal: 3273 harmonic: 2847 Sorted by residual: dihedral pdb=" CA VAL A 255 " pdb=" C VAL A 255 " pdb=" N ASN A 256 " pdb=" CA ASN A 256 " ideal model delta harmonic sigma weight residual 180.00 -154.28 -25.72 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ILE A 66 " pdb=" C ILE A 66 " pdb=" N TYR A 67 " pdb=" CA TYR A 67 " ideal model delta harmonic sigma weight residual 180.00 155.20 24.80 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ALA D 11 " pdb=" C ALA D 11 " pdb=" N HIS D 12 " pdb=" CA HIS D 12 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 6117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 719 0.098 - 0.196: 230 0.196 - 0.294: 28 0.294 - 0.391: 7 0.391 - 0.489: 3 Chirality restraints: 987 Sorted by residual: chirality pdb=" CA THR A 41 " pdb=" N THR A 41 " pdb=" C THR A 41 " pdb=" CB THR A 41 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CA THR A 155 " pdb=" N THR A 155 " pdb=" C THR A 155 " pdb=" CB THR A 155 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" CA GLN C 27 " pdb=" N GLN C 27 " pdb=" C GLN C 27 " pdb=" CB GLN C 27 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.95e+00 ... (remaining 984 not shown) Planarity restraints: 1928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 12 " -0.161 2.00e-02 2.50e+03 8.34e-02 1.57e+02 pdb=" CG HIS D 12 " 0.131 2.00e-02 2.50e+03 pdb=" ND1 HIS D 12 " 0.076 2.00e-02 2.50e+03 pdb=" CD2 HIS D 12 " 0.059 2.00e-02 2.50e+03 pdb=" CE1 HIS D 12 " -0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS D 12 " -0.033 2.00e-02 2.50e+03 pdb=" HD1 HIS D 12 " 0.038 2.00e-02 2.50e+03 pdb=" HD2 HIS D 12 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 HIS D 12 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 153 " -0.136 2.00e-02 2.50e+03 5.82e-02 1.35e+02 pdb=" CG TRP A 153 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 153 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 153 " 0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP A 153 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TRP A 153 " 0.063 2.00e-02 2.50e+03 pdb=" CE3 TRP A 153 " 0.062 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 153 " 0.022 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 153 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A 153 " -0.033 2.00e-02 2.50e+03 pdb=" HD1 TRP A 153 " -0.055 2.00e-02 2.50e+03 pdb=" HE1 TRP A 153 " 0.020 2.00e-02 2.50e+03 pdb=" HE3 TRP A 153 " 0.066 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 153 " -0.009 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 153 " -0.021 2.00e-02 2.50e+03 pdb=" HH2 TRP A 153 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 185 " 0.154 2.00e-02 2.50e+03 6.67e-02 1.33e+02 pdb=" CG TYR B 185 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR B 185 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR B 185 " -0.053 2.00e-02 2.50e+03 pdb=" CE1 TYR B 185 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR B 185 " -0.043 2.00e-02 2.50e+03 pdb=" CZ TYR B 185 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 185 " 0.135 2.00e-02 2.50e+03 pdb=" HD1 TYR B 185 " -0.017 2.00e-02 2.50e+03 pdb=" HD2 TYR B 185 " -0.019 2.00e-02 2.50e+03 pdb=" HE1 TYR B 185 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 TYR B 185 " -0.010 2.00e-02 2.50e+03 ... (remaining 1925 not shown) Histogram of nonbonded interaction distances: 1.28 - 1.95: 119 1.95 - 2.61: 13096 2.61 - 3.27: 37617 3.27 - 3.94: 50623 3.94 - 4.60: 76602 Nonbonded interactions: 178057 Sorted by model distance: nonbonded pdb=" H LYS D 51 " pdb=" H PHE D 52 " model vdw 1.283 2.100 nonbonded pdb=" H ALA C 91 " pdb=" H SER C 92 " model vdw 1.363 2.100 nonbonded pdb=" H ALA A 73 " pdb=" H GLU A 74 " model vdw 1.399 2.100 nonbonded pdb=" H ALA C 139 " pdb=" H GLY C 140 " model vdw 1.407 2.100 nonbonded pdb=" H MET C 78 " pdb=" H GLY C 79 " model vdw 1.413 2.100 ... (remaining 178052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.190 Find NCS groups from input model: 0.050 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 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 : 0.019 0.061 6557 Z= 1.288 Angle : 1.985 9.499 8935 Z= 1.332 Chirality : 0.098 0.489 987 Planarity : 0.014 0.097 1163 Dihedral : 14.128 89.757 2360 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 0.32 Ramachandran Plot: Outliers : 2.98 % Allowed : 5.58 % Favored : 91.44 % Rotamer: Outliers : 2.12 % Allowed : 3.95 % Favored : 93.94 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.24), residues: 806 helix: -4.10 (0.49), residues: 51 sheet: -1.39 (0.31), residues: 219 loop : -2.00 (0.21), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 95 TYR 0.144 0.020 TYR B 185 PHE 0.042 0.010 PHE C 120 TRP 0.095 0.019 TRP A 153 HIS 0.008 0.002 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.01870 ( 6557) covalent geometry : angle 1.98480 ( 8935) hydrogen bonds : bond 0.25007 ( 121) hydrogen bonds : angle 10.08272 ( 348) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 270 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7138 (mtt180) cc_final: 0.6716 (ttp-170) REVERT: A 226 THR cc_start: 0.7709 (t) cc_final: 0.7464 (t) REVERT: B 195 ASN cc_start: 0.7485 (p0) cc_final: 0.7272 (p0) REVERT: C 149 MET cc_start: 0.6419 (pp-130) cc_final: 0.6133 (pp-130) REVERT: D 7 GLN cc_start: 0.5299 (mt0) cc_final: 0.4743 (mm-40) outliers start: 15 outliers final: 7 residues processed: 277 average time/residue: 0.1549 time to fit residues: 59.2288 Evaluate side-chains 213 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 206 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 59 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 125 ASN A 131 GLN A 154 GLN B 30 ASN B 119 GLN B 206 ASN C 20 GLN C 27 GLN C 35 ASN C 42 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.112817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.097939 restraints weight = 32426.148| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.88 r_work: 0.3019 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 6557 Z= 0.266 Angle : 0.818 6.751 8935 Z= 0.446 Chirality : 0.052 0.185 987 Planarity : 0.007 0.052 1163 Dihedral : 7.597 76.720 903 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.83 % Favored : 93.55 % Rotamer: Outliers : 3.39 % Allowed : 12.83 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.25), residues: 806 helix: -4.57 (0.40), residues: 52 sheet: -0.65 (0.35), residues: 196 loop : -1.82 (0.22), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 62 TYR 0.035 0.002 TYR A 67 PHE 0.017 0.002 PHE C 236 TRP 0.022 0.002 TRP B 80 HIS 0.009 0.002 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00612 ( 6557) covalent geometry : angle 0.81825 ( 8935) hydrogen bonds : bond 0.04292 ( 121) hydrogen bonds : angle 6.31354 ( 348) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8593 (mt-10) REVERT: A 79 LYS cc_start: 0.7573 (mmmm) cc_final: 0.7178 (mmmm) REVERT: A 108 MET cc_start: 0.9012 (mmt) cc_final: 0.8562 (mmt) REVERT: A 109 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8138 (mt-10) REVERT: A 132 THR cc_start: 0.9238 (OUTLIER) cc_final: 0.9007 (m) REVERT: A 171 ARG cc_start: 0.8527 (ptp-170) cc_final: 0.6426 (ptt-90) REVERT: A 188 ASP cc_start: 0.9152 (t0) cc_final: 0.8895 (t0) REVERT: A 251 LYS cc_start: 0.8333 (mmtm) cc_final: 0.7997 (mmmm) REVERT: B 50 GLU cc_start: 0.4453 (pm20) cc_final: 0.3525 (pm20) REVERT: B 72 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7754 (mt-10) REVERT: B 74 GLN cc_start: 0.8650 (mp10) cc_final: 0.8433 (mm-40) REVERT: B 121 CYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8552 (m) REVERT: B 131 GLU cc_start: 0.8881 (tt0) cc_final: 0.8630 (tt0) REVERT: B 138 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8483 (mm-30) REVERT: B 150 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8063 (mt-10) REVERT: B 156 GLU cc_start: 0.7607 (tp30) cc_final: 0.7170 (tp30) REVERT: B 211 ASP cc_start: 0.7928 (t0) cc_final: 0.7631 (t0) REVERT: B 230 ASP cc_start: 0.9167 (t0) cc_final: 0.8895 (t0) REVERT: B 256 ARG cc_start: 0.6750 (pmt-80) cc_final: 0.4176 (mtt-85) REVERT: C 73 ARG cc_start: 0.7851 (ptm-80) cc_final: 0.7240 (ptt-90) REVERT: C 113 SER cc_start: 0.8728 (m) cc_final: 0.8442 (p) REVERT: D 7 GLN cc_start: 0.8772 (mt0) cc_final: 0.6306 (mm-40) REVERT: D 8 LYS cc_start: 0.8845 (tptt) cc_final: 0.6583 (mtpt) REVERT: D 30 ASN cc_start: 0.9226 (m-40) cc_final: 0.8740 (m-40) outliers start: 24 outliers final: 14 residues processed: 234 average time/residue: 0.1635 time to fit residues: 51.4163 Evaluate side-chains 216 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.098725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.083532 restraints weight = 33641.028| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.90 r_work: 0.2823 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.6354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6557 Z= 0.208 Angle : 0.589 4.789 8935 Z= 0.321 Chirality : 0.045 0.150 987 Planarity : 0.005 0.052 1163 Dihedral : 6.168 49.971 896 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.07 % Favored : 92.43 % Rotamer: Outliers : 3.24 % Allowed : 15.66 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.26), residues: 806 helix: -4.36 (0.43), residues: 52 sheet: -0.39 (0.36), residues: 216 loop : -1.81 (0.23), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 12 TYR 0.018 0.001 TYR A 67 PHE 0.015 0.001 PHE A 257 TRP 0.018 0.002 TRP B 80 HIS 0.005 0.001 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 6557) covalent geometry : angle 0.58879 ( 8935) hydrogen bonds : bond 0.04504 ( 121) hydrogen bonds : angle 5.58226 ( 348) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.7953 (mmmm) cc_final: 0.7517 (mmmm) REVERT: A 108 MET cc_start: 0.9034 (mmt) cc_final: 0.8565 (mmt) REVERT: A 119 GLU cc_start: 0.7345 (pt0) cc_final: 0.7050 (pt0) REVERT: A 137 TYR cc_start: 0.9396 (t80) cc_final: 0.9183 (t80) REVERT: A 152 VAL cc_start: 0.8680 (t) cc_final: 0.8406 (t) REVERT: A 251 LYS cc_start: 0.8362 (mmtm) cc_final: 0.8080 (mmmm) REVERT: B 72 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7780 (mt-10) REVERT: B 131 GLU cc_start: 0.8929 (tt0) cc_final: 0.8655 (tt0) REVERT: B 132 MET cc_start: 0.9474 (mmm) cc_final: 0.9104 (mmm) REVERT: B 138 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8670 (mm-30) REVERT: B 145 ASP cc_start: 0.8353 (m-30) cc_final: 0.7957 (m-30) REVERT: B 222 MET cc_start: 0.9330 (OUTLIER) cc_final: 0.9056 (mtt) REVERT: B 256 ARG cc_start: 0.7837 (pmt-80) cc_final: 0.5156 (mtt180) REVERT: C 33 GLU cc_start: 0.6803 (pm20) cc_final: 0.6529 (pm20) REVERT: D 8 LYS cc_start: 0.9067 (tptt) cc_final: 0.6958 (mtpt) outliers start: 23 outliers final: 15 residues processed: 203 average time/residue: 0.1656 time to fit residues: 45.1199 Evaluate side-chains 193 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 55 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.096451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.081513 restraints weight = 33307.503| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.81 r_work: 0.2761 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.7099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6557 Z= 0.144 Angle : 0.537 4.685 8935 Z= 0.287 Chirality : 0.044 0.156 987 Planarity : 0.004 0.044 1163 Dihedral : 5.538 40.628 896 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.46 % Favored : 94.04 % Rotamer: Outliers : 2.96 % Allowed : 15.09 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.27), residues: 806 helix: -4.19 (0.46), residues: 50 sheet: -0.20 (0.35), residues: 221 loop : -1.80 (0.23), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 266 TYR 0.021 0.001 TYR A 67 PHE 0.013 0.001 PHE A 257 TRP 0.015 0.001 TRP B 80 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6557) covalent geometry : angle 0.53661 ( 8935) hydrogen bonds : bond 0.03543 ( 121) hydrogen bonds : angle 5.19320 ( 348) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 HIS cc_start: 0.8809 (t70) cc_final: 0.8528 (t70) REVERT: A 79 LYS cc_start: 0.8118 (mmmm) cc_final: 0.7796 (mmmm) REVERT: A 108 MET cc_start: 0.9024 (mmt) cc_final: 0.8558 (mmt) REVERT: A 119 GLU cc_start: 0.7390 (pt0) cc_final: 0.6975 (pt0) REVERT: A 137 TYR cc_start: 0.9394 (t80) cc_final: 0.9159 (t80) REVERT: A 152 VAL cc_start: 0.8787 (t) cc_final: 0.8540 (t) REVERT: A 251 LYS cc_start: 0.8438 (mmtm) cc_final: 0.8113 (mmmm) REVERT: B 89 MET cc_start: 0.8816 (mmm) cc_final: 0.8349 (mmm) REVERT: B 138 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8714 (mm-30) REVERT: B 145 ASP cc_start: 0.8276 (m-30) cc_final: 0.7889 (m-30) REVERT: B 156 GLU cc_start: 0.7854 (tp30) cc_final: 0.7568 (tp30) REVERT: B 222 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.9077 (mtt) REVERT: B 256 ARG cc_start: 0.7951 (pmt-80) cc_final: 0.5189 (mtt-85) REVERT: C 33 GLU cc_start: 0.6573 (pm20) cc_final: 0.6284 (pm20) REVERT: C 57 ASN cc_start: 0.9043 (p0) cc_final: 0.8766 (p0) REVERT: C 125 MET cc_start: 0.9183 (mmm) cc_final: 0.8884 (mmm) REVERT: C 210 ILE cc_start: 0.9054 (mm) cc_final: 0.8841 (mm) REVERT: D 8 LYS cc_start: 0.9196 (tptt) cc_final: 0.7336 (mtmt) outliers start: 21 outliers final: 18 residues processed: 192 average time/residue: 0.1706 time to fit residues: 44.0489 Evaluate side-chains 196 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 32 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 4 optimal weight: 0.4980 chunk 64 optimal weight: 10.0000 chunk 1 optimal weight: 0.0020 chunk 19 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 overall best weight: 4.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.090262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.075694 restraints weight = 34207.951| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.76 r_work: 0.2665 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.8027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6557 Z= 0.233 Angle : 0.573 4.962 8935 Z= 0.308 Chirality : 0.045 0.159 987 Planarity : 0.005 0.046 1163 Dihedral : 5.550 46.610 896 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.68 % Favored : 90.94 % Rotamer: Outliers : 3.67 % Allowed : 16.36 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.27), residues: 806 helix: -4.02 (0.50), residues: 50 sheet: -0.06 (0.36), residues: 217 loop : -1.89 (0.23), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 11 TYR 0.016 0.001 TYR C 194 PHE 0.016 0.001 PHE A 257 TRP 0.016 0.001 TRP B 80 HIS 0.006 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 6557) covalent geometry : angle 0.57289 ( 8935) hydrogen bonds : bond 0.04440 ( 121) hydrogen bonds : angle 5.16029 ( 348) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9256 (m-30) cc_final: 0.8966 (m-30) REVERT: A 79 LYS cc_start: 0.8675 (mmmm) cc_final: 0.8404 (mmmm) REVERT: A 119 GLU cc_start: 0.7782 (pt0) cc_final: 0.7299 (pt0) REVERT: A 152 VAL cc_start: 0.9108 (t) cc_final: 0.8819 (t) REVERT: A 177 MET cc_start: 0.8878 (ptm) cc_final: 0.8113 (ppp) REVERT: A 207 MET cc_start: 0.9135 (mmm) cc_final: 0.8908 (tpp) REVERT: B 50 GLU cc_start: 0.5070 (OUTLIER) cc_final: 0.2902 (tp30) REVERT: B 72 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8072 (mt-10) REVERT: B 145 ASP cc_start: 0.8390 (m-30) cc_final: 0.8088 (m-30) REVERT: B 156 GLU cc_start: 0.8069 (tp30) cc_final: 0.7783 (tp30) REVERT: B 185 TYR cc_start: 0.9080 (m-80) cc_final: 0.8876 (m-80) REVERT: B 222 MET cc_start: 0.9388 (OUTLIER) cc_final: 0.9173 (mtt) REVERT: C 33 GLU cc_start: 0.6659 (pm20) cc_final: 0.6300 (pm20) REVERT: C 66 GLU cc_start: 0.8602 (tp30) cc_final: 0.7971 (tp30) REVERT: C 125 MET cc_start: 0.9333 (mmm) cc_final: 0.9092 (mmm) REVERT: C 160 LEU cc_start: 0.9112 (mp) cc_final: 0.8726 (tp) REVERT: D 8 LYS cc_start: 0.9459 (tptt) cc_final: 0.7462 (mtmt) REVERT: D 28 ASN cc_start: 0.8731 (t0) cc_final: 0.8344 (t0) outliers start: 26 outliers final: 18 residues processed: 180 average time/residue: 0.1711 time to fit residues: 41.2653 Evaluate side-chains 168 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 12 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 65 optimal weight: 0.0370 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 248 GLN B 109 HIS C 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.091750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.077199 restraints weight = 33739.761| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.79 r_work: 0.2716 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.8250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6557 Z= 0.116 Angle : 0.516 7.891 8935 Z= 0.269 Chirality : 0.043 0.152 987 Planarity : 0.004 0.043 1163 Dihedral : 5.336 51.413 896 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.45 % Favored : 93.18 % Rotamer: Outliers : 2.68 % Allowed : 17.21 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.27), residues: 806 helix: -4.00 (0.50), residues: 50 sheet: -0.00 (0.35), residues: 225 loop : -1.78 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 12 TYR 0.018 0.001 TYR A 67 PHE 0.014 0.001 PHE A 257 TRP 0.012 0.001 TRP B 80 HIS 0.017 0.001 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6557) covalent geometry : angle 0.51609 ( 8935) hydrogen bonds : bond 0.03508 ( 121) hydrogen bonds : angle 4.95233 ( 348) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9149 (m-30) cc_final: 0.8877 (m-30) REVERT: A 79 LYS cc_start: 0.8672 (mmmm) cc_final: 0.8394 (mmmm) REVERT: A 93 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8389 (mm-40) REVERT: A 119 GLU cc_start: 0.7763 (pt0) cc_final: 0.7338 (pt0) REVERT: A 131 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8727 (mm-40) REVERT: A 152 VAL cc_start: 0.8997 (t) cc_final: 0.8699 (t) REVERT: A 177 MET cc_start: 0.8831 (ptm) cc_final: 0.8078 (ppp) REVERT: B 12 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.8027 (mmm-85) REVERT: B 50 GLU cc_start: 0.4846 (OUTLIER) cc_final: 0.2780 (tp30) REVERT: B 72 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8096 (mt-10) REVERT: B 145 ASP cc_start: 0.8359 (m-30) cc_final: 0.8055 (m-30) REVERT: B 156 GLU cc_start: 0.7982 (tp30) cc_final: 0.7695 (tp30) REVERT: C 33 GLU cc_start: 0.6629 (pm20) cc_final: 0.6289 (pm20) REVERT: C 66 GLU cc_start: 0.8545 (tp30) cc_final: 0.8326 (tp30) REVERT: C 160 LEU cc_start: 0.9106 (mp) cc_final: 0.8735 (tp) REVERT: D 8 LYS cc_start: 0.9475 (tptt) cc_final: 0.7484 (mttt) REVERT: D 28 ASN cc_start: 0.8741 (t0) cc_final: 0.8340 (t0) outliers start: 19 outliers final: 15 residues processed: 164 average time/residue: 0.1796 time to fit residues: 39.0618 Evaluate side-chains 164 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 0.0570 chunk 78 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 overall best weight: 2.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.091022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.076612 restraints weight = 33740.259| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.76 r_work: 0.2687 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.8369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6557 Z= 0.136 Angle : 0.504 3.992 8935 Z= 0.264 Chirality : 0.043 0.149 987 Planarity : 0.004 0.052 1163 Dihedral : 5.189 49.820 896 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.69 % Favored : 91.94 % Rotamer: Outliers : 2.40 % Allowed : 17.35 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.27), residues: 806 helix: -4.05 (0.48), residues: 50 sheet: 0.01 (0.35), residues: 225 loop : -1.75 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 73 TYR 0.015 0.001 TYR A 67 PHE 0.015 0.001 PHE A 257 TRP 0.011 0.001 TRP B 80 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6557) covalent geometry : angle 0.50407 ( 8935) hydrogen bonds : bond 0.03472 ( 121) hydrogen bonds : angle 4.88328 ( 348) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9078 (m-30) cc_final: 0.8800 (m-30) REVERT: A 60 CYS cc_start: 0.9232 (t) cc_final: 0.8574 (t) REVERT: A 79 LYS cc_start: 0.8699 (mmmm) cc_final: 0.8414 (mmmm) REVERT: A 119 GLU cc_start: 0.7771 (pt0) cc_final: 0.7312 (pt0) REVERT: A 131 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8715 (mm-40) REVERT: A 152 VAL cc_start: 0.9036 (t) cc_final: 0.8771 (t) REVERT: A 177 MET cc_start: 0.8874 (ptm) cc_final: 0.8025 (ppp) REVERT: B 50 GLU cc_start: 0.4843 (OUTLIER) cc_final: 0.2681 (tp30) REVERT: B 72 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8092 (mt-10) REVERT: B 145 ASP cc_start: 0.8279 (m-30) cc_final: 0.7977 (m-30) REVERT: B 230 ASP cc_start: 0.9143 (t0) cc_final: 0.8862 (t0) REVERT: C 33 GLU cc_start: 0.6580 (pm20) cc_final: 0.6254 (pm20) REVERT: C 66 GLU cc_start: 0.8520 (tp30) cc_final: 0.8275 (tp30) REVERT: C 160 LEU cc_start: 0.9103 (mp) cc_final: 0.8728 (tp) REVERT: C 227 ASP cc_start: 0.7849 (m-30) cc_final: 0.7441 (m-30) REVERT: D 8 LYS cc_start: 0.9479 (tptt) cc_final: 0.7535 (mttt) REVERT: D 28 ASN cc_start: 0.8724 (t0) cc_final: 0.8329 (t0) outliers start: 17 outliers final: 14 residues processed: 159 average time/residue: 0.1511 time to fit residues: 32.6998 Evaluate side-chains 160 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 56 optimal weight: 7.9990 chunk 52 optimal weight: 0.0000 chunk 12 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.090832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.076492 restraints weight = 33334.861| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.72 r_work: 0.2691 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.8643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6557 Z= 0.160 Angle : 0.520 7.759 8935 Z= 0.272 Chirality : 0.043 0.143 987 Planarity : 0.005 0.062 1163 Dihedral : 5.138 54.940 896 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.32 % Favored : 92.31 % Rotamer: Outliers : 2.26 % Allowed : 17.91 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.27), residues: 806 helix: -4.05 (0.49), residues: 50 sheet: -0.01 (0.35), residues: 225 loop : -1.77 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 73 TYR 0.017 0.001 TYR A 67 PHE 0.015 0.001 PHE A 257 TRP 0.011 0.001 TRP B 80 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 6557) covalent geometry : angle 0.52011 ( 8935) hydrogen bonds : bond 0.03572 ( 121) hydrogen bonds : angle 4.81611 ( 348) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8808 (tp) cc_final: 0.8547 (pt) REVERT: A 37 ASP cc_start: 0.9166 (m-30) cc_final: 0.8892 (m-30) REVERT: A 60 CYS cc_start: 0.9215 (t) cc_final: 0.8633 (t) REVERT: A 79 LYS cc_start: 0.8807 (mmmm) cc_final: 0.8540 (mmmm) REVERT: A 119 GLU cc_start: 0.8001 (pt0) cc_final: 0.7576 (pt0) REVERT: A 177 MET cc_start: 0.8914 (ptm) cc_final: 0.8020 (ppp) REVERT: B 50 GLU cc_start: 0.4725 (OUTLIER) cc_final: 0.2486 (tp30) REVERT: B 72 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8141 (mt-10) REVERT: B 145 ASP cc_start: 0.8406 (m-30) cc_final: 0.8117 (m-30) REVERT: C 33 GLU cc_start: 0.6657 (pm20) cc_final: 0.6298 (pm20) REVERT: C 59 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: C 66 GLU cc_start: 0.8583 (tp30) cc_final: 0.8358 (tp30) REVERT: C 160 LEU cc_start: 0.9117 (mp) cc_final: 0.8582 (tt) REVERT: C 227 ASP cc_start: 0.7800 (m-30) cc_final: 0.7325 (m-30) REVERT: D 8 LYS cc_start: 0.9479 (tptt) cc_final: 0.7571 (mttt) REVERT: D 28 ASN cc_start: 0.8800 (t0) cc_final: 0.8395 (t0) outliers start: 16 outliers final: 13 residues processed: 167 average time/residue: 0.1623 time to fit residues: 36.8771 Evaluate side-chains 165 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 64 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 52 optimal weight: 0.0170 chunk 37 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 6 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.093025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.078396 restraints weight = 33271.816| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.77 r_work: 0.2735 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.8725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6557 Z= 0.087 Angle : 0.493 5.866 8935 Z= 0.253 Chirality : 0.043 0.145 987 Planarity : 0.004 0.038 1163 Dihedral : 4.888 55.200 896 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.33 % Favored : 94.29 % Rotamer: Outliers : 1.41 % Allowed : 19.46 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.27), residues: 806 helix: -3.95 (0.50), residues: 50 sheet: 0.09 (0.35), residues: 225 loop : -1.68 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 12 TYR 0.013 0.001 TYR A 67 PHE 0.014 0.001 PHE A 257 TRP 0.010 0.001 TRP B 80 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 6557) covalent geometry : angle 0.49284 ( 8935) hydrogen bonds : bond 0.02977 ( 121) hydrogen bonds : angle 4.60257 ( 348) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8803 (tp) cc_final: 0.8595 (pt) REVERT: A 29 HIS cc_start: 0.8518 (t70) cc_final: 0.8225 (t-90) REVERT: A 37 ASP cc_start: 0.9151 (m-30) cc_final: 0.8856 (m-30) REVERT: A 60 CYS cc_start: 0.9188 (t) cc_final: 0.8768 (t) REVERT: A 79 LYS cc_start: 0.8782 (mmmm) cc_final: 0.8502 (mmmm) REVERT: A 100 MET cc_start: 0.9075 (mtp) cc_final: 0.8754 (mtm) REVERT: A 119 GLU cc_start: 0.8094 (pt0) cc_final: 0.7606 (pt0) REVERT: A 177 MET cc_start: 0.8838 (ptm) cc_final: 0.7989 (ppp) REVERT: A 251 LYS cc_start: 0.8629 (mmmm) cc_final: 0.8429 (mmmm) REVERT: B 50 GLU cc_start: 0.4421 (OUTLIER) cc_final: 0.2464 (tp30) REVERT: B 72 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8103 (mt-10) REVERT: B 145 ASP cc_start: 0.8418 (m-30) cc_final: 0.8122 (m-30) REVERT: B 156 GLU cc_start: 0.8036 (tp30) cc_final: 0.7664 (tp30) REVERT: C 33 GLU cc_start: 0.6611 (pm20) cc_final: 0.6267 (pm20) REVERT: C 59 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: C 66 GLU cc_start: 0.8449 (tp30) cc_final: 0.8210 (tp30) REVERT: C 160 LEU cc_start: 0.9127 (mp) cc_final: 0.8620 (tt) REVERT: C 227 ASP cc_start: 0.7638 (m-30) cc_final: 0.7007 (m-30) REVERT: D 8 LYS cc_start: 0.9427 (tptt) cc_final: 0.7556 (mttt) REVERT: D 28 ASN cc_start: 0.8801 (t0) cc_final: 0.8388 (t0) outliers start: 10 outliers final: 8 residues processed: 163 average time/residue: 0.1741 time to fit residues: 38.2130 Evaluate side-chains 161 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 63 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.091174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.076531 restraints weight = 33827.723| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.77 r_work: 0.2693 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.8872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6557 Z= 0.173 Angle : 0.525 5.873 8935 Z= 0.271 Chirality : 0.043 0.139 987 Planarity : 0.004 0.041 1163 Dihedral : 4.711 55.662 894 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.44 % Favored : 92.18 % Rotamer: Outliers : 1.69 % Allowed : 19.18 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.27), residues: 806 helix: -3.96 (0.49), residues: 50 sheet: 0.04 (0.35), residues: 225 loop : -1.70 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 73 TYR 0.015 0.001 TYR A 67 PHE 0.016 0.001 PHE A 257 TRP 0.010 0.001 TRP B 80 HIS 0.006 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 6557) covalent geometry : angle 0.52504 ( 8935) hydrogen bonds : bond 0.03579 ( 121) hydrogen bonds : angle 4.66481 ( 348) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9223 (m-30) cc_final: 0.8960 (m-30) REVERT: A 60 CYS cc_start: 0.9216 (t) cc_final: 0.8689 (t) REVERT: A 79 LYS cc_start: 0.8903 (mmmm) cc_final: 0.8648 (mmmm) REVERT: A 100 MET cc_start: 0.9123 (mtp) cc_final: 0.8811 (mtm) REVERT: A 119 GLU cc_start: 0.8163 (pt0) cc_final: 0.7685 (pt0) REVERT: A 177 MET cc_start: 0.8933 (ptm) cc_final: 0.8044 (ppp) REVERT: B 50 GLU cc_start: 0.4812 (OUTLIER) cc_final: 0.2424 (tp30) REVERT: B 72 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8163 (mt-10) REVERT: B 145 ASP cc_start: 0.8434 (m-30) cc_final: 0.8152 (m-30) REVERT: B 156 GLU cc_start: 0.8142 (tp30) cc_final: 0.7771 (tp30) REVERT: B 230 ASP cc_start: 0.9115 (t0) cc_final: 0.8745 (t0) REVERT: C 33 GLU cc_start: 0.6638 (pm20) cc_final: 0.6271 (pm20) REVERT: C 59 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: C 66 GLU cc_start: 0.8573 (tp30) cc_final: 0.8341 (tp30) REVERT: C 160 LEU cc_start: 0.9135 (mp) cc_final: 0.8826 (tp) REVERT: C 227 ASP cc_start: 0.7790 (m-30) cc_final: 0.7055 (m-30) REVERT: D 8 LYS cc_start: 0.9479 (tptt) cc_final: 0.7599 (mttt) REVERT: D 28 ASN cc_start: 0.8797 (t0) cc_final: 0.8397 (t0) outliers start: 12 outliers final: 10 residues processed: 155 average time/residue: 0.1587 time to fit residues: 33.7881 Evaluate side-chains 158 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 1 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.092020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.077525 restraints weight = 33364.513| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.74 r_work: 0.2680 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.8911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6557 Z= 0.116 Angle : 0.506 5.788 8935 Z= 0.261 Chirality : 0.043 0.141 987 Planarity : 0.004 0.040 1163 Dihedral : 4.665 58.466 894 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.83 % Favored : 93.80 % Rotamer: Outliers : 1.55 % Allowed : 19.04 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.27), residues: 806 helix: -3.91 (0.49), residues: 50 sheet: 0.06 (0.35), residues: 225 loop : -1.67 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 73 TYR 0.012 0.001 TYR A 67 PHE 0.015 0.001 PHE A 257 TRP 0.010 0.001 TRP B 80 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6557) covalent geometry : angle 0.50644 ( 8935) hydrogen bonds : bond 0.03232 ( 121) hydrogen bonds : angle 4.57989 ( 348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3166.57 seconds wall clock time: 54 minutes 22.65 seconds (3262.65 seconds total)