Starting phenix.real_space_refine on Wed Jul 30 13:24:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zms_11300/07_2025/6zms_11300.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zms_11300/07_2025/6zms_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6zms_11300/07_2025/6zms_11300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zms_11300/07_2025/6zms_11300.map" model { file = "/net/cci-nas-00/data/ceres_data/6zms_11300/07_2025/6zms_11300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zms_11300/07_2025/6zms_11300.cif" } resolution = 3.4 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= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.23, per 1000 atoms: 0.58 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: 2.94 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.05 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: 4.33 Time building geometry restraints manager: 3.67 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: 3.260 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: 0.240 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.260 Find NCS groups from input model: 0.130 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: 0.010 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: 37.690 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.095 0.019 TRP A 153 HIS 0.008 0.002 HIS B 99 PHE 0.042 0.010 PHE C 120 TYR 0.144 0.020 TYR B 185 ARG 0.006 0.001 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.25007 ( 121) hydrogen bonds : angle 10.08272 ( 348) covalent geometry : bond 0.01870 ( 6557) covalent geometry : angle 1.98480 ( 8935) *********************** 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 : 0.938 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: A 61 ARG cc_start: 0.7138 (mtt180) cc_final: 0.6715 (ttp-170) REVERT: A 226 THR cc_start: 0.7709 (t) cc_final: 0.7464 (t) REVERT: B 195 ASN cc_start: 0.7484 (p0) cc_final: 0.7271 (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: 0.4731 (mm-40) outliers start: 15 outliers final: 7 residues processed: 277 average time/residue: 0.3228 time to fit residues: 123.5800 Evaluate side-chains 211 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 204 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 67 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3305 r_free = 0.3305 target = 0.110393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.095489 restraints weight = 32741.173| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.87 r_work: 0.3005 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 6557 Z= 0.291 Angle : 0.788 7.497 8935 Z= 0.426 Chirality : 0.052 0.191 987 Planarity : 0.006 0.048 1163 Dihedral : 7.834 77.637 903 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.21 % Favored : 94.17 % Rotamer: Outliers : 3.10 % Allowed : 13.40 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.44 (0.25), residues: 806 helix: -4.57 (0.40), residues: 53 sheet: -0.51 (0.35), residues: 196 loop : -1.84 (0.22), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 80 HIS 0.008 0.002 HIS A 214 PHE 0.012 0.002 PHE C 85 TYR 0.040 0.002 TYR A 67 ARG 0.005 0.001 ARG A 50 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 121) hydrogen bonds : angle 6.33148 ( 348) covalent geometry : bond 0.00675 ( 6557) covalent geometry : angle 0.78846 ( 8935) *********************** 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 241 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 219 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 THR cc_start: 0.9111 (m) cc_final: 0.8905 (p) REVERT: A 52 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8604 (mt-10) REVERT: A 79 LYS cc_start: 0.7596 (mmmm) cc_final: 0.7191 (mmmm) REVERT: A 108 MET cc_start: 0.9030 (mmt) cc_final: 0.8577 (mmt) REVERT: A 109 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8235 (mt-10) REVERT: A 152 VAL cc_start: 0.8435 (t) cc_final: 0.8153 (t) REVERT: A 171 ARG cc_start: 0.8652 (ptp-170) cc_final: 0.6600 (ptt-90) REVERT: A 251 LYS cc_start: 0.8369 (mmtm) cc_final: 0.8020 (mmmm) REVERT: B 50 GLU cc_start: 0.4392 (pm20) cc_final: 0.3416 (pm20) REVERT: B 121 CYS cc_start: 0.8957 (t) cc_final: 0.8615 (m) REVERT: B 131 GLU cc_start: 0.8882 (tt0) cc_final: 0.8420 (tt0) REVERT: B 138 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8573 (mm-30) REVERT: B 150 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8041 (mt-10) REVERT: B 156 GLU cc_start: 0.7620 (tp30) cc_final: 0.7180 (tp30) REVERT: B 211 ASP cc_start: 0.7969 (t0) cc_final: 0.7652 (t0) REVERT: B 230 ASP cc_start: 0.9183 (t0) cc_final: 0.8913 (t0) REVERT: B 256 ARG cc_start: 0.6844 (pmt-80) cc_final: 0.4234 (mtt-85) REVERT: C 73 ARG cc_start: 0.7870 (ptm-80) cc_final: 0.7306 (ptt-90) REVERT: C 113 SER cc_start: 0.8844 (m) cc_final: 0.8543 (p) REVERT: C 162 SER cc_start: 0.8115 (t) cc_final: 0.7915 (p) REVERT: D 7 GLN cc_start: 0.8833 (mt0) cc_final: 0.6378 (mm-40) REVERT: D 8 LYS cc_start: 0.8867 (tptt) cc_final: 0.6606 (mtpt) REVERT: D 34 ASP cc_start: 0.9156 (m-30) cc_final: 0.8908 (m-30) outliers start: 22 outliers final: 13 residues processed: 228 average time/residue: 0.3565 time to fit residues: 110.2510 Evaluate side-chains 213 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 149 ASN 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 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 47 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3160 r_free = 0.3160 target = 0.099667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.084808 restraints weight = 33324.445| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.79 r_work: 0.2844 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.6254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6557 Z= 0.177 Angle : 0.585 4.910 8935 Z= 0.318 Chirality : 0.044 0.146 987 Planarity : 0.005 0.074 1163 Dihedral : 6.066 49.311 896 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.82 % Favored : 92.68 % Rotamer: Outliers : 2.40 % Allowed : 15.66 % 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 (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: -2.16 (0.26), residues: 806 helix: -4.31 (0.43), residues: 52 sheet: -0.14 (0.36), residues: 208 loop : -1.77 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 80 HIS 0.005 0.001 HIS C 109 PHE 0.015 0.001 PHE A 257 TYR 0.020 0.002 TYR A 67 ARG 0.003 0.000 ARG C 73 Details of bonding type rmsd hydrogen bonds : bond 0.04401 ( 121) hydrogen bonds : angle 5.59779 ( 348) covalent geometry : bond 0.00397 ( 6557) covalent geometry : angle 0.58543 ( 8935) *********************** 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 204 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.9020 (mp0) cc_final: 0.8800 (mp0) REVERT: A 37 ASP cc_start: 0.9204 (m-30) cc_final: 0.8664 (m-30) REVERT: A 79 LYS cc_start: 0.7899 (mmmm) cc_final: 0.7451 (mmmm) REVERT: A 108 MET cc_start: 0.9042 (mmt) cc_final: 0.8581 (mmt) REVERT: A 119 GLU cc_start: 0.7114 (pt0) cc_final: 0.6802 (pt0) REVERT: A 137 TYR cc_start: 0.9381 (t80) cc_final: 0.9178 (t80) REVERT: A 152 VAL cc_start: 0.8690 (t) cc_final: 0.8415 (t) REVERT: A 251 LYS cc_start: 0.8256 (mmtm) cc_final: 0.7997 (mmmm) REVERT: B 131 GLU cc_start: 0.8894 (tt0) cc_final: 0.8638 (tt0) REVERT: B 132 MET cc_start: 0.9392 (mmm) cc_final: 0.9031 (mmm) REVERT: B 138 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8695 (mm-30) REVERT: B 145 ASP cc_start: 0.8245 (m-30) cc_final: 0.7855 (m-30) REVERT: B 156 GLU cc_start: 0.7778 (tp30) cc_final: 0.7499 (tp30) REVERT: B 256 ARG cc_start: 0.7710 (pmt-80) cc_final: 0.4998 (mtt180) REVERT: C 33 GLU cc_start: 0.6777 (pm20) cc_final: 0.6494 (pm20) REVERT: C 163 SER cc_start: 0.9067 (m) cc_final: 0.8698 (p) REVERT: D 8 LYS cc_start: 0.9053 (tptt) cc_final: 0.6945 (mtpt) REVERT: D 34 ASP cc_start: 0.9051 (m-30) cc_final: 0.8846 (m-30) outliers start: 17 outliers final: 13 residues processed: 196 average time/residue: 0.3601 time to fit residues: 95.6074 Evaluate side-chains 192 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain B residue 104 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 C residue 23 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 56 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 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 = 0.3107 r_free = 0.3107 target = 0.095946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.081182 restraints weight = 33382.934| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.78 r_work: 0.2770 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6557 Z= 0.170 Angle : 0.539 4.581 8935 Z= 0.289 Chirality : 0.044 0.157 987 Planarity : 0.004 0.044 1163 Dihedral : 5.593 42.434 896 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.83 % Favored : 93.80 % Rotamer: Outliers : 3.39 % Allowed : 14.81 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.15 (0.27), residues: 806 helix: -4.13 (0.47), residues: 50 sheet: -0.18 (0.35), residues: 221 loop : -1.81 (0.23), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 80 HIS 0.005 0.001 HIS A 214 PHE 0.012 0.001 PHE A 257 TYR 0.021 0.001 TYR A 67 ARG 0.003 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 121) hydrogen bonds : angle 5.24850 ( 348) covalent geometry : bond 0.00387 ( 6557) covalent geometry : angle 0.53946 ( 8935) *********************** 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 209 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 23 THR cc_start: 0.8277 (m) cc_final: 0.7904 (t) REVERT: A 29 HIS cc_start: 0.8921 (t70) cc_final: 0.8682 (t70) REVERT: A 37 ASP cc_start: 0.9079 (m-30) cc_final: 0.8681 (m-30) REVERT: A 79 LYS cc_start: 0.8162 (mmmm) cc_final: 0.7845 (mmmm) REVERT: A 108 MET cc_start: 0.9061 (mmt) cc_final: 0.8627 (mmt) REVERT: A 119 GLU cc_start: 0.7424 (pt0) cc_final: 0.7113 (pt0) REVERT: A 152 VAL cc_start: 0.8838 (t) cc_final: 0.8598 (t) REVERT: A 177 MET cc_start: 0.8861 (ptm) cc_final: 0.8029 (ppp) REVERT: A 251 LYS cc_start: 0.8541 (mmtm) cc_final: 0.8215 (mmmm) REVERT: B 89 MET cc_start: 0.8851 (mmm) cc_final: 0.8400 (mmm) REVERT: B 138 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8607 (mm-30) REVERT: B 145 ASP cc_start: 0.8272 (m-30) cc_final: 0.7956 (m-30) REVERT: B 156 GLU cc_start: 0.7893 (tp30) cc_final: 0.7618 (tp30) REVERT: B 256 ARG cc_start: 0.8139 (pmt-80) cc_final: 0.5259 (mtt90) REVERT: C 57 ASN cc_start: 0.9138 (p0) cc_final: 0.8891 (p0) REVERT: C 125 MET cc_start: 0.9224 (mmm) cc_final: 0.8950 (mmm) REVERT: C 163 SER cc_start: 0.9216 (m) cc_final: 0.8718 (p) REVERT: C 210 ILE cc_start: 0.9102 (mm) cc_final: 0.8889 (mt) REVERT: C 227 ASP cc_start: 0.7604 (m-30) cc_final: 0.7395 (m-30) REVERT: D 7 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.6385 (mm-40) REVERT: D 8 LYS cc_start: 0.9138 (tptt) cc_final: 0.7317 (mtmt) outliers start: 24 outliers final: 20 residues processed: 199 average time/residue: 0.3691 time to fit residues: 98.9944 Evaluate side-chains 200 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 56 GLU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 107 THR 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 C residue 16 SER 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 D residue 7 GLN Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 12 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 HIS D 12 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.089970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.075219 restraints weight = 33982.082| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.79 r_work: 0.2707 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.7734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6557 Z= 0.160 Angle : 0.522 4.547 8935 Z= 0.278 Chirality : 0.043 0.152 987 Planarity : 0.004 0.046 1163 Dihedral : 5.315 47.993 896 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.58 % Favored : 93.05 % Rotamer: Outliers : 3.39 % Allowed : 15.09 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.05 (0.27), residues: 806 helix: -4.02 (0.50), residues: 50 sheet: -0.09 (0.35), residues: 221 loop : -1.75 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 80 HIS 0.005 0.001 HIS A 214 PHE 0.014 0.001 PHE A 257 TYR 0.015 0.001 TYR A 67 ARG 0.003 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 121) hydrogen bonds : angle 5.06272 ( 348) covalent geometry : bond 0.00375 ( 6557) covalent geometry : angle 0.52217 ( 8935) *********************** 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 188 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.8573 (ptm-80) cc_final: 0.8319 (ptm-80) REVERT: A 23 THR cc_start: 0.8252 (m) cc_final: 0.8027 (t) REVERT: A 37 ASP cc_start: 0.9091 (m-30) cc_final: 0.8803 (m-30) REVERT: A 79 LYS cc_start: 0.8382 (mmmm) cc_final: 0.8083 (mmmm) REVERT: A 119 GLU cc_start: 0.7678 (pt0) cc_final: 0.7183 (pt0) REVERT: A 152 VAL cc_start: 0.8983 (t) cc_final: 0.8740 (t) REVERT: A 177 MET cc_start: 0.8922 (ptm) cc_final: 0.8010 (ppp) REVERT: A 251 LYS cc_start: 0.8506 (mmtm) cc_final: 0.8200 (mmmm) REVERT: B 21 SER cc_start: 0.8537 (m) cc_final: 0.7791 (p) REVERT: B 50 GLU cc_start: 0.4530 (OUTLIER) cc_final: 0.2783 (tp30) REVERT: B 131 GLU cc_start: 0.8842 (tt0) cc_final: 0.8607 (tt0) REVERT: B 138 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8617 (mm-30) REVERT: B 145 ASP cc_start: 0.8235 (m-30) cc_final: 0.7917 (m-30) REVERT: B 156 GLU cc_start: 0.7886 (tp30) cc_final: 0.7596 (tp30) REVERT: B 185 TYR cc_start: 0.9007 (m-80) cc_final: 0.8794 (m-80) REVERT: C 57 ASN cc_start: 0.9345 (p0) cc_final: 0.8970 (p0) REVERT: C 78 MET cc_start: 0.7958 (tpt) cc_final: 0.7709 (tpt) REVERT: C 125 MET cc_start: 0.9270 (mmm) cc_final: 0.9031 (mmm) REVERT: C 160 LEU cc_start: 0.9061 (mp) cc_final: 0.8669 (tp) REVERT: C 163 SER cc_start: 0.9338 (m) cc_final: 0.8823 (p) REVERT: C 203 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8550 (mm-30) REVERT: C 227 ASP cc_start: 0.7665 (m-30) cc_final: 0.7331 (m-30) REVERT: D 8 LYS cc_start: 0.9298 (tptt) cc_final: 0.7441 (mttt) outliers start: 24 outliers final: 18 residues processed: 179 average time/residue: 0.3771 time to fit residues: 90.3267 Evaluate side-chains 181 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 50 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 104 SER 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 16 SER 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 111 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain D residue 5 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 70 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3008 r_free = 0.3008 target = 0.089281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.074673 restraints weight = 34454.765| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.78 r_work: 0.2610 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.8144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 6557 Z= 0.236 Angle : 0.568 10.504 8935 Z= 0.298 Chirality : 0.045 0.154 987 Planarity : 0.004 0.044 1163 Dihedral : 5.400 52.168 896 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.20 % Favored : 92.43 % Rotamer: Outliers : 3.53 % Allowed : 15.23 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.13 (0.27), residues: 806 helix: -4.02 (0.50), residues: 50 sheet: -0.13 (0.36), residues: 220 loop : -1.82 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 80 HIS 0.005 0.001 HIS A 214 PHE 0.015 0.001 PHE A 257 TYR 0.019 0.001 TYR A 67 ARG 0.003 0.000 ARG C 73 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 121) hydrogen bonds : angle 5.07226 ( 348) covalent geometry : bond 0.00554 ( 6557) covalent geometry : angle 0.56783 ( 8935) *********************** 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 184 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9127 (m-30) cc_final: 0.8853 (m-30) REVERT: A 79 LYS cc_start: 0.8632 (mmmm) cc_final: 0.8338 (mmmm) REVERT: A 119 GLU cc_start: 0.7793 (pt0) cc_final: 0.7274 (pt0) REVERT: A 152 VAL cc_start: 0.9058 (t) cc_final: 0.8853 (t) REVERT: A 177 MET cc_start: 0.8967 (ptm) cc_final: 0.8010 (ppp) REVERT: A 251 LYS cc_start: 0.8571 (mmtm) cc_final: 0.8239 (mmmm) REVERT: B 12 ARG cc_start: 0.8125 (mmm-85) cc_final: 0.7889 (mmm-85) REVERT: B 50 GLU cc_start: 0.4541 (OUTLIER) cc_final: 0.2362 (tp30) REVERT: B 131 GLU cc_start: 0.8787 (tt0) cc_final: 0.8586 (tt0) REVERT: B 138 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8639 (mm-30) REVERT: B 145 ASP cc_start: 0.8328 (m-30) cc_final: 0.8021 (m-30) REVERT: B 156 GLU cc_start: 0.7889 (tp30) cc_final: 0.7598 (tp30) REVERT: C 33 GLU cc_start: 0.6510 (pm20) cc_final: 0.6070 (pm20) REVERT: C 66 GLU cc_start: 0.8556 (tp30) cc_final: 0.8348 (tp30) REVERT: C 125 MET cc_start: 0.9270 (mmm) cc_final: 0.9039 (mmm) REVERT: C 160 LEU cc_start: 0.9081 (mp) cc_final: 0.8511 (tt) REVERT: C 163 SER cc_start: 0.9375 (m) cc_final: 0.8944 (p) REVERT: C 227 ASP cc_start: 0.7712 (m-30) cc_final: 0.7430 (m-30) REVERT: D 8 LYS cc_start: 0.9442 (tptt) cc_final: 0.7572 (mttt) REVERT: D 28 ASN cc_start: 0.8725 (t0) cc_final: 0.8272 (t0) outliers start: 25 outliers final: 18 residues processed: 174 average time/residue: 0.3609 time to fit residues: 84.6290 Evaluate side-chains 173 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 43 SER Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 104 SER 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 194 THR Chi-restraints excluded: chain C residue 16 SER 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 D residue 5 SER Chi-restraints excluded: chain D residue 9 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 70 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3036 r_free = 0.3036 target = 0.091278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.076773 restraints weight = 33642.550| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 2.75 r_work: 0.2649 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.8308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6557 Z= 0.105 Angle : 0.501 6.931 8935 Z= 0.261 Chirality : 0.043 0.146 987 Planarity : 0.004 0.042 1163 Dihedral : 5.060 49.647 896 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.83 % Favored : 93.80 % Rotamer: Outliers : 1.83 % Allowed : 16.78 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.27), residues: 806 helix: -3.99 (0.50), residues: 50 sheet: -0.00 (0.36), residues: 220 loop : -1.72 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 80 HIS 0.004 0.001 HIS A 214 PHE 0.014 0.001 PHE A 231 TYR 0.014 0.001 TYR A 67 ARG 0.003 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 121) hydrogen bonds : angle 4.87684 ( 348) covalent geometry : bond 0.00252 ( 6557) covalent geometry : angle 0.50077 ( 8935) *********************** 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 180 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9120 (m-30) cc_final: 0.8835 (m-30) REVERT: A 60 CYS cc_start: 0.9237 (t) cc_final: 0.8585 (t) REVERT: A 79 LYS cc_start: 0.8660 (mmmm) cc_final: 0.8370 (mmmm) REVERT: A 119 GLU cc_start: 0.7797 (pt0) cc_final: 0.7292 (pt0) REVERT: A 152 VAL cc_start: 0.9031 (t) cc_final: 0.8759 (t) REVERT: A 177 MET cc_start: 0.8964 (ptm) cc_final: 0.8030 (ppp) REVERT: A 251 LYS cc_start: 0.8558 (mmtm) cc_final: 0.8246 (mmmm) REVERT: B 50 GLU cc_start: 0.4279 (OUTLIER) cc_final: 0.2421 (tp30) REVERT: B 131 GLU cc_start: 0.8797 (tt0) cc_final: 0.8580 (tt0) REVERT: B 138 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8676 (mm-30) REVERT: B 145 ASP cc_start: 0.8272 (m-30) cc_final: 0.7980 (m-30) REVERT: B 230 ASP cc_start: 0.9119 (t0) cc_final: 0.8859 (t0) REVERT: C 33 GLU cc_start: 0.6534 (pm20) cc_final: 0.6042 (pm20) REVERT: C 59 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: C 66 GLU cc_start: 0.8455 (tp30) cc_final: 0.8238 (tp30) REVERT: C 160 LEU cc_start: 0.9097 (mp) cc_final: 0.8550 (tt) REVERT: C 163 SER cc_start: 0.9318 (m) cc_final: 0.8964 (p) REVERT: C 227 ASP cc_start: 0.7754 (m-30) cc_final: 0.7335 (m-30) REVERT: D 8 LYS cc_start: 0.9460 (tptt) cc_final: 0.7512 (mtmt) REVERT: D 28 ASN cc_start: 0.8736 (t0) cc_final: 0.8282 (t0) outliers start: 13 outliers final: 9 residues processed: 175 average time/residue: 0.3436 time to fit residues: 82.0107 Evaluate side-chains 172 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 104 SER 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 55 ILE Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain D residue 5 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 35 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 46 optimal weight: 0.0980 chunk 15 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3058 r_free = 0.3058 target = 0.092613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.078036 restraints weight = 33507.438| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.75 r_work: 0.2695 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.8449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6557 Z= 0.084 Angle : 0.487 5.174 8935 Z= 0.250 Chirality : 0.043 0.146 987 Planarity : 0.004 0.054 1163 Dihedral : 4.849 53.705 896 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.96 % Favored : 93.67 % Rotamer: Outliers : 1.83 % Allowed : 18.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.27), residues: 806 helix: -3.93 (0.51), residues: 50 sheet: 0.08 (0.35), residues: 220 loop : -1.66 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 80 HIS 0.004 0.001 HIS A 214 PHE 0.014 0.001 PHE A 257 TYR 0.016 0.001 TYR A 67 ARG 0.007 0.000 ARG B 12 Details of bonding type rmsd hydrogen bonds : bond 0.03005 ( 121) hydrogen bonds : angle 4.67049 ( 348) covalent geometry : bond 0.00204 ( 6557) covalent geometry : angle 0.48691 ( 8935) *********************** 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 181 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9104 (m-30) cc_final: 0.8768 (m-30) REVERT: A 60 CYS cc_start: 0.9212 (t) cc_final: 0.8768 (t) REVERT: A 79 LYS cc_start: 0.8657 (mmmm) cc_final: 0.8356 (mmmm) REVERT: A 119 GLU cc_start: 0.7825 (pt0) cc_final: 0.7330 (pt0) REVERT: A 152 VAL cc_start: 0.9020 (t) cc_final: 0.8724 (t) REVERT: A 177 MET cc_start: 0.8912 (ptm) cc_final: 0.8003 (ppp) REVERT: A 251 LYS cc_start: 0.8564 (mmtm) cc_final: 0.8237 (mmmm) REVERT: B 50 GLU cc_start: 0.4184 (OUTLIER) cc_final: 0.2447 (tp30) REVERT: B 131 GLU cc_start: 0.8801 (tt0) cc_final: 0.8569 (tt0) REVERT: B 138 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8650 (mm-30) REVERT: B 145 ASP cc_start: 0.8235 (m-30) cc_final: 0.7936 (m-30) REVERT: B 230 ASP cc_start: 0.9151 (t0) cc_final: 0.8904 (t0) REVERT: C 33 GLU cc_start: 0.6426 (pm20) cc_final: 0.5912 (pm20) REVERT: C 59 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: C 66 GLU cc_start: 0.8321 (tp30) cc_final: 0.8085 (tp30) REVERT: C 160 LEU cc_start: 0.9094 (mp) cc_final: 0.8658 (tp) REVERT: C 163 SER cc_start: 0.9290 (m) cc_final: 0.8982 (p) REVERT: C 227 ASP cc_start: 0.7654 (m-30) cc_final: 0.7402 (m-30) REVERT: D 8 LYS cc_start: 0.9470 (tptt) cc_final: 0.7482 (mtmt) REVERT: D 28 ASN cc_start: 0.8741 (t0) cc_final: 0.8295 (t0) outliers start: 13 outliers final: 10 residues processed: 176 average time/residue: 0.4602 time to fit residues: 111.7827 Evaluate side-chains 167 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 104 SER 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 51 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 47 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 48 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 15 optimal weight: 0.0970 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- 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 = 0.3015 r_free = 0.3015 target = 0.090038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.075410 restraints weight = 33980.146| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.75 r_work: 0.2672 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.8602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6557 Z= 0.128 Angle : 0.496 5.311 8935 Z= 0.257 Chirality : 0.043 0.148 987 Planarity : 0.004 0.052 1163 Dihedral : 4.544 51.980 894 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.58 % Favored : 93.05 % Rotamer: Outliers : 1.97 % Allowed : 18.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.28), residues: 806 helix: -3.91 (0.50), residues: 50 sheet: 0.10 (0.36), residues: 220 loop : -1.66 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 80 HIS 0.005 0.001 HIS A 214 PHE 0.015 0.001 PHE A 257 TYR 0.013 0.001 TYR A 67 ARG 0.006 0.000 ARG B 12 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 121) hydrogen bonds : angle 4.63906 ( 348) covalent geometry : bond 0.00305 ( 6557) covalent geometry : angle 0.49585 ( 8935) *********************** 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 170 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9117 (m-30) cc_final: 0.8838 (m-30) REVERT: A 60 CYS cc_start: 0.9230 (t) cc_final: 0.8789 (t) REVERT: A 79 LYS cc_start: 0.8742 (mmmm) cc_final: 0.8446 (mmmm) REVERT: A 119 GLU cc_start: 0.7960 (pt0) cc_final: 0.7429 (pt0) REVERT: A 152 VAL cc_start: 0.9020 (t) cc_final: 0.8757 (t) REVERT: A 177 MET cc_start: 0.8986 (ptm) cc_final: 0.8014 (ppp) REVERT: A 251 LYS cc_start: 0.8564 (mmtm) cc_final: 0.8261 (mmmm) REVERT: B 50 GLU cc_start: 0.4355 (OUTLIER) cc_final: 0.2269 (tp30) REVERT: B 131 GLU cc_start: 0.8788 (tt0) cc_final: 0.8583 (tt0) REVERT: B 138 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8676 (mm-30) REVERT: B 145 ASP cc_start: 0.8209 (m-30) cc_final: 0.7917 (m-30) REVERT: B 156 GLU cc_start: 0.7944 (tp30) cc_final: 0.7575 (tp30) REVERT: B 211 ASP cc_start: 0.8138 (t0) cc_final: 0.7901 (t0) REVERT: B 230 ASP cc_start: 0.9166 (t0) cc_final: 0.8907 (t0) REVERT: C 33 GLU cc_start: 0.6436 (pm20) cc_final: 0.5890 (pm20) REVERT: C 59 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: C 66 GLU cc_start: 0.8388 (tp30) cc_final: 0.8154 (tp30) REVERT: C 160 LEU cc_start: 0.9108 (mp) cc_final: 0.8691 (tp) REVERT: C 163 SER cc_start: 0.9410 (m) cc_final: 0.9088 (p) REVERT: C 227 ASP cc_start: 0.7678 (m-30) cc_final: 0.7378 (m-30) REVERT: D 8 LYS cc_start: 0.9435 (tptt) cc_final: 0.7530 (mtmt) REVERT: D 28 ASN cc_start: 0.8730 (t0) cc_final: 0.8288 (t0) outliers start: 14 outliers final: 10 residues processed: 166 average time/residue: 0.3503 time to fit residues: 79.2814 Evaluate side-chains 166 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 104 SER 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 187 SER 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 62 optimal weight: 3.9990 chunk 15 optimal weight: 0.0370 chunk 52 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 56 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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 = 0.3091 r_free = 0.3091 target = 0.094779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.080651 restraints weight = 33104.238| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.66 r_work: 0.2757 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.8711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6557 Z= 0.082 Angle : 0.479 5.196 8935 Z= 0.245 Chirality : 0.043 0.143 987 Planarity : 0.004 0.065 1163 Dihedral : 4.400 53.993 894 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.96 % Favored : 94.67 % Rotamer: Outliers : 1.69 % Allowed : 18.62 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.28), residues: 806 helix: -3.84 (0.51), residues: 50 sheet: 0.23 (0.36), residues: 220 loop : -1.61 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 80 HIS 0.004 0.001 HIS A 214 PHE 0.015 0.001 PHE A 257 TYR 0.018 0.001 TYR A 67 ARG 0.006 0.000 ARG B 12 Details of bonding type rmsd hydrogen bonds : bond 0.02802 ( 121) hydrogen bonds : angle 4.45270 ( 348) covalent geometry : bond 0.00202 ( 6557) covalent geometry : angle 0.47922 ( 8935) ********************** 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 171 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 HIS cc_start: 0.8534 (t70) cc_final: 0.8242 (t70) REVERT: A 37 ASP cc_start: 0.9119 (m-30) cc_final: 0.8773 (m-30) REVERT: A 60 CYS cc_start: 0.9171 (t) cc_final: 0.8751 (t) REVERT: A 79 LYS cc_start: 0.8754 (mmmm) cc_final: 0.8528 (mmmm) REVERT: A 119 GLU cc_start: 0.8018 (pt0) cc_final: 0.7500 (pt0) REVERT: A 152 VAL cc_start: 0.9045 (t) cc_final: 0.8764 (t) REVERT: A 177 MET cc_start: 0.8870 (ptm) cc_final: 0.8024 (ppp) REVERT: A 251 LYS cc_start: 0.8630 (mmtm) cc_final: 0.8311 (mmmm) REVERT: B 50 GLU cc_start: 0.4231 (OUTLIER) cc_final: 0.2467 (tp30) REVERT: B 131 GLU cc_start: 0.8811 (tt0) cc_final: 0.8593 (tt0) REVERT: B 138 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8633 (mm-30) REVERT: B 145 ASP cc_start: 0.8252 (m-30) cc_final: 0.7965 (m-30) REVERT: B 156 GLU cc_start: 0.8021 (tp30) cc_final: 0.7664 (tp30) REVERT: B 211 ASP cc_start: 0.8334 (t0) cc_final: 0.8122 (t0) REVERT: B 230 ASP cc_start: 0.9166 (t0) cc_final: 0.8928 (t0) REVERT: C 33 GLU cc_start: 0.6514 (pm20) cc_final: 0.6022 (pm20) REVERT: C 59 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: C 66 GLU cc_start: 0.8311 (tp30) cc_final: 0.8087 (tp30) REVERT: C 160 LEU cc_start: 0.9110 (mp) cc_final: 0.8704 (tt) REVERT: C 163 SER cc_start: 0.9305 (m) cc_final: 0.9092 (p) REVERT: C 227 ASP cc_start: 0.7703 (m-30) cc_final: 0.7146 (m-30) REVERT: C 237 TYR cc_start: 0.8789 (m-80) cc_final: 0.8360 (m-80) REVERT: D 8 LYS cc_start: 0.9457 (tptt) cc_final: 0.7569 (mttt) REVERT: D 28 ASN cc_start: 0.8796 (t0) cc_final: 0.8360 (t0) outliers start: 12 outliers final: 9 residues processed: 166 average time/residue: 0.3772 time to fit residues: 86.3355 Evaluate side-chains 170 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 104 SER 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 51 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 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 0 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 52 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- 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 = 0.3040 r_free = 0.3040 target = 0.091300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.076823 restraints weight = 33973.266| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.74 r_work: 0.2710 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.8814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6557 Z= 0.164 Angle : 0.507 5.715 8935 Z= 0.262 Chirality : 0.043 0.142 987 Planarity : 0.004 0.052 1163 Dihedral : 4.475 52.939 894 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.07 % Favored : 92.56 % Rotamer: Outliers : 2.26 % Allowed : 17.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.28), residues: 806 helix: -3.90 (0.48), residues: 50 sheet: 0.16 (0.36), residues: 220 loop : -1.64 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 80 HIS 0.005 0.001 HIS A 214 PHE 0.015 0.001 PHE A 257 TYR 0.015 0.001 TYR A 67 ARG 0.005 0.000 ARG B 12 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 121) hydrogen bonds : angle 4.54044 ( 348) covalent geometry : bond 0.00388 ( 6557) covalent geometry : angle 0.50698 ( 8935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6304.70 seconds wall clock time: 109 minutes 6.45 seconds (6546.45 seconds total)