Starting phenix.real_space_refine on Tue Aug 4 19:04:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ruf_54270/08_2026/9ruf_54270.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ruf_54270/08_2026/9ruf_54270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ruf_54270/08_2026/9ruf_54270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ruf_54270/08_2026/9ruf_54270.map" model { file = "/net/cci-nas-00/data/ceres_data/9ruf_54270/08_2026/9ruf_54270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ruf_54270/08_2026/9ruf_54270.cif" } resolution = 2.9 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= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 3833 2.51 5 N 1023 2.21 5 O 1168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6045 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1457 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Chain: "B" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1400 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 10, 'TRANS': 157} Chain breaks: 2 Chain: "H" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1546 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 193} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1592 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Chain breaks: 1 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 1.23, per 1000 atoms: 0.20 Number of scatterers: 6045 At special positions: 0 Unit cell: (56.1, 82.11, 146.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 1168 8.00 N 1023 7.00 C 3833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 79 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 173 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 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: 0.44 Conformation dependent library (CDL) restraints added in 177.8 milliseconds 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1446 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 18 sheets defined 13.1% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 49 through 54 removed outlier: 3.729A pdb=" N GLN A 53 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 79 removed outlier: 3.930A pdb=" N ALA A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 22 Processing helix chain 'B' and resid 54 through 64 removed outlier: 3.531A pdb=" N TYR B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 78 removed outlier: 4.177A pdb=" N LEU B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASP B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 89 removed outlier: 3.750A pdb=" N GLN B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 93 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 207 through 210 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.914A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 191 removed outlier: 3.733A pdb=" N HIS L 191 " --> pdb=" O ASP L 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.408A pdb=" N HIS A 27 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR A 36 " --> pdb=" O TYR A 25 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N TYR A 25 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ASP A 38 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N GLY A 23 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU A 28 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR A 11 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS A 7 " --> pdb=" O PHE B 17 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALA B 13 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL A 13 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE B 11 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU A 15 " --> pdb=" O TYR B 9 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR B 9 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR B 32 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLU B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP B 41 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL B 46 " --> pdb=" O ASP B 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 95 removed outlier: 6.289A pdb=" N PHE A 148 " --> pdb=" O PHE A 139 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE A 139 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE A 150 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.184A pdb=" N TRP A 123 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 102 removed outlier: 5.954A pdb=" N PHE B 155 " --> pdb=" O ASP B 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 102 removed outlier: 5.954A pdb=" N PHE B 155 " --> pdb=" O ASP B 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 136 through 138 removed outlier: 4.604A pdb=" N TRP B 131 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 130 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.534A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.503A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 157 through 160 Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.505A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB7, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AB8, first strand: chain 'L' and resid 118 through 120 removed outlier: 3.599A pdb=" N VAL L 134 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 147 through 152 removed outlier: 3.764A pdb=" N TYR L 194 " --> pdb=" O PHE L 211 " (cutoff:3.500A) 270 hydrogen bonds defined for protein. 663 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: 0.76 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1949 1.34 - 1.46: 1532 1.46 - 1.58: 2684 1.58 - 1.71: 0 1.71 - 1.83: 27 Bond restraints: 6192 Sorted by residual: bond pdb=" C TRP L 94 " pdb=" N PRO L 95 " ideal model delta sigma weight residual 1.329 1.370 -0.040 1.18e-02 7.18e+03 1.17e+01 bond pdb=" N SER H 105 " pdb=" CA SER H 105 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.69e+00 bond pdb=" CA GLU B 36 " pdb=" C GLU B 36 " ideal model delta sigma weight residual 1.525 1.497 0.028 1.25e-02 6.40e+03 5.07e+00 bond pdb=" CA TYR H 104 " pdb=" C TYR H 104 " ideal model delta sigma weight residual 1.522 1.549 -0.027 1.31e-02 5.83e+03 4.31e+00 bond pdb=" C PHE H 152 " pdb=" O PHE H 152 " ideal model delta sigma weight residual 1.244 1.226 0.018 1.00e-02 1.00e+04 3.24e+00 ... (remaining 6187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 8263 2.50 - 4.99: 135 4.99 - 7.49: 26 7.49 - 9.99: 6 9.99 - 12.48: 1 Bond angle restraints: 8431 Sorted by residual: angle pdb=" N ASN L 31 " pdb=" CA ASN L 31 " pdb=" C ASN L 31 " ideal model delta sigma weight residual 111.87 105.20 6.67 1.41e+00 5.03e-01 2.24e+01 angle pdb=" C GLU H 154 " pdb=" N PRO H 155 " pdb=" CA PRO H 155 " ideal model delta sigma weight residual 119.76 115.07 4.69 1.03e+00 9.43e-01 2.07e+01 angle pdb=" C ASP B 152 " pdb=" CA ASP B 152 " pdb=" CB ASP B 152 " ideal model delta sigma weight residual 111.22 105.67 5.55 1.23e+00 6.61e-01 2.04e+01 angle pdb=" C PHE H 152 " pdb=" N PRO H 153 " pdb=" CA PRO H 153 " ideal model delta sigma weight residual 119.99 115.14 4.85 1.08e+00 8.57e-01 2.02e+01 angle pdb=" N TYR L 32 " pdb=" CA TYR L 32 " pdb=" C TYR L 32 " ideal model delta sigma weight residual 110.68 104.54 6.14 1.39e+00 5.18e-01 1.95e+01 ... (remaining 8426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.65: 3133 15.65 - 31.29: 384 31.29 - 46.94: 123 46.94 - 62.59: 33 62.59 - 78.23: 12 Dihedral angle restraints: 3685 sinusoidal: 1439 harmonic: 2246 Sorted by residual: dihedral pdb=" CB CYS L 136 " pdb=" SG CYS L 136 " pdb=" SG CYS L 196 " pdb=" CB CYS L 196 " ideal model delta sinusoidal sigma weight residual -86.00 -163.26 77.26 1 1.00e+01 1.00e-02 7.48e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 79 " pdb=" CB CYS B 79 " ideal model delta sinusoidal sigma weight residual -86.00 -157.01 71.01 1 1.00e+01 1.00e-02 6.48e+01 dihedral pdb=" CB CYS B 117 " pdb=" SG CYS B 117 " pdb=" SG CYS B 173 " pdb=" CB CYS B 173 " ideal model delta sinusoidal sigma weight residual 93.00 59.00 34.00 1 1.00e+01 1.00e-02 1.64e+01 ... (remaining 3682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 793 0.068 - 0.135: 131 0.135 - 0.203: 9 0.203 - 0.270: 3 0.270 - 0.338: 2 Chirality restraints: 938 Sorted by residual: chirality pdb=" CA PHE H 152 " pdb=" N PHE H 152 " pdb=" C PHE H 152 " pdb=" CB PHE H 152 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA GLU H 154 " pdb=" N GLU H 154 " pdb=" C GLU H 154 " pdb=" CB GLU H 154 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CG LEU A 153 " pdb=" CB LEU A 153 " pdb=" CD1 LEU A 153 " pdb=" CD2 LEU A 153 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 935 not shown) Planarity restraints: 1085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 152 " 0.048 5.00e-02 4.00e+02 7.33e-02 8.61e+00 pdb=" N PRO H 153 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO H 153 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO H 153 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 123 " -0.017 2.00e-02 2.50e+03 1.70e-02 7.19e+00 pdb=" CG TRP A 123 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 123 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 123 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 123 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 123 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 123 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 123 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 123 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 123 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 94 " -0.013 2.00e-02 2.50e+03 1.53e-02 4.69e+00 pdb=" CG TYR H 94 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR H 94 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR H 94 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR H 94 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR H 94 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR H 94 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR H 94 " -0.000 2.00e-02 2.50e+03 ... (remaining 1082 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 517 2.74 - 3.28: 5876 3.28 - 3.82: 10374 3.82 - 4.36: 12552 4.36 - 4.90: 21410 Nonbonded interactions: 50729 Sorted by model distance: nonbonded pdb=" O PRO H 129 " pdb=" OG SER L 123 " model vdw 2.201 3.040 nonbonded pdb=" O VAL B 78 " pdb=" ND2 ASN B 82 " model vdw 2.203 3.120 nonbonded pdb=" OG1 THR B 172 " pdb=" OE1 GLU B 187 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASP A 112 " pdb=" CB PHE A 148 " model vdw 2.207 3.440 nonbonded pdb=" O THR A 82 " pdb=" OH TYR B 32 " model vdw 2.220 3.040 ... (remaining 50724 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=1.00 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: 8.670 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.090 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6199 Z= 0.214 Angle : 0.804 12.483 8445 Z= 0.432 Chirality : 0.051 0.338 938 Planarity : 0.005 0.073 1085 Dihedral : 16.155 78.234 2218 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.60 % Allowed : 28.70 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.32), residues: 743 helix: -0.31 (0.64), residues: 76 sheet: 0.08 (0.30), residues: 313 loop : -0.18 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 88 TYR 0.037 0.002 TYR H 94 PHE 0.028 0.002 PHE A 35 TRP 0.045 0.003 TRP A 123 HIS 0.011 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 ( 6192) covalent geometry : angle 0.80172 / 0.43 ( 8431) SS BOND : bond 0.00346 / 0.18 ( 7) SS BOND : angle 1.73908 / 1.21 ( 14) hydrogen bonds : bond 0.24984 / 17.43 ( 250) hydrogen bonds : angle 9.17840 / 6.45 ( 663) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.142 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 102 average time/residue: 0.3712 time to fit residues: 40.0003 Evaluate side-chains 90 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain L residue 196 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN B 150 ASN H 39 GLN L 28 ASN L 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.162783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.127537 restraints weight = 9707.532| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.68 r_work: 0.3747 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6199 Z= 0.232 Angle : 0.736 10.083 8445 Z= 0.386 Chirality : 0.048 0.155 938 Planarity : 0.006 0.049 1085 Dihedral : 5.548 49.404 841 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.73 % Allowed : 22.12 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.40 (0.32), residues: 743 helix: -0.60 (0.61), residues: 79 sheet: 0.03 (0.29), residues: 316 loop : -0.32 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 88 TYR 0.035 0.002 TYR H 94 PHE 0.017 0.002 PHE H 27 TRP 0.026 0.002 TRP L 150 HIS 0.009 0.002 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.23 ( 6192) covalent geometry : angle 0.73498 / 0.39 ( 8431) SS BOND : bond 0.00550 / 0.28 ( 7) SS BOND : angle 1.17152 / 0.58 ( 14) hydrogen bonds : bond 0.05159 / 3.53 ( 250) hydrogen bonds : angle 6.83691 / 4.90 ( 663) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 97 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: B 87 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7069 (mp) REVERT: H 89 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7788 (mm-30) outliers start: 45 outliers final: 21 residues processed: 126 average time/residue: 0.3564 time to fit residues: 47.5684 Evaluate side-chains 109 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 46 TRP Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN L 30 ASN L 37 GLN L 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.164959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.130326 restraints weight = 9652.482| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.68 r_work: 0.3795 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6199 Z= 0.159 Angle : 0.680 10.199 8445 Z= 0.351 Chirality : 0.046 0.148 938 Planarity : 0.005 0.045 1085 Dihedral : 5.306 49.915 838 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.68 % Allowed : 23.32 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.32 (0.32), residues: 743 helix: -0.54 (0.62), residues: 79 sheet: 0.16 (0.29), residues: 315 loop : -0.36 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 144 TYR 0.030 0.002 TYR H 94 PHE 0.013 0.002 PHE L 211 TRP 0.023 0.002 TRP L 150 HIS 0.007 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 6192) covalent geometry : angle 0.67965 / 0.35 ( 8431) SS BOND : bond 0.00503 / 0.25 ( 7) SS BOND : angle 1.02206 / 0.50 ( 14) hydrogen bonds : bond 0.04229 / 2.87 ( 250) hydrogen bonds : angle 6.33348 / 4.55 ( 663) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.8109 (m-40) REVERT: A 103 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8467 (tp-100) REVERT: A 152 TYR cc_start: 0.6223 (OUTLIER) cc_final: 0.5959 (m-80) REVERT: B 87 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7078 (mp) REVERT: H 216 LYS cc_start: 0.4483 (OUTLIER) cc_final: 0.4201 (mmtt) REVERT: L 145 GLU cc_start: 0.7503 (mm-30) cc_final: 0.6879 (pt0) REVERT: L 147 LYS cc_start: 0.8183 (mppt) cc_final: 0.7938 (mmpt) REVERT: L 175 TYR cc_start: 0.8681 (m-80) cc_final: 0.8461 (m-80) outliers start: 38 outliers final: 20 residues processed: 117 average time/residue: 0.3888 time to fit residues: 48.1656 Evaluate side-chains 110 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 46 TRP Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 52 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 30 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN L 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.165936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.131380 restraints weight = 9690.175| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.68 r_work: 0.3803 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6199 Z= 0.149 Angle : 0.659 10.831 8445 Z= 0.338 Chirality : 0.046 0.148 938 Planarity : 0.005 0.045 1085 Dihedral : 5.216 52.265 838 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 7.47 % Allowed : 22.57 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.32), residues: 743 helix: -0.26 (0.65), residues: 72 sheet: 0.26 (0.29), residues: 325 loop : -0.37 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 88 TYR 0.030 0.002 TYR H 94 PHE 0.014 0.002 PHE L 211 TRP 0.024 0.002 TRP L 150 HIS 0.008 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 6192) covalent geometry : angle 0.65818 / 0.34 ( 8431) SS BOND : bond 0.00505 / 0.26 ( 7) SS BOND : angle 0.97519 / 0.48 ( 14) hydrogen bonds : bond 0.03867 / 2.62 ( 250) hydrogen bonds : angle 6.04212 / 4.35 ( 663) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 95 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7234 (t80) REVERT: H 216 LYS cc_start: 0.4480 (OUTLIER) cc_final: 0.4253 (mmtp) REVERT: L 107 GLU cc_start: 0.6482 (pt0) cc_final: 0.5942 (pt0) outliers start: 50 outliers final: 24 residues processed: 127 average time/residue: 0.3893 time to fit residues: 52.2213 Evaluate side-chains 114 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 TRP Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 52 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.0000 chunk 66 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 69 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 ASN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.164311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.129664 restraints weight = 9807.445| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.69 r_work: 0.3777 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6199 Z= 0.190 Angle : 0.695 10.511 8445 Z= 0.356 Chirality : 0.046 0.148 938 Planarity : 0.005 0.048 1085 Dihedral : 4.971 19.784 837 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.68 % Allowed : 25.11 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.32), residues: 743 helix: -0.21 (0.66), residues: 71 sheet: 0.24 (0.29), residues: 325 loop : -0.36 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 88 TYR 0.034 0.002 TYR H 94 PHE 0.016 0.002 PHE A 35 TRP 0.023 0.002 TRP L 150 HIS 0.008 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 6192) covalent geometry : angle 0.69413 / 0.36 ( 8431) SS BOND : bond 0.00567 / 0.29 ( 7) SS BOND : angle 0.98065 / 0.47 ( 14) hydrogen bonds : bond 0.04000 / 2.70 ( 250) hydrogen bonds : angle 6.10132 / 4.39 ( 663) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 TYR cc_start: 0.8182 (OUTLIER) cc_final: 0.7296 (t80) REVERT: A 130 VAL cc_start: 0.8860 (m) cc_final: 0.8640 (p) REVERT: A 161 GLU cc_start: 0.6633 (tp30) cc_final: 0.6331 (tp30) REVERT: B 26 TYR cc_start: 0.7829 (t80) cc_final: 0.7464 (t80) REVERT: H 89 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7796 (mm-30) REVERT: H 216 LYS cc_start: 0.4506 (OUTLIER) cc_final: 0.4266 (mmtp) REVERT: L 107 GLU cc_start: 0.6501 (pt0) cc_final: 0.5855 (pt0) REVERT: L 145 GLU cc_start: 0.7651 (mm-30) cc_final: 0.6695 (pt0) REVERT: L 175 TYR cc_start: 0.8724 (m-80) cc_final: 0.8197 (m-80) outliers start: 38 outliers final: 24 residues processed: 120 average time/residue: 0.3883 time to fit residues: 49.1545 Evaluate side-chains 116 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 46 TRP Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 52 ARG Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.163094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.128354 restraints weight = 9631.423| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.72 r_work: 0.3752 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6199 Z= 0.204 Angle : 0.712 11.300 8445 Z= 0.364 Chirality : 0.047 0.148 938 Planarity : 0.005 0.049 1085 Dihedral : 5.083 18.968 837 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.28 % Allowed : 24.66 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.32), residues: 743 helix: -0.26 (0.66), residues: 71 sheet: 0.16 (0.29), residues: 326 loop : -0.47 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 88 TYR 0.036 0.002 TYR H 94 PHE 0.024 0.002 PHE H 27 TRP 0.029 0.002 TRP L 150 HIS 0.008 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 6192) covalent geometry : angle 0.71136 / 0.36 ( 8431) SS BOND : bond 0.00494 / 0.26 ( 7) SS BOND : angle 0.97187 / 0.47 ( 14) hydrogen bonds : bond 0.04083 / 2.78 ( 250) hydrogen bonds : angle 6.13719 / 4.41 ( 663) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 94 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 TYR cc_start: 0.8210 (OUTLIER) cc_final: 0.7299 (t80) REVERT: B 26 TYR cc_start: 0.7815 (t80) cc_final: 0.7588 (t80) REVERT: H 89 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7806 (mm-30) REVERT: H 216 LYS cc_start: 0.4476 (OUTLIER) cc_final: 0.4236 (mmtp) REVERT: L 107 GLU cc_start: 0.6610 (pt0) cc_final: 0.5882 (pt0) REVERT: L 145 GLU cc_start: 0.7596 (mm-30) cc_final: 0.6702 (pt0) REVERT: L 147 LYS cc_start: 0.8297 (mppt) cc_final: 0.8074 (mmpt) REVERT: L 175 TYR cc_start: 0.8757 (m-80) cc_final: 0.7918 (m-80) outliers start: 42 outliers final: 26 residues processed: 120 average time/residue: 0.3574 time to fit residues: 45.3151 Evaluate side-chains 118 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 TRP Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 52 ARG Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.162400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.127380 restraints weight = 9803.938| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.76 r_work: 0.3740 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6199 Z= 0.214 Angle : 0.727 11.462 8445 Z= 0.372 Chirality : 0.048 0.154 938 Planarity : 0.005 0.050 1085 Dihedral : 5.162 18.711 837 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.98 % Allowed : 25.71 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.32), residues: 743 helix: -0.39 (0.65), residues: 71 sheet: 0.07 (0.29), residues: 315 loop : -0.47 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 88 TYR 0.037 0.002 TYR H 94 PHE 0.021 0.002 PHE H 27 TRP 0.032 0.002 TRP L 150 HIS 0.009 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 ( 6192) covalent geometry : angle 0.72609 / 0.37 ( 8431) SS BOND : bond 0.00522 / 0.27 ( 7) SS BOND : angle 0.96470 / 0.49 ( 14) hydrogen bonds : bond 0.04126 / 2.82 ( 250) hydrogen bonds : angle 6.19102 / 4.44 ( 663) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7281 (t80) REVERT: H 89 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7824 (mm-30) REVERT: H 216 LYS cc_start: 0.4483 (OUTLIER) cc_final: 0.4249 (mmtp) REVERT: L 107 GLU cc_start: 0.6670 (pt0) cc_final: 0.6359 (pt0) REVERT: L 145 GLU cc_start: 0.7698 (mm-30) cc_final: 0.6803 (pt0) outliers start: 40 outliers final: 26 residues processed: 124 average time/residue: 0.3947 time to fit residues: 51.7514 Evaluate side-chains 116 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 52 ARG Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 0.0970 chunk 58 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.166502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.132136 restraints weight = 9665.506| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.70 r_work: 0.3818 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6199 Z= 0.142 Angle : 0.701 12.632 8445 Z= 0.354 Chirality : 0.046 0.148 938 Planarity : 0.005 0.046 1085 Dihedral : 4.954 19.445 837 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.33 % Allowed : 27.80 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.27 (0.32), residues: 743 helix: -0.33 (0.64), residues: 71 sheet: 0.19 (0.29), residues: 330 loop : -0.39 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 88 TYR 0.027 0.002 TYR H 94 PHE 0.018 0.002 PHE L 118 TRP 0.030 0.002 TRP L 150 HIS 0.010 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 6192) covalent geometry : angle 0.69987 / 0.35 ( 8431) SS BOND : bond 0.00498 / 0.26 ( 7) SS BOND : angle 1.14230 / 0.77 ( 14) hydrogen bonds : bond 0.03687 / 2.52 ( 250) hydrogen bonds : angle 5.89400 / 4.21 ( 663) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.156 Fit side-chains REVERT: A 19 TYR cc_start: 0.8170 (OUTLIER) cc_final: 0.7256 (t80) REVERT: B 22 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.5363 (mp0) REVERT: H 216 LYS cc_start: 0.4463 (OUTLIER) cc_final: 0.4228 (mmtp) REVERT: L 107 GLU cc_start: 0.6636 (pt0) cc_final: 0.5954 (pt0) REVERT: L 145 GLU cc_start: 0.7634 (mm-30) cc_final: 0.6737 (pt0) REVERT: L 175 TYR cc_start: 0.8499 (m-80) cc_final: 0.7739 (m-80) outliers start: 29 outliers final: 15 residues processed: 118 average time/residue: 0.3710 time to fit residues: 46.0787 Evaluate side-chains 106 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain H residue 52 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 3 optimal weight: 4.9990 chunk 46 optimal weight: 0.0980 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 ASN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.165284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.131015 restraints weight = 9681.786| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.71 r_work: 0.3801 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6199 Z= 0.166 Angle : 0.735 12.527 8445 Z= 0.370 Chirality : 0.046 0.145 938 Planarity : 0.005 0.045 1085 Dihedral : 5.023 19.749 837 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.04 % Allowed : 27.95 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.32), residues: 743 helix: -0.32 (0.66), residues: 69 sheet: 0.24 (0.30), residues: 320 loop : -0.52 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 88 TYR 0.025 0.002 TYR H 94 PHE 0.023 0.002 PHE A 35 TRP 0.037 0.002 TRP L 150 HIS 0.010 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 6192) covalent geometry : angle 0.73424 / 0.37 ( 8431) SS BOND : bond 0.00425 / 0.22 ( 7) SS BOND : angle 0.93404 / 0.46 ( 14) hydrogen bonds : bond 0.03780 / 2.59 ( 250) hydrogen bonds : angle 5.95069 / 4.26 ( 663) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 19 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7282 (t80) REVERT: H 216 LYS cc_start: 0.4479 (OUTLIER) cc_final: 0.4246 (mmtp) REVERT: L 107 GLU cc_start: 0.6627 (pt0) cc_final: 0.5945 (pt0) REVERT: L 145 GLU cc_start: 0.7653 (mm-30) cc_final: 0.6735 (pt0) REVERT: L 147 LYS cc_start: 0.8162 (mppt) cc_final: 0.7899 (mmpt) REVERT: L 175 TYR cc_start: 0.8494 (m-80) cc_final: 0.7655 (m-80) outliers start: 27 outliers final: 16 residues processed: 110 average time/residue: 0.3374 time to fit residues: 39.2435 Evaluate side-chains 106 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain H residue 52 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 66 optimal weight: 0.0070 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 68 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.167970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.134016 restraints weight = 9618.363| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.70 r_work: 0.3850 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6199 Z= 0.140 Angle : 0.727 13.648 8445 Z= 0.365 Chirality : 0.046 0.192 938 Planarity : 0.005 0.044 1085 Dihedral : 4.911 20.227 837 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.99 % Allowed : 28.85 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.32), residues: 743 helix: -0.36 (0.65), residues: 69 sheet: 0.22 (0.28), residues: 339 loop : -0.46 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 88 TYR 0.021 0.002 TYR H 94 PHE 0.030 0.002 PHE L 118 TRP 0.038 0.002 TRP L 150 HIS 0.011 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 6192) covalent geometry : angle 0.72678 / 0.36 ( 8431) SS BOND : bond 0.00442 / 0.23 ( 7) SS BOND : angle 1.03288 / 0.53 ( 14) hydrogen bonds : bond 0.03582 / 2.48 ( 250) hydrogen bonds : angle 5.85832 / 4.18 ( 663) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 19 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7360 (t80) REVERT: A 92 THR cc_start: 0.7960 (m) cc_final: 0.7634 (p) REVERT: H 216 LYS cc_start: 0.4488 (OUTLIER) cc_final: 0.4248 (mmtp) REVERT: L 107 GLU cc_start: 0.6620 (pt0) cc_final: 0.5941 (pt0) REVERT: L 145 GLU cc_start: 0.7573 (mm-30) cc_final: 0.6712 (pt0) REVERT: L 175 TYR cc_start: 0.8344 (m-80) cc_final: 0.7644 (m-80) outliers start: 20 outliers final: 14 residues processed: 113 average time/residue: 0.3609 time to fit residues: 43.0685 Evaluate side-chains 103 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 3 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.164898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.130660 restraints weight = 9571.972| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.67 r_work: 0.3798 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.141 6199 Z= 0.217 Angle : 1.096 44.287 8445 Z= 0.605 Chirality : 0.047 0.145 938 Planarity : 0.006 0.057 1085 Dihedral : 5.092 19.780 837 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.54 % Allowed : 29.90 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.41 (0.32), residues: 743 helix: -0.28 (0.67), residues: 69 sheet: 0.18 (0.29), residues: 331 loop : -0.62 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 144 TYR 0.026 0.002 TYR H 94 PHE 0.097 0.003 PHE A 35 TRP 0.050 0.003 TRP A 123 HIS 0.008 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.22 ( 6192) covalent geometry : angle 1.09644 / 0.61 ( 8431) SS BOND : bond 0.00416 / 0.22 ( 7) SS BOND : angle 0.94871 / 0.46 ( 14) hydrogen bonds : bond 0.03861 / 2.68 ( 250) hydrogen bonds : angle 6.00052 / 4.28 ( 663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1993.78 seconds wall clock time: 34 minutes 47.21 seconds (2087.21 seconds total)