Starting phenix.real_space_refine on Wed Jul 1 22:49:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tlz_25991/07_2026/7tlz_25991.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tlz_25991/07_2026/7tlz_25991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tlz_25991/07_2026/7tlz_25991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tlz_25991/07_2026/7tlz_25991.map" model { file = "/net/cci-nas-00/data/ceres_data/7tlz_25991/07_2026/7tlz_25991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tlz_25991/07_2026/7tlz_25991.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tlz_25991/07_2026/7tlz_25991.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tlz_25991/07_2026/7tlz_25991.cif" } resolution = 3.3 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= 0.049 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 14 5.16 5 C 2359 2.51 5 N 603 2.21 5 O 645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3621 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 761 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1873 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 15, 'TRANS': 235} Chain breaks: 5 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 10, 'GLU:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 0.99, per 1000 atoms: 0.27 Number of scatterers: 3621 At special positions: 0 Unit cell: (84.3, 69.126, 76.713, 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 14 16.00 O 645 8.00 N 603 7.00 C 2359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.20 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 15 " - pdb=" SG CYS J 136 " distance=2.04 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 166 " distance=2.03 Simple disulfide: pdb=" SG CYS J 291 " - pdb=" SG CYS J 301 " distance=2.02 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 Links applied NAG-ASN " NAG J1401 " - " ASN J 165 " " NAG J1402 " - " ASN J 282 " " NAG J1403 " - " ASN J 17 " " NAG J1404 " - " ASN J 234 " " NAG J1405 " - " ASN J 61 " " NAG J1406 " - " ASN J 122 " Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 163.5 milliseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 884 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 11 sheets defined 4.2% alpha, 50.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'J' and resid 294 through 303 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 4.086A pdb=" N ASP A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 67 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 6.651A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 33 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 97 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 removed outlier: 6.651A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 33 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.702A pdb=" N MET B 34 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'J' and resid 27 through 30 Processing sheet with id=AA8, first strand: chain 'J' and resid 27 through 30 removed outlier: 8.184A pdb=" N ASN J 61 " --> pdb=" O TYR J 269 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR J 269 " --> pdb=" O ASN J 61 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE J 201 " --> pdb=" O ASP J 228 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP J 228 " --> pdb=" O PHE J 201 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE J 203 " --> pdb=" O LEU J 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 47 through 55 removed outlier: 4.067A pdb=" N ASP J 287 " --> pdb=" O LYS J 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 84 through 85 removed outlier: 13.167A pdb=" N PHE J 238 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 13.074A pdb=" N PHE J 135 " --> pdb=" O PHE J 238 " (cutoff:3.500A) removed outlier: 13.017A pdb=" N THR J 240 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 11.290A pdb=" N ASN J 137 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N LEU J 242 " --> pdb=" O ASN J 137 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LEU J 244 " --> pdb=" O PRO J 139 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU J 141 " --> pdb=" O LEU J 244 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER J 162 " --> pdb=" O GLN J 134 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N CYS J 136 " --> pdb=" O TYR J 160 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR J 160 " --> pdb=" O CYS J 136 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP J 138 " --> pdb=" O ARG J 158 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ARG J 158 " --> pdb=" O ASP J 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 84 through 85 removed outlier: 3.576A pdb=" N GLY J 103 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA J 243 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE J 101 " --> pdb=" O ALA J 243 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ARG J 102 " --> pdb=" O ASN J 121 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE J 168 " --> pdb=" O VAL J 130 " (cutoff:3.500A) 178 hydrogen bonds defined for protein. 423 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: 0.50 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 636 1.32 - 1.45: 1067 1.45 - 1.58: 1993 1.58 - 1.71: 1 1.71 - 1.84: 18 Bond restraints: 3715 Sorted by residual: bond pdb=" CA ASN J 165 " pdb=" C ASN J 165 " ideal model delta sigma weight residual 1.523 1.582 -0.059 1.42e-02 4.96e+03 1.73e+01 bond pdb=" CA CYS J 131 " pdb=" C CYS J 131 " ideal model delta sigma weight residual 1.522 1.567 -0.046 1.24e-02 6.50e+03 1.36e+01 bond pdb=" C ASN J 165 " pdb=" O ASN J 165 " ideal model delta sigma weight residual 1.235 1.195 0.040 1.20e-02 6.94e+03 1.10e+01 bond pdb=" C5 NAG J1406 " pdb=" O5 NAG J1406 " ideal model delta sigma weight residual 1.413 1.473 -0.060 2.00e-02 2.50e+03 9.10e+00 bond pdb=" C5 NAG J1401 " pdb=" O5 NAG J1401 " ideal model delta sigma weight residual 1.413 1.473 -0.060 2.00e-02 2.50e+03 8.89e+00 ... (remaining 3710 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 4328 1.66 - 3.31: 596 3.31 - 4.97: 88 4.97 - 6.63: 36 6.63 - 8.28: 14 Bond angle restraints: 5062 Sorted by residual: angle pdb=" C LEU J 24 " pdb=" N PRO J 25 " pdb=" CA PRO J 25 " ideal model delta sigma weight residual 119.66 125.78 -6.12 7.20e-01 1.93e+00 7.23e+01 angle pdb=" C ASP J 138 " pdb=" N PRO J 139 " pdb=" CA PRO J 139 " ideal model delta sigma weight residual 119.76 127.46 -7.70 1.00e+00 1.00e+00 5.93e+01 angle pdb=" C PRO J 25 " pdb=" N PRO J 26 " pdb=" CA PRO J 26 " ideal model delta sigma weight residual 119.85 127.21 -7.36 1.01e+00 9.80e-01 5.32e+01 angle pdb=" C GLY A 99 " pdb=" N PRO A 100 " pdb=" CA PRO A 100 " ideal model delta sigma weight residual 119.32 127.60 -8.28 1.14e+00 7.69e-01 5.28e+01 angle pdb=" C ASP J 294 " pdb=" N PRO J 295 " pdb=" CA PRO J 295 " ideal model delta sigma weight residual 119.56 126.43 -6.87 1.02e+00 9.61e-01 4.54e+01 ... (remaining 5057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.38: 2007 14.38 - 28.75: 67 28.75 - 43.13: 17 43.13 - 57.51: 6 57.51 - 71.88: 4 Dihedral angle restraints: 2101 sinusoidal: 723 harmonic: 1378 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 50.62 42.38 1 1.00e+01 1.00e-02 2.51e+01 dihedral pdb=" CA TYR B 95 " pdb=" C TYR B 95 " pdb=" N CYS B 96 " pdb=" CA CYS B 96 " ideal model delta harmonic sigma weight residual 180.00 164.28 15.72 0 5.00e+00 4.00e-02 9.88e+00 dihedral pdb=" CG ARG B 67 " pdb=" CD ARG B 67 " pdb=" NE ARG B 67 " pdb=" CZ ARG B 67 " ideal model delta sinusoidal sigma weight residual 180.00 139.40 40.60 2 1.50e+01 4.44e-03 9.03e+00 ... (remaining 2098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 409 0.071 - 0.142: 128 0.142 - 0.212: 24 0.212 - 0.283: 9 0.283 - 0.354: 5 Chirality restraints: 575 Sorted by residual: chirality pdb=" C2 NAG J1405 " pdb=" C1 NAG J1405 " pdb=" C3 NAG J1405 " pdb=" N2 NAG J1405 " both_signs ideal model delta sigma weight residual False -2.49 -2.85 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C2 NAG J1401 " pdb=" C1 NAG J1401 " pdb=" C3 NAG J1401 " pdb=" N2 NAG J1401 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C2 NAG J1403 " pdb=" C1 NAG J1403 " pdb=" C3 NAG J1403 " pdb=" N2 NAG J1403 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 572 not shown) Planarity restraints: 650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN J 282 " 0.026 2.00e-02 2.50e+03 2.85e-02 1.01e+01 pdb=" CG ASN J 282 " -0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN J 282 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN J 282 " -0.045 2.00e-02 2.50e+03 pdb=" C1 NAG J1402 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 269 " 0.033 2.00e-02 2.50e+03 1.66e-02 5.54e+00 pdb=" CG TYR J 269 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR J 269 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR J 269 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR J 269 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR J 269 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR J 269 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR J 269 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 17 " 0.019 2.00e-02 2.50e+03 1.99e-02 4.94e+00 pdb=" CG ASN J 17 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN J 17 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN J 17 " -0.031 2.00e-02 2.50e+03 pdb=" C1 NAG J1403 " 0.024 2.00e-02 2.50e+03 ... (remaining 647 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.04: 2061 3.04 - 3.51: 3034 3.51 - 3.97: 5566 3.97 - 4.44: 6349 4.44 - 4.90: 10682 Nonbonded interactions: 27692 Sorted by model distance: nonbonded pdb=" O ASP A 92 " pdb=" NH1 ARG B 103 " model vdw 2.581 3.120 nonbonded pdb=" C ASP B 101 " pdb=" OD1 ASP B 101 " model vdw 2.611 3.270 nonbonded pdb=" N ASN J 165 " pdb=" OD1 ASN J 165 " model vdw 2.617 3.120 nonbonded pdb=" N LYS B 76 " pdb=" N ASN B 77 " model vdw 2.628 2.560 nonbonded pdb=" N GLY B 33 " pdb=" O GLY B 33 " model vdw 2.641 2.496 ... (remaining 27687 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: 12.560 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.280 Find NCS groups from input model: 0.010 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: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.011 0.165 3726 Z= 0.621 Angle : 1.309 8.282 5090 Z= 0.878 Chirality : 0.078 0.354 575 Planarity : 0.005 0.021 644 Dihedral : 9.171 71.882 1202 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.31 % Allowed : 0.31 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.38), residues: 457 helix: -0.12 (1.59), residues: 11 sheet: 1.60 (0.36), residues: 187 loop : 0.04 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 34 TYR 0.033 0.005 TYR J 269 PHE 0.016 0.003 PHE A 98 TRP 0.024 0.005 TRP J 64 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.01068 / 0.60 ( 3715) covalent geometry : angle 1.30058 / 0.88 ( 5062) SS BOND : bond 0.07408 / 3.90 ( 5) SS BOND : angle 2.89817 / 1.77 ( 10) hydrogen bonds : bond 0.17709 / 12.11 ( 154) hydrogen bonds : angle 8.00612 / 5.42 ( 423) link_NAG-ASN : bond 0.04434 / 2.53 ( 6) link_NAG-ASN : angle 1.96985 / 1.36 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 202 LYS cc_start: 0.8602 (mttm) cc_final: 0.8380 (mttp) outliers start: 1 outliers final: 1 residues processed: 84 average time/residue: 0.0984 time to fit residues: 9.6405 Evaluate side-chains 60 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 165 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN B 74 ASN J 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.150039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.118636 restraints weight = 4552.470| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.69 r_work: 0.3164 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3726 Z= 0.146 Angle : 0.612 9.811 5090 Z= 0.321 Chirality : 0.047 0.199 575 Planarity : 0.004 0.024 644 Dihedral : 4.401 17.263 513 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.62 % Allowed : 6.56 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.80 (0.38), residues: 457 helix: 1.65 (1.49), residues: 11 sheet: 1.37 (0.39), residues: 174 loop : -0.04 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 87 TYR 0.022 0.002 TYR J 265 PHE 0.014 0.002 PHE A 98 TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS J 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 3715) covalent geometry : angle 0.59990 / 0.32 ( 5062) SS BOND : bond 0.00343 / 0.19 ( 5) SS BOND : angle 2.09235 / 1.52 ( 10) hydrogen bonds : bond 0.03891 / 2.50 ( 154) hydrogen bonds : angle 6.07758 / 4.19 ( 423) link_NAG-ASN : bond 0.00225 / 0.11 ( 6) link_NAG-ASN : angle 1.54599 / 1.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.137 Fit side-chains REVERT: J 41 LYS cc_start: 0.7782 (mttt) cc_final: 0.7111 (mtpt) outliers start: 2 outliers final: 0 residues processed: 54 average time/residue: 0.0957 time to fit residues: 6.1152 Evaluate side-chains 51 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.147962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117888 restraints weight = 4543.810| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.67 r_work: 0.3134 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3726 Z= 0.134 Angle : 0.550 6.069 5090 Z= 0.290 Chirality : 0.046 0.192 575 Planarity : 0.004 0.032 644 Dihedral : 4.136 14.746 511 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.85 (0.39), residues: 457 helix: 2.45 (1.65), residues: 11 sheet: 1.34 (0.38), residues: 186 loop : -0.07 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 102 TYR 0.020 0.002 TYR J 265 PHE 0.014 0.002 PHE A 98 TRP 0.010 0.001 TRP B 47 HIS 0.003 0.001 HIS J 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 ( 3715) covalent geometry : angle 0.54521 / 0.29 ( 5062) SS BOND : bond 0.00330 / 0.18 ( 5) SS BOND : angle 1.15300 / 0.80 ( 10) hydrogen bonds : bond 0.03722 / 2.37 ( 154) hydrogen bonds : angle 5.39268 / 3.77 ( 423) link_NAG-ASN : bond 0.00261 / 0.13 ( 6) link_NAG-ASN : angle 1.04765 / 0.67 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.099 Fit side-chains REVERT: J 205 SER cc_start: 0.9192 (p) cc_final: 0.8932 (t) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1043 time to fit residues: 6.5292 Evaluate side-chains 48 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 16 optimal weight: 0.0040 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.146695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.116288 restraints weight = 4537.192| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.56 r_work: 0.3126 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3726 Z= 0.133 Angle : 0.535 5.996 5090 Z= 0.279 Chirality : 0.046 0.191 575 Planarity : 0.004 0.032 644 Dihedral : 4.083 14.350 511 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.31 % Allowed : 8.75 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.78 (0.39), residues: 457 helix: 2.52 (1.70), residues: 11 sheet: 1.64 (0.39), residues: 169 loop : -0.30 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 87 TYR 0.020 0.002 TYR J 265 PHE 0.012 0.001 PHE J 92 TRP 0.012 0.001 TRP B 47 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 ( 3715) covalent geometry : angle 0.53065 / 0.28 ( 5062) SS BOND : bond 0.00328 / 0.17 ( 5) SS BOND : angle 0.95974 / 0.67 ( 10) hydrogen bonds : bond 0.03443 / 2.23 ( 154) hydrogen bonds : angle 5.24781 / 3.67 ( 423) link_NAG-ASN : bond 0.00229 / 0.11 ( 6) link_NAG-ASN : angle 1.07754 / 0.72 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.132 Fit side-chains REVERT: A 42 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8354 (mmmm) REVERT: J 205 SER cc_start: 0.9187 (p) cc_final: 0.8914 (t) outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.1000 time to fit residues: 5.5853 Evaluate side-chains 48 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.0040 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.144732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.114321 restraints weight = 4518.275| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.59 r_work: 0.3100 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3726 Z= 0.164 Angle : 0.567 6.727 5090 Z= 0.294 Chirality : 0.047 0.204 575 Planarity : 0.004 0.031 644 Dihedral : 4.168 14.403 511 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.62 % Allowed : 8.75 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.86 (0.40), residues: 457 helix: 2.16 (1.75), residues: 11 sheet: 1.87 (0.36), residues: 204 loop : -0.74 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 237 TYR 0.021 0.002 TYR J 265 PHE 0.015 0.002 PHE J 92 TRP 0.014 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.16 ( 3715) covalent geometry : angle 0.56261 / 0.29 ( 5062) SS BOND : bond 0.00347 / 0.19 ( 5) SS BOND : angle 1.05489 / 0.73 ( 10) hydrogen bonds : bond 0.03704 / 2.40 ( 154) hydrogen bonds : angle 5.25989 / 3.69 ( 423) link_NAG-ASN : bond 0.00189 / 0.10 ( 6) link_NAG-ASN : angle 1.08320 / 0.73 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.115 Fit side-chains REVERT: J 205 SER cc_start: 0.9206 (p) cc_final: 0.8908 (t) outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.0926 time to fit residues: 5.1505 Evaluate side-chains 46 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 31 optimal weight: 0.0370 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.114881 restraints weight = 4539.643| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.64 r_work: 0.3114 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3726 Z= 0.136 Angle : 0.527 6.031 5090 Z= 0.274 Chirality : 0.046 0.199 575 Planarity : 0.004 0.029 644 Dihedral : 4.068 13.560 511 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.62 % Allowed : 9.06 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.72 (0.39), residues: 457 helix: 1.98 (1.77), residues: 11 sheet: 1.78 (0.36), residues: 204 loop : -0.82 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 102 TYR 0.020 0.002 TYR J 265 PHE 0.013 0.001 PHE J 92 TRP 0.011 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 3715) covalent geometry : angle 0.52363 / 0.27 ( 5062) SS BOND : bond 0.00286 / 0.16 ( 5) SS BOND : angle 0.83647 / 0.58 ( 10) hydrogen bonds : bond 0.03373 / 2.19 ( 154) hydrogen bonds : angle 5.12839 / 3.60 ( 423) link_NAG-ASN : bond 0.00222 / 0.11 ( 6) link_NAG-ASN : angle 1.06596 / 0.71 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.135 Fit side-chains REVERT: J 41 LYS cc_start: 0.7833 (mttt) cc_final: 0.7221 (mtpt) REVERT: J 205 SER cc_start: 0.9196 (p) cc_final: 0.8926 (t) outliers start: 2 outliers final: 1 residues processed: 50 average time/residue: 0.1177 time to fit residues: 6.8038 Evaluate side-chains 48 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 0.0370 chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 0.0000 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.146372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.114787 restraints weight = 4623.865| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.76 r_work: 0.3111 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3726 Z= 0.110 Angle : 0.508 5.973 5090 Z= 0.263 Chirality : 0.045 0.194 575 Planarity : 0.003 0.028 644 Dihedral : 3.912 13.388 511 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.31 % Allowed : 10.00 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.81 (0.39), residues: 457 helix: 2.20 (1.77), residues: 11 sheet: 1.82 (0.36), residues: 203 loop : -0.74 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.019 0.001 TYR J 265 PHE 0.012 0.001 PHE J 92 TRP 0.011 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 3715) covalent geometry : angle 0.50432 / 0.26 ( 5062) SS BOND : bond 0.00267 / 0.15 ( 5) SS BOND : angle 0.71649 / 0.49 ( 10) hydrogen bonds : bond 0.03149 / 2.05 ( 154) hydrogen bonds : angle 5.01078 / 3.52 ( 423) link_NAG-ASN : bond 0.00243 / 0.12 ( 6) link_NAG-ASN : angle 1.05615 / 0.71 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.133 Fit side-chains REVERT: J 41 LYS cc_start: 0.7892 (mttt) cc_final: 0.7184 (mtpt) REVERT: J 205 SER cc_start: 0.9204 (p) cc_final: 0.8929 (t) REVERT: J 304 LYS cc_start: 0.8631 (mmtm) cc_final: 0.8219 (mptt) outliers start: 1 outliers final: 0 residues processed: 50 average time/residue: 0.1083 time to fit residues: 6.3049 Evaluate side-chains 48 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.145101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113633 restraints weight = 4575.585| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.74 r_work: 0.3108 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3726 Z= 0.141 Angle : 0.540 6.547 5090 Z= 0.279 Chirality : 0.046 0.200 575 Planarity : 0.004 0.029 644 Dihedral : 4.025 13.611 511 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.71 (0.39), residues: 457 helix: 2.01 (1.75), residues: 11 sheet: 1.75 (0.36), residues: 204 loop : -0.82 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.021 0.002 TYR J 265 PHE 0.014 0.001 PHE J 92 TRP 0.011 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 ( 3715) covalent geometry : angle 0.53658 / 0.28 ( 5062) SS BOND : bond 0.00288 / 0.16 ( 5) SS BOND : angle 0.82241 / 0.55 ( 10) hydrogen bonds : bond 0.03401 / 2.22 ( 154) hydrogen bonds : angle 5.05045 / 3.53 ( 423) link_NAG-ASN : bond 0.00204 / 0.10 ( 6) link_NAG-ASN : angle 1.08955 / 0.74 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.135 Fit side-chains REVERT: J 41 LYS cc_start: 0.7890 (mttt) cc_final: 0.7191 (mtpt) REVERT: J 205 SER cc_start: 0.9221 (p) cc_final: 0.8928 (t) REVERT: J 304 LYS cc_start: 0.8699 (mmtm) cc_final: 0.8302 (mptt) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1072 time to fit residues: 5.9390 Evaluate side-chains 44 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.144337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.114257 restraints weight = 4546.655| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.62 r_work: 0.3116 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3726 Z= 0.143 Angle : 0.540 6.383 5090 Z= 0.278 Chirality : 0.046 0.198 575 Planarity : 0.004 0.029 644 Dihedral : 4.023 13.558 511 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.31 % Allowed : 10.00 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.64 (0.39), residues: 457 helix: 1.98 (1.74), residues: 11 sheet: 1.74 (0.36), residues: 204 loop : -0.89 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.020 0.002 TYR J 265 PHE 0.014 0.001 PHE J 92 TRP 0.011 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.14 ( 3715) covalent geometry : angle 0.53575 / 0.28 ( 5062) SS BOND : bond 0.00287 / 0.16 ( 5) SS BOND : angle 0.91078 / 0.59 ( 10) hydrogen bonds : bond 0.03362 / 2.20 ( 154) hydrogen bonds : angle 5.05172 / 3.54 ( 423) link_NAG-ASN : bond 0.00198 / 0.10 ( 6) link_NAG-ASN : angle 1.08645 / 0.73 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.132 Fit side-chains REVERT: J 41 LYS cc_start: 0.7891 (mttt) cc_final: 0.7193 (mtpt) REVERT: J 205 SER cc_start: 0.9230 (p) cc_final: 0.8954 (t) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.1060 time to fit residues: 5.3521 Evaluate side-chains 43 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 38 optimal weight: 0.0470 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.144649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.114396 restraints weight = 4554.908| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.63 r_work: 0.3119 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3726 Z= 0.138 Angle : 0.537 6.439 5090 Z= 0.277 Chirality : 0.046 0.196 575 Planarity : 0.004 0.029 644 Dihedral : 4.025 13.242 511 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.63 (0.39), residues: 457 helix: 2.03 (1.75), residues: 11 sheet: 1.74 (0.36), residues: 204 loop : -0.91 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.021 0.002 TYR J 265 PHE 0.013 0.001 PHE J 92 TRP 0.011 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 3715) covalent geometry : angle 0.53276 / 0.28 ( 5062) SS BOND : bond 0.00269 / 0.15 ( 5) SS BOND : angle 0.85495 / 0.56 ( 10) hydrogen bonds : bond 0.03343 / 2.19 ( 154) hydrogen bonds : angle 5.03743 / 3.52 ( 423) link_NAG-ASN : bond 0.00212 / 0.11 ( 6) link_NAG-ASN : angle 1.08949 / 0.74 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.135 Fit side-chains REVERT: J 41 LYS cc_start: 0.7893 (mttt) cc_final: 0.7191 (mtpt) REVERT: J 97 LYS cc_start: 0.8798 (ttmm) cc_final: 0.8353 (mtmm) REVERT: J 205 SER cc_start: 0.9236 (p) cc_final: 0.8949 (t) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1131 time to fit residues: 5.8111 Evaluate side-chains 43 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.143303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113458 restraints weight = 4514.362| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.57 r_work: 0.3112 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3726 Z= 0.154 Angle : 0.552 6.591 5090 Z= 0.284 Chirality : 0.046 0.199 575 Planarity : 0.004 0.030 644 Dihedral : 4.088 13.342 511 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.58 (0.39), residues: 457 helix: 1.96 (1.75), residues: 11 sheet: 1.72 (0.36), residues: 204 loop : -0.95 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.021 0.002 TYR J 265 PHE 0.014 0.001 PHE J 92 TRP 0.012 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.15 ( 3715) covalent geometry : angle 0.54804 / 0.28 ( 5062) SS BOND : bond 0.00288 / 0.17 ( 5) SS BOND : angle 1.00117 / 0.64 ( 10) hydrogen bonds : bond 0.03458 / 2.26 ( 154) hydrogen bonds : angle 5.08765 / 3.56 ( 423) link_NAG-ASN : bond 0.00195 / 0.10 ( 6) link_NAG-ASN : angle 1.10056 / 0.75 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1113.99 seconds wall clock time: 19 minutes 51.35 seconds (1191.35 seconds total)