Starting phenix.real_space_refine on Tue Mar 3 11:59:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tlz_25991/03_2026/7tlz_25991.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tlz_25991/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tlz_25991/03_2026/7tlz_25991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tlz_25991/03_2026/7tlz_25991.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tlz_25991/03_2026/7tlz_25991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tlz_25991/03_2026/7tlz_25991.map" } 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-5986/lib/python3.9/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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 0.91, per 1000 atoms: 0.25 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: 0.26 Conformation dependent library (CDL) restraints added in 134.4 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: 0.15 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: 0.59 Time building geometry restraints manager: 0.35 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: 2120 14.38 - 28.75: 80 28.75 - 43.13: 17 43.13 - 57.51: 6 57.51 - 71.88: 4 Dihedral angle restraints: 2227 sinusoidal: 849 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 2224 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: 12.570 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: 0.020 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.530 Find NCS groups from input model: 0.020 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 9.091 71.882 1328 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 covalent geometry : bond 0.01068 ( 3715) covalent geometry : angle 1.30058 ( 5062) SS BOND : bond 0.07408 ( 5) SS BOND : angle 2.89817 ( 10) hydrogen bonds : bond 0.17709 ( 154) hydrogen bonds : angle 8.00612 ( 423) link_NAG-ASN : bond 0.04434 ( 6) link_NAG-ASN : angle 1.96985 ( 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 : 0.095 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: 0.1099 time to fit residues: 10.6522 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 : 0.131 ------------------------------------------------------------------------------- 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: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3685 r_free = 0.3685 target = 0.149397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.117719 restraints weight = 4559.805| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.73 r_work: 0.3158 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3726 Z= 0.169 Angle : 0.623 9.200 5090 Z= 0.329 Chirality : 0.048 0.224 575 Planarity : 0.004 0.024 644 Dihedral : 4.895 25.370 639 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: 1.47 (1.49), residues: 11 sheet: 1.40 (0.39), residues: 171 loop : -0.05 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 87 TYR 0.022 0.002 TYR J 265 PHE 0.016 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 covalent geometry : bond 0.00404 ( 3715) covalent geometry : angle 0.61294 ( 5062) SS BOND : bond 0.00680 ( 5) SS BOND : angle 1.67776 ( 10) hydrogen bonds : bond 0.04095 ( 154) hydrogen bonds : angle 6.17284 ( 423) link_NAG-ASN : bond 0.00247 ( 6) link_NAG-ASN : angle 1.60120 ( 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 56 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.135 Fit side-chains REVERT: J 41 LYS cc_start: 0.7761 (mttt) cc_final: 0.7106 (mtpt) outliers start: 2 outliers final: 0 residues processed: 55 average time/residue: 0.1103 time to fit residues: 7.0027 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 : 0.106 ------------------------------------------------------------------------------- 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: 1.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116485 restraints weight = 4553.952| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.66 r_work: 0.3089 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2661 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= 0.170 Angle : 0.595 7.537 5090 Z= 0.311 Chirality : 0.047 0.212 575 Planarity : 0.004 0.032 644 Dihedral : 4.422 28.967 637 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.31 % Allowed : 7.19 % Favored : 92.50 % 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: 1.00 (0.39), residues: 457 helix: 2.04 (1.61), residues: 11 sheet: 1.74 (0.37), residues: 197 loop : -0.32 (0.39), residues: 249 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 A 98 TRP 0.012 0.001 TRP B 47 HIS 0.004 0.001 HIS J 66 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 3715) covalent geometry : angle 0.58838 ( 5062) SS BOND : bond 0.00471 ( 5) SS BOND : angle 1.44710 ( 10) hydrogen bonds : bond 0.03974 ( 154) hydrogen bonds : angle 5.60910 ( 423) link_NAG-ASN : bond 0.00269 ( 6) link_NAG-ASN : angle 1.27879 ( 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 54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.136 Fit side-chains REVERT: J 205 SER cc_start: 0.9212 (p) cc_final: 0.8927 (t) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.1030 time to fit residues: 6.4070 Evaluate side-chains 50 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 27 optimal weight: 0.0040 chunk 39 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.3932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.147580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.116680 restraints weight = 4515.628| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.59 r_work: 0.3138 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3726 Z= 0.111 Angle : 0.518 5.671 5090 Z= 0.271 Chirality : 0.045 0.190 575 Planarity : 0.004 0.032 644 Dihedral : 4.148 30.832 637 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.62 % Allowed : 8.12 % Favored : 91.25 % 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: 0.74 (0.39), residues: 457 helix: 2.38 (1.69), residues: 11 sheet: 1.63 (0.40), residues: 169 loop : -0.33 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 102 TYR 0.017 0.001 TYR J 265 PHE 0.011 0.001 PHE J 92 TRP 0.010 0.001 TRP B 47 HIS 0.002 0.001 HIS J 66 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 3715) covalent geometry : angle 0.51378 ( 5062) SS BOND : bond 0.00314 ( 5) SS BOND : angle 0.90229 ( 10) hydrogen bonds : bond 0.03338 ( 154) hydrogen bonds : angle 5.26409 ( 423) link_NAG-ASN : bond 0.00300 ( 6) link_NAG-ASN : angle 1.08221 ( 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 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: A 42 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8328 (mmmm) REVERT: J 205 SER cc_start: 0.9164 (p) cc_final: 0.8911 (t) outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.1021 time to fit residues: 5.9831 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 : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain J residue 227 VAL 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: 0.9990 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113542 restraints weight = 4521.051| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.67 r_work: 0.3089 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3726 Z= 0.186 Angle : 0.590 6.672 5090 Z= 0.304 Chirality : 0.047 0.204 575 Planarity : 0.004 0.035 644 Dihedral : 4.421 36.258 637 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.62 % Allowed : 8.12 % Favored : 91.25 % 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: 0.79 (0.39), residues: 457 helix: 2.04 (1.77), residues: 11 sheet: 1.79 (0.37), residues: 199 loop : -0.68 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 237 TYR 0.022 0.002 TYR J 265 PHE 0.017 0.002 PHE J 92 TRP 0.013 0.001 TRP B 47 HIS 0.003 0.002 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 3715) covalent geometry : angle 0.58461 ( 5062) SS BOND : bond 0.00376 ( 5) SS BOND : angle 1.17177 ( 10) hydrogen bonds : bond 0.03875 ( 154) hydrogen bonds : angle 5.33133 ( 423) link_NAG-ASN : bond 0.00181 ( 6) link_NAG-ASN : angle 1.18982 ( 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 : 0.160 Fit side-chains REVERT: A 42 LYS cc_start: 0.8651 (mmmt) cc_final: 0.8361 (mmmm) REVERT: J 205 SER cc_start: 0.9211 (p) cc_final: 0.8890 (t) outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.0994 time to fit residues: 5.5335 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 : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 28 optimal weight: 0.3980 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.111264 restraints weight = 4573.644| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.55 r_work: 0.3073 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 3726 Z= 0.249 Angle : 0.652 7.485 5090 Z= 0.335 Chirality : 0.049 0.214 575 Planarity : 0.004 0.031 644 Dihedral : 4.903 43.329 637 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.94 % Allowed : 9.06 % 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: 0.38 (0.39), residues: 457 helix: 1.62 (1.78), residues: 11 sheet: 1.54 (0.36), residues: 205 loop : -1.05 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 237 TYR 0.023 0.002 TYR J 265 PHE 0.019 0.002 PHE J 92 TRP 0.015 0.002 TRP B 47 HIS 0.004 0.002 HIS J 143 Details of bonding type rmsd covalent geometry : bond 0.00625 ( 3715) covalent geometry : angle 0.64658 ( 5062) SS BOND : bond 0.00434 ( 5) SS BOND : angle 1.30295 ( 10) hydrogen bonds : bond 0.04291 ( 154) hydrogen bonds : angle 5.46757 ( 423) link_NAG-ASN : bond 0.00151 ( 6) link_NAG-ASN : angle 1.31747 ( 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 51 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.085 Fit side-chains REVERT: A 42 LYS cc_start: 0.8672 (mmmt) cc_final: 0.8466 (mmmm) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.1104 time to fit residues: 6.4044 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 : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain J residue 227 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 0.0470 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 0.0770 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.144512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.114213 restraints weight = 4591.701| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.60 r_work: 0.3102 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3726 Z= 0.143 Angle : 0.547 6.103 5090 Z= 0.282 Chirality : 0.046 0.195 575 Planarity : 0.004 0.028 644 Dihedral : 4.515 40.774 637 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: 0.48 (0.39), residues: 457 helix: 1.74 (1.78), residues: 11 sheet: 1.60 (0.36), residues: 205 loop : -0.97 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 72 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 0.004 0.002 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3715) covalent geometry : angle 0.54244 ( 5062) SS BOND : bond 0.00330 ( 5) SS BOND : angle 0.89134 ( 10) hydrogen bonds : bond 0.03465 ( 154) hydrogen bonds : angle 5.22348 ( 423) link_NAG-ASN : bond 0.00224 ( 6) link_NAG-ASN : angle 1.15874 ( 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 53 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.095 Fit side-chains REVERT: J 41 LYS cc_start: 0.7875 (mttt) cc_final: 0.7239 (mtpt) REVERT: J 97 LYS cc_start: 0.8707 (mtmm) cc_final: 0.8432 (ttmm) REVERT: J 205 SER cc_start: 0.9207 (p) cc_final: 0.8902 (t) REVERT: J 304 LYS cc_start: 0.8625 (mmtm) cc_final: 0.8217 (mptt) outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 0.1121 time to fit residues: 6.4810 Evaluate side-chains 47 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.114332 restraints weight = 4528.524| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.60 r_work: 0.3112 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3725 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= 0.138 Angle : 0.546 6.002 5090 Z= 0.281 Chirality : 0.046 0.195 575 Planarity : 0.004 0.030 644 Dihedral : 4.423 39.738 637 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.31 % Allowed : 9.38 % 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: 0.53 (0.39), residues: 457 helix: 1.83 (1.77), residues: 11 sheet: 1.70 (0.37), residues: 195 loop : -0.90 (0.36), residues: 251 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 covalent geometry : bond 0.00336 ( 3715) covalent geometry : angle 0.54213 ( 5062) SS BOND : bond 0.00307 ( 5) SS BOND : angle 0.87707 ( 10) hydrogen bonds : bond 0.03402 ( 154) hydrogen bonds : angle 5.17066 ( 423) link_NAG-ASN : bond 0.00221 ( 6) link_NAG-ASN : angle 1.11616 ( 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: 1 poor density : 46 time to evaluate : 0.113 Fit side-chains REVERT: J 41 LYS cc_start: 0.7865 (mttt) cc_final: 0.7218 (mtpt) REVERT: J 205 SER cc_start: 0.9203 (p) cc_final: 0.8871 (t) outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.1086 time to fit residues: 5.8012 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 : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 46 optimal weight: 0.0770 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 24 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.146416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.116337 restraints weight = 4489.837| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.54 r_work: 0.3120 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3726 Z= 0.102 Angle : 0.511 5.442 5090 Z= 0.264 Chirality : 0.045 0.187 575 Planarity : 0.003 0.027 644 Dihedral : 4.233 37.827 637 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.62 % Allowed : 9.38 % 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: 0.65 (0.39), residues: 457 helix: 1.97 (1.77), residues: 11 sheet: 1.73 (0.36), residues: 204 loop : -0.88 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.020 0.001 TYR J 265 PHE 0.010 0.001 PHE J 92 TRP 0.010 0.001 TRP B 47 HIS 0.003 0.002 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 3715) covalent geometry : angle 0.50780 ( 5062) SS BOND : bond 0.00256 ( 5) SS BOND : angle 0.75378 ( 10) hydrogen bonds : bond 0.03102 ( 154) hydrogen bonds : angle 5.01413 ( 423) link_NAG-ASN : bond 0.00267 ( 6) link_NAG-ASN : angle 1.05941 ( 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 46 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.133 Fit side-chains REVERT: J 41 LYS cc_start: 0.7842 (mttt) cc_final: 0.7200 (mtpt) REVERT: J 205 SER cc_start: 0.9192 (p) cc_final: 0.8901 (t) outliers start: 2 outliers final: 1 residues processed: 44 average time/residue: 0.1190 time to fit residues: 6.0554 Evaluate side-chains 45 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET 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: 0.0980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 0.0170 chunk 41 optimal weight: 0.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.114183 restraints weight = 4555.846| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.74 r_work: 0.3105 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3726 Z= 0.124 Angle : 0.531 5.640 5090 Z= 0.273 Chirality : 0.046 0.193 575 Planarity : 0.004 0.030 644 Dihedral : 4.246 37.524 637 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.47 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: 0.63 (0.39), residues: 457 helix: 1.95 (1.76), residues: 11 sheet: 1.73 (0.36), residues: 204 loop : -0.89 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.021 0.001 TYR J 265 PHE 0.012 0.001 PHE J 92 TRP 0.011 0.001 TRP B 47 HIS 0.003 0.002 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3715) covalent geometry : angle 0.52784 ( 5062) SS BOND : bond 0.00255 ( 5) SS BOND : angle 0.82045 ( 10) hydrogen bonds : bond 0.03260 ( 154) hydrogen bonds : angle 5.02241 ( 423) link_NAG-ASN : bond 0.00243 ( 6) link_NAG-ASN : angle 1.06792 ( 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 45 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.107 Fit side-chains REVERT: J 41 LYS cc_start: 0.7883 (mttt) cc_final: 0.7191 (mtpt) REVERT: J 205 SER cc_start: 0.9220 (p) cc_final: 0.8905 (t) outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.1119 time to fit residues: 5.7544 Evaluate side-chains 45 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET 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: 1.9990 chunk 34 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.143969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.112315 restraints weight = 4517.626| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.73 r_work: 0.3078 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3726 Z= 0.179 Angle : 0.587 6.549 5090 Z= 0.301 Chirality : 0.047 0.204 575 Planarity : 0.004 0.030 644 Dihedral : 4.537 39.690 637 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.31 % Allowed : 10.31 % Favored : 89.38 % 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: 0.46 (0.39), residues: 457 helix: 1.74 (1.77), residues: 11 sheet: 1.68 (0.37), residues: 195 loop : -0.97 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.023 0.002 TYR J 265 PHE 0.016 0.002 PHE J 92 TRP 0.012 0.001 TRP B 47 HIS 0.008 0.002 HIS J 143 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 3715) covalent geometry : angle 0.58301 ( 5062) SS BOND : bond 0.00325 ( 5) SS BOND : angle 1.08380 ( 10) hydrogen bonds : bond 0.03719 ( 154) hydrogen bonds : angle 5.18205 ( 423) link_NAG-ASN : bond 0.00202 ( 6) link_NAG-ASN : angle 1.13341 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1124.02 seconds wall clock time: 19 minutes 53.36 seconds (1193.36 seconds total)