Starting phenix.real_space_refine on Wed Jun 4 18:09:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tlz_25991/06_2025/7tlz_25991.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tlz_25991/06_2025/7tlz_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_25991/06_2025/7tlz_25991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tlz_25991/06_2025/7tlz_25991.map" model { file = "/net/cci-nas-00/data/ceres_data/7tlz_25991/06_2025/7tlz_25991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tlz_25991/06_2025/7tlz_25991.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 2, 'GLU:plan': 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, 'ASP:plan': 10, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} 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: 5.60, per 1000 atoms: 1.55 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: 0.92 Conformation dependent library (CDL) restraints added in 446.2 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: 0.56 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: 1.16 Time building geometry restraints manager: 1.12 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: 11.250 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.060 Find NCS groups from input model: 0.030 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.510 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (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 TRP 0.024 0.005 TRP J 64 HIS 0.002 0.001 HIS B 35 PHE 0.016 0.003 PHE A 98 TYR 0.033 0.005 TYR J 269 ARG 0.004 0.001 ARG J 34 Details of bonding type rmsd link_NAG-ASN : bond 0.04434 ( 6) link_NAG-ASN : angle 1.96985 ( 18) hydrogen bonds : bond 0.17709 ( 154) hydrogen bonds : angle 8.00612 ( 423) SS BOND : bond 0.07408 ( 5) SS BOND : angle 2.89817 ( 10) covalent geometry : bond 0.01068 ( 3715) covalent geometry : angle 1.30058 ( 5062) *********************** 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 : 0.420 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: 0.2394 time to fit residues: 23.2723 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 : 0.387 ------------------------------------------------------------------------------- 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 39 optimal weight: 0.0070 chunk 35 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.0060 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.2814 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.154282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.124222 restraints weight = 4447.175| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.54 r_work: 0.3232 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3726 Z= 0.118 Angle : 0.582 8.821 5090 Z= 0.307 Chirality : 0.046 0.204 575 Planarity : 0.004 0.026 644 Dihedral : 4.797 25.467 639 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.31 % Allowed : 6.56 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.38), residues: 457 helix: 1.76 (1.53), residues: 11 sheet: 1.51 (0.39), residues: 171 loop : -0.01 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 47 HIS 0.002 0.001 HIS J 66 PHE 0.014 0.001 PHE J 79 TYR 0.020 0.001 TYR J 265 ARG 0.004 0.001 ARG B 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 6) link_NAG-ASN : angle 1.61525 ( 18) hydrogen bonds : bond 0.03807 ( 154) hydrogen bonds : angle 6.22650 ( 423) SS BOND : bond 0.00387 ( 5) SS BOND : angle 1.96814 ( 10) covalent geometry : bond 0.00273 ( 3715) covalent geometry : angle 0.56886 ( 5062) *********************** 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 54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.416 Fit side-chains REVERT: J 41 LYS cc_start: 0.7706 (mttt) cc_final: 0.7058 (mtpt) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.2142 time to fit residues: 13.5285 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 : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 41 optimal weight: 0.0070 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.150190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.119680 restraints weight = 4444.666| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.55 r_work: 0.3178 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2420 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= 0.120 Angle : 0.544 6.238 5090 Z= 0.284 Chirality : 0.046 0.205 575 Planarity : 0.004 0.028 644 Dihedral : 4.003 21.461 637 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.39), residues: 457 helix: 2.46 (1.58), residues: 11 sheet: 1.33 (0.39), residues: 180 loop : 0.03 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS J 66 PHE 0.013 0.001 PHE A 98 TYR 0.019 0.001 TYR J 265 ARG 0.002 0.001 ARG B 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 6) link_NAG-ASN : angle 1.16165 ( 18) hydrogen bonds : bond 0.03537 ( 154) hydrogen bonds : angle 5.49829 ( 423) SS BOND : bond 0.00315 ( 5) SS BOND : angle 1.20189 ( 10) covalent geometry : bond 0.00280 ( 3715) covalent geometry : angle 0.53809 ( 5062) *********************** 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 52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.409 Fit side-chains REVERT: J 41 LYS cc_start: 0.7787 (mttt) cc_final: 0.7081 (mtpt) REVERT: J 129 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.8039 (ptmm) REVERT: J 205 SER cc_start: 0.9177 (p) cc_final: 0.8878 (t) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.1995 time to fit residues: 12.4672 Evaluate side-chains 49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 129 LYS 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 38 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.143869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.112936 restraints weight = 4538.861| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.63 r_work: 0.3054 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3726 Z= 0.190 Angle : 0.615 7.038 5090 Z= 0.318 Chirality : 0.048 0.214 575 Planarity : 0.004 0.039 644 Dihedral : 4.437 30.585 637 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.94 % Allowed : 8.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.39), residues: 457 helix: 2.21 (1.71), residues: 11 sheet: 1.78 (0.37), residues: 196 loop : -0.49 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 47 HIS 0.003 0.001 HIS J 66 PHE 0.017 0.002 PHE A 98 TYR 0.019 0.002 TYR J 265 ARG 0.002 0.001 ARG J 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 6) link_NAG-ASN : angle 1.26649 ( 18) hydrogen bonds : bond 0.04025 ( 154) hydrogen bonds : angle 5.50631 ( 423) SS BOND : bond 0.00352 ( 5) SS BOND : angle 1.42809 ( 10) covalent geometry : bond 0.00467 ( 3715) covalent geometry : angle 0.60904 ( 5062) *********************** 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 51 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.421 Fit side-chains REVERT: J 129 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8114 (ptmm) REVERT: J 205 SER cc_start: 0.9218 (p) cc_final: 0.8885 (t) outliers start: 3 outliers final: 0 residues processed: 50 average time/residue: 0.2445 time to fit residues: 14.3508 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 : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 129 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.144353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113688 restraints weight = 4572.432| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.60 r_work: 0.3099 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3726 Z= 0.188 Angle : 0.590 6.785 5090 Z= 0.305 Chirality : 0.048 0.197 575 Planarity : 0.004 0.030 644 Dihedral : 4.588 38.450 637 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.31 % Allowed : 9.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.39), residues: 457 helix: 1.94 (1.77), residues: 11 sheet: 1.77 (0.36), residues: 204 loop : -0.83 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.016 0.002 PHE J 92 TYR 0.021 0.002 TYR J 265 ARG 0.003 0.001 ARG J 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00154 ( 6) link_NAG-ASN : angle 1.12686 ( 18) hydrogen bonds : bond 0.03835 ( 154) hydrogen bonds : angle 5.33785 ( 423) SS BOND : bond 0.00283 ( 5) SS BOND : angle 1.20851 ( 10) covalent geometry : bond 0.00465 ( 3715) covalent geometry : angle 0.58488 ( 5062) *********************** 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 48 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.376 Fit side-chains REVERT: A 42 LYS cc_start: 0.8670 (mmmt) cc_final: 0.8380 (mmmm) REVERT: J 129 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8162 (ptmm) REVERT: J 205 SER cc_start: 0.9213 (p) cc_final: 0.8887 (t) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.2257 time to fit residues: 12.7994 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 : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 129 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.143650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.113434 restraints weight = 4537.557| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.57 r_work: 0.3102 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3726 Z= 0.162 Angle : 0.561 6.298 5090 Z= 0.290 Chirality : 0.047 0.196 575 Planarity : 0.004 0.032 644 Dihedral : 4.547 40.362 637 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.62 % Allowed : 8.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.39), residues: 457 helix: 1.90 (1.77), residues: 11 sheet: 1.76 (0.36), residues: 204 loop : -0.96 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.015 0.002 PHE J 92 TYR 0.021 0.002 TYR J 265 ARG 0.002 0.000 ARG J 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 6) link_NAG-ASN : angle 1.13489 ( 18) hydrogen bonds : bond 0.03612 ( 154) hydrogen bonds : angle 5.26095 ( 423) SS BOND : bond 0.00372 ( 5) SS BOND : angle 0.97761 ( 10) covalent geometry : bond 0.00398 ( 3715) covalent geometry : angle 0.55656 ( 5062) *********************** 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 50 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.416 Fit side-chains REVERT: A 42 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8421 (mmmm) REVERT: J 41 LYS cc_start: 0.7863 (mttt) cc_final: 0.7241 (mtpt) REVERT: J 129 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8138 (ptmm) REVERT: J 205 SER cc_start: 0.9203 (p) cc_final: 0.8898 (t) outliers start: 2 outliers final: 1 residues processed: 49 average time/residue: 0.2534 time to fit residues: 14.5346 Evaluate side-chains 47 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 129 LYS 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 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.144386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112914 restraints weight = 4596.794| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.71 r_work: 0.3050 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3726 Z= 0.185 Angle : 0.583 6.608 5090 Z= 0.300 Chirality : 0.047 0.202 575 Planarity : 0.004 0.030 644 Dihedral : 4.626 40.894 637 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.39), residues: 457 helix: 1.73 (1.78), residues: 11 sheet: 1.75 (0.37), residues: 195 loop : -1.00 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.016 0.002 PHE J 92 TYR 0.022 0.002 TYR J 265 ARG 0.002 0.000 ARG J 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00154 ( 6) link_NAG-ASN : angle 1.17977 ( 18) hydrogen bonds : bond 0.03763 ( 154) hydrogen bonds : angle 5.27767 ( 423) SS BOND : bond 0.00353 ( 5) SS BOND : angle 0.97828 ( 10) covalent geometry : bond 0.00457 ( 3715) covalent geometry : angle 0.57901 ( 5062) *********************** 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 49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.436 Fit side-chains REVERT: A 42 LYS cc_start: 0.8660 (mmmt) cc_final: 0.8447 (mmmm) REVERT: J 41 LYS cc_start: 0.7900 (mttt) cc_final: 0.7244 (mtpt) REVERT: J 129 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8123 (ptmm) REVERT: J 205 SER cc_start: 0.9212 (p) cc_final: 0.8898 (t) REVERT: J 304 LYS cc_start: 0.8682 (mmtm) cc_final: 0.8278 (mptt) outliers start: 2 outliers final: 1 residues processed: 48 average time/residue: 0.2521 time to fit residues: 14.1894 Evaluate side-chains 48 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 129 LYS Chi-restraints excluded: chain J residue 227 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 0.0470 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 0.0970 chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.144636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.114503 restraints weight = 4482.817| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.58 r_work: 0.3109 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3687 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= 0.122 Angle : 0.525 5.763 5090 Z= 0.271 Chirality : 0.046 0.190 575 Planarity : 0.004 0.028 644 Dihedral : 4.366 39.126 637 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.62 % Allowed : 9.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.39), residues: 457 helix: 1.88 (1.77), residues: 11 sheet: 1.81 (0.37), residues: 194 loop : -0.93 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.012 0.001 PHE J 92 TYR 0.020 0.001 TYR J 265 ARG 0.002 0.000 ARG J 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 6) link_NAG-ASN : angle 1.09736 ( 18) hydrogen bonds : bond 0.03232 ( 154) hydrogen bonds : angle 5.12319 ( 423) SS BOND : bond 0.00282 ( 5) SS BOND : angle 0.74858 ( 10) covalent geometry : bond 0.00291 ( 3715) covalent geometry : angle 0.52094 ( 5062) *********************** 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: 2 poor density : 45 time to evaluate : 0.417 Fit side-chains REVERT: A 42 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8405 (mmmm) REVERT: J 41 LYS cc_start: 0.7854 (mttt) cc_final: 0.7213 (mtpt) REVERT: J 129 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8097 (ptmm) REVERT: J 205 SER cc_start: 0.9194 (p) cc_final: 0.8917 (t) outliers start: 2 outliers final: 1 residues processed: 46 average time/residue: 0.2669 time to fit residues: 14.4130 Evaluate side-chains 44 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 129 LYS Chi-restraints excluded: chain J residue 227 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.142842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.113714 restraints weight = 4494.043| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.64 r_work: 0.3039 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 3726 Z= 0.216 Angle : 0.614 7.001 5090 Z= 0.315 Chirality : 0.048 0.211 575 Planarity : 0.004 0.033 644 Dihedral : 4.696 41.100 637 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.62 % Allowed : 9.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.38), residues: 457 helix: 1.57 (1.78), residues: 11 sheet: 1.67 (0.37), residues: 196 loop : -1.06 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 47 HIS 0.003 0.002 HIS B 35 PHE 0.019 0.002 PHE J 92 TYR 0.024 0.002 TYR J 265 ARG 0.002 0.001 ARG J 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 6) link_NAG-ASN : angle 1.21536 ( 18) hydrogen bonds : bond 0.03937 ( 154) hydrogen bonds : angle 5.32683 ( 423) SS BOND : bond 0.00377 ( 5) SS BOND : angle 1.06912 ( 10) covalent geometry : bond 0.00538 ( 3715) covalent geometry : angle 0.60933 ( 5062) *********************** 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 47 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.395 Fit side-chains REVERT: J 41 LYS cc_start: 0.7904 (mttt) cc_final: 0.7260 (mtpt) REVERT: J 129 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8108 (ptmm) REVERT: J 205 SER cc_start: 0.9221 (p) cc_final: 0.8882 (t) outliers start: 2 outliers final: 1 residues processed: 46 average time/residue: 0.2595 time to fit residues: 14.1811 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 : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 129 LYS Chi-restraints excluded: chain J residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.144354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113148 restraints weight = 4509.346| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.67 r_work: 0.3055 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3726 Z= 0.174 Angle : 0.579 6.585 5090 Z= 0.298 Chirality : 0.047 0.201 575 Planarity : 0.004 0.029 644 Dihedral : 4.620 40.437 637 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.62 % Allowed : 10.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.38), residues: 457 helix: 1.54 (1.78), residues: 11 sheet: 1.62 (0.36), residues: 196 loop : -1.11 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.016 0.002 PHE J 92 TYR 0.022 0.002 TYR J 265 ARG 0.002 0.000 ARG J 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 6) link_NAG-ASN : angle 1.16883 ( 18) hydrogen bonds : bond 0.03667 ( 154) hydrogen bonds : angle 5.23350 ( 423) SS BOND : bond 0.00323 ( 5) SS BOND : angle 0.98319 ( 10) covalent geometry : bond 0.00429 ( 3715) covalent geometry : angle 0.57494 ( 5062) ********************** 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 46 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.410 Fit side-chains REVERT: J 41 LYS cc_start: 0.7898 (mttt) cc_final: 0.7238 (mtpt) REVERT: J 129 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8124 (ptmm) REVERT: J 205 SER cc_start: 0.9202 (p) cc_final: 0.8868 (t) outliers start: 2 outliers final: 1 residues processed: 45 average time/residue: 0.2499 time to fit residues: 13.2435 Evaluate side-chains 44 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 129 LYS Chi-restraints excluded: chain J residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 28 optimal weight: 0.4980 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.143517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113453 restraints weight = 4504.784| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.58 r_work: 0.3092 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3726 Z= 0.174 Angle : 0.576 6.509 5090 Z= 0.296 Chirality : 0.047 0.200 575 Planarity : 0.004 0.030 644 Dihedral : 4.604 39.940 637 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.62 % Allowed : 10.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.38), residues: 457 helix: 1.56 (1.78), residues: 11 sheet: 1.63 (0.37), residues: 195 loop : -1.12 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 47 HIS 0.003 0.002 HIS B 35 PHE 0.015 0.002 PHE J 92 TYR 0.022 0.002 TYR J 265 ARG 0.002 0.000 ARG J 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 6) link_NAG-ASN : angle 1.16311 ( 18) hydrogen bonds : bond 0.03637 ( 154) hydrogen bonds : angle 5.19525 ( 423) SS BOND : bond 0.00308 ( 5) SS BOND : angle 1.02476 ( 10) covalent geometry : bond 0.00431 ( 3715) covalent geometry : angle 0.57113 ( 5062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2337.08 seconds wall clock time: 41 minutes 8.78 seconds (2468.78 seconds total)