Starting phenix.real_space_refine on Wed Jul 23 20:17:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rbu_24402/07_2025/7rbu_24402.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rbu_24402/07_2025/7rbu_24402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rbu_24402/07_2025/7rbu_24402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rbu_24402/07_2025/7rbu_24402.map" model { file = "/net/cci-nas-00/data/ceres_data/7rbu_24402/07_2025/7rbu_24402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rbu_24402/07_2025/7rbu_24402.cif" } resolution = 3.7 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= 0.008 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 13 5.16 5 C 2629 2.51 5 N 665 2.21 5 O 800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4107 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2241 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 14, 'TRANS': 263} Chain: "H" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 968 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 800 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.85, per 1000 atoms: 1.91 Number of scatterers: 4107 At special positions: 0 Unit cell: (86.8, 66.64, 81.2, 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 13 16.00 O 800 8.00 N 665 7.00 C 2629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.06 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 1 " - " ASN B 122 " " NAG B 401 " - " ASN B 234 " " NAG B 402 " - " ASN B 61 " " NAG B 403 " - " ASN B 149 " " NAG C 1 " - " ASN B 17 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 496.4 milliseconds 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 44.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.501A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.769A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.501A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR B 76 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.575A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.555A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.266A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 9.987A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.829A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.621A pdb=" N LEU B 176 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER H 110 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ARG H 101 " --> pdb=" O TYR H 111 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP H 113 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG H 99 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ASP H 115 " --> pdb=" O CYS H 97 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N CYS H 97 " --> pdb=" O ASP H 115 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY H 37 " --> pdb=" O ALA H 98 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER H 52 " --> pdb=" O TYR H 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.621A pdb=" N LEU B 176 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER H 110 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ARG H 101 " --> pdb=" O TYR H 111 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP H 113 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG H 99 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ASP H 115 " --> pdb=" O CYS H 97 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N CYS H 97 " --> pdb=" O ASP H 115 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA H 93 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR H 121 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.784A pdb=" N GLN H 5 " --> pdb=" O THR H 23 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR H 23 " --> pdb=" O GLN H 5 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN H 79 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6 removed outlier: 4.013A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.330A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 116 hydrogen bonds defined for protein. 303 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: 1.10 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1264 1.34 - 1.47: 1167 1.47 - 1.59: 1771 1.59 - 1.71: 0 1.71 - 1.83: 16 Bond restraints: 4218 Sorted by residual: bond pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.30e-02 5.92e+03 8.81e+00 bond pdb=" N PHE B 168 " pdb=" CA PHE B 168 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.17e-02 7.31e+03 8.10e+00 bond pdb=" N SER B 162 " pdb=" CA SER B 162 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.20e-02 6.94e+03 6.98e+00 bond pdb=" N THR B 167 " pdb=" CA THR B 167 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.68e+00 bond pdb=" N ASN B 164 " pdb=" CA ASN B 164 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.16e-02 7.43e+03 4.84e+00 ... (remaining 4213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 5204 1.24 - 2.48: 403 2.48 - 3.71: 102 3.71 - 4.95: 25 4.95 - 6.19: 7 Bond angle restraints: 5741 Sorted by residual: angle pdb=" CA ASN B 165 " pdb=" C ASN B 165 " pdb=" O ASN B 165 " ideal model delta sigma weight residual 121.84 116.48 5.36 1.16e+00 7.43e-01 2.14e+01 angle pdb=" N VAL B 213 " pdb=" CA VAL B 213 " pdb=" C VAL B 213 " ideal model delta sigma weight residual 113.71 109.41 4.30 9.50e-01 1.11e+00 2.05e+01 angle pdb=" C SER L 56 " pdb=" CA SER L 56 " pdb=" CB SER L 56 " ideal model delta sigma weight residual 116.34 110.15 6.19 1.40e+00 5.10e-01 1.95e+01 angle pdb=" CA ASN B 165 " pdb=" C ASN B 165 " pdb=" N CYS B 166 " ideal model delta sigma weight residual 115.51 119.95 -4.44 1.30e+00 5.92e-01 1.17e+01 angle pdb=" CA ASN B 164 " pdb=" C ASN B 164 " pdb=" O ASN B 164 " ideal model delta sigma weight residual 121.38 117.77 3.61 1.06e+00 8.90e-01 1.16e+01 ... (remaining 5736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 2315 17.16 - 34.32: 178 34.32 - 51.48: 45 51.48 - 68.64: 10 68.64 - 85.80: 2 Dihedral angle restraints: 2550 sinusoidal: 1072 harmonic: 1478 Sorted by residual: dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual 93.00 178.80 -85.80 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 97 " pdb=" CB CYS H 97 " ideal model delta sinusoidal sigma weight residual 93.00 151.53 -58.53 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CA CYS B 136 " pdb=" C CYS B 136 " pdb=" N ASN B 137 " pdb=" CA ASN B 137 " ideal model delta harmonic sigma weight residual -180.00 -160.72 -19.28 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 2547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 462 0.046 - 0.092: 136 0.092 - 0.138: 42 0.138 - 0.184: 5 0.184 - 0.230: 2 Chirality restraints: 647 Sorted by residual: chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA GLU B 169 " pdb=" N GLU B 169 " pdb=" C GLU B 169 " pdb=" CB GLU B 169 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA SER L 7 " pdb=" N SER L 7 " pdb=" C SER L 7 " pdb=" CB SER L 7 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 644 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 208 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.81e+00 pdb=" N PRO B 209 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 209 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 209 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO L 59 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 161 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C SER B 161 " -0.026 2.00e-02 2.50e+03 pdb=" O SER B 161 " 0.010 2.00e-02 2.50e+03 pdb=" N SER B 162 " 0.009 2.00e-02 2.50e+03 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 204 2.71 - 3.26: 3673 3.26 - 3.81: 5933 3.81 - 4.35: 6871 4.35 - 4.90: 12578 Nonbonded interactions: 29259 Sorted by model distance: nonbonded pdb=" OG SER L 52 " pdb=" O GLY L 64 " model vdw 2.167 3.040 nonbonded pdb=" O ASN B 17 " pdb=" OG SER B 255 " model vdw 2.211 3.040 nonbonded pdb=" NH1 ARG L 61 " pdb=" OE1 GLN L 79 " model vdw 2.229 3.120 nonbonded pdb=" NH2 ARG L 61 " pdb=" OE2 GLU L 81 " model vdw 2.231 3.120 nonbonded pdb=" OG SER L 12 " pdb=" OE2 GLU L 105 " model vdw 2.275 3.040 ... (remaining 29254 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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 group one per residue 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: 42.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 19.510 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 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 : 0.006 0.043 4229 Z= 0.269 Angle : 0.826 7.155 5770 Z= 0.462 Chirality : 0.049 0.230 647 Planarity : 0.005 0.055 721 Dihedral : 12.814 68.971 1598 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.13 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.06 (0.38), residues: 196 loop : -3.05 (0.29), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 117 HIS 0.004 0.001 HIS B 66 PHE 0.021 0.002 PHE B 59 TYR 0.021 0.002 TYR B 204 ARG 0.003 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 5) link_NAG-ASN : angle 2.87375 ( 15) link_BETA1-4 : bond 0.00037 ( 2) link_BETA1-4 : angle 2.55091 ( 6) hydrogen bonds : bond 0.19615 ( 109) hydrogen bonds : angle 7.26158 ( 303) SS BOND : bond 0.01351 ( 4) SS BOND : angle 3.12040 ( 8) covalent geometry : bond 0.00555 ( 4218) covalent geometry : angle 0.80236 ( 5741) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.411 Fit side-chains REVERT: H 110 SER cc_start: 0.7742 (p) cc_final: 0.7538 (p) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1227 time to fit residues: 10.7754 Evaluate side-chains 58 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.1980 chunk 25 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 44 optimal weight: 0.0670 overall best weight: 0.1918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.125288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.100678 restraints weight = 6353.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.103988 restraints weight = 3465.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.106244 restraints weight = 2338.407| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4229 Z= 0.127 Angle : 0.674 9.382 5770 Z= 0.337 Chirality : 0.044 0.213 647 Planarity : 0.004 0.044 721 Dihedral : 7.915 56.056 703 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.13 % Favored : 91.67 % Rotamer: Outliers : 1.79 % Allowed : 8.07 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.24 (0.37), residues: 207 loop : -2.93 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.002 0.001 HIS B 69 PHE 0.012 0.001 PHE H 80 TYR 0.015 0.001 TYR B 265 ARG 0.002 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00123 ( 5) link_NAG-ASN : angle 2.37374 ( 15) link_BETA1-4 : bond 0.00488 ( 2) link_BETA1-4 : angle 2.29819 ( 6) hydrogen bonds : bond 0.05417 ( 109) hydrogen bonds : angle 6.11639 ( 303) SS BOND : bond 0.00916 ( 4) SS BOND : angle 1.73584 ( 8) covalent geometry : bond 0.00273 ( 4218) covalent geometry : angle 0.65691 ( 5741) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.487 Fit side-chains REVERT: B 97 LYS cc_start: 0.8340 (mtmt) cc_final: 0.8043 (mtmm) REVERT: B 278 LYS cc_start: 0.7710 (ttpp) cc_final: 0.7169 (ttpp) outliers start: 8 outliers final: 7 residues processed: 70 average time/residue: 0.1466 time to fit residues: 13.6048 Evaluate side-chains 67 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 20 optimal weight: 0.2980 chunk 34 optimal weight: 0.0370 chunk 5 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.0770 chunk 32 optimal weight: 0.6980 chunk 47 optimal weight: 0.0870 overall best weight: 0.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.102034 restraints weight = 6235.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.105150 restraints weight = 3493.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.107457 restraints weight = 2426.938| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4229 Z= 0.109 Angle : 0.632 9.560 5770 Z= 0.312 Chirality : 0.043 0.229 647 Planarity : 0.004 0.045 721 Dihedral : 7.333 55.969 703 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.02 % Allowed : 13.45 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.36 (0.37), residues: 207 loop : -2.89 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.002 0.001 HIS B 69 PHE 0.016 0.001 PHE B 133 TYR 0.016 0.001 TYR B 265 ARG 0.001 0.000 ARG H 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00097 ( 5) link_NAG-ASN : angle 2.38443 ( 15) link_BETA1-4 : bond 0.00569 ( 2) link_BETA1-4 : angle 1.98776 ( 6) hydrogen bonds : bond 0.04466 ( 109) hydrogen bonds : angle 5.76865 ( 303) SS BOND : bond 0.00349 ( 4) SS BOND : angle 2.07162 ( 8) covalent geometry : bond 0.00239 ( 4218) covalent geometry : angle 0.61330 ( 5741) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: B 97 LYS cc_start: 0.8331 (mtmt) cc_final: 0.8013 (mtmm) REVERT: B 160 TYR cc_start: 0.8679 (p90) cc_final: 0.8321 (p90) REVERT: B 278 LYS cc_start: 0.7696 (ttpp) cc_final: 0.7177 (ttpp) outliers start: 9 outliers final: 6 residues processed: 63 average time/residue: 0.1766 time to fit residues: 14.4422 Evaluate side-chains 64 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 108 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 45 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.099286 restraints weight = 6228.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.102676 restraints weight = 3307.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.104947 restraints weight = 2207.738| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 4229 Z= 0.261 Angle : 0.759 9.594 5770 Z= 0.384 Chirality : 0.046 0.245 647 Planarity : 0.005 0.053 721 Dihedral : 7.286 56.692 703 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 3.36 % Allowed : 15.70 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.26 (0.37), residues: 208 loop : -2.96 (0.30), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 104 HIS 0.004 0.001 HIS B 49 PHE 0.024 0.003 PHE B 59 TYR 0.024 0.002 TYR B 204 ARG 0.003 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 5) link_NAG-ASN : angle 2.55274 ( 15) link_BETA1-4 : bond 0.00502 ( 2) link_BETA1-4 : angle 1.71433 ( 6) hydrogen bonds : bond 0.07385 ( 109) hydrogen bonds : angle 5.99193 ( 303) SS BOND : bond 0.00775 ( 4) SS BOND : angle 3.11662 ( 8) covalent geometry : bond 0.00638 ( 4218) covalent geometry : angle 0.73840 ( 5741) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.438 Fit side-chains REVERT: L 65 SER cc_start: 0.8361 (p) cc_final: 0.8159 (m) outliers start: 15 outliers final: 10 residues processed: 63 average time/residue: 0.1086 time to fit residues: 10.4623 Evaluate side-chains 69 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 9 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.0270 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 0.0870 chunk 7 optimal weight: 0.0980 chunk 25 optimal weight: 0.1980 chunk 0 optimal weight: 0.9980 overall best weight: 0.1416 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.126364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.101421 restraints weight = 6458.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.104754 restraints weight = 3540.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.107032 restraints weight = 2394.637| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 4229 Z= 0.111 Angle : 0.653 9.540 5770 Z= 0.322 Chirality : 0.043 0.236 647 Planarity : 0.004 0.043 721 Dihedral : 6.624 55.515 703 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.59 % Allowed : 17.26 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.46 (0.37), residues: 207 loop : -2.96 (0.29), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.002 0.000 HIS B 69 PHE 0.020 0.001 PHE B 133 TYR 0.016 0.001 TYR B 265 ARG 0.001 0.000 ARG H 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00090 ( 5) link_NAG-ASN : angle 2.37843 ( 15) link_BETA1-4 : bond 0.00562 ( 2) link_BETA1-4 : angle 1.96884 ( 6) hydrogen bonds : bond 0.04482 ( 109) hydrogen bonds : angle 5.66355 ( 303) SS BOND : bond 0.00410 ( 4) SS BOND : angle 3.34007 ( 8) covalent geometry : bond 0.00241 ( 4218) covalent geometry : angle 0.62828 ( 5741) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 LYS cc_start: 0.8363 (mtmt) cc_final: 0.8015 (mtmm) REVERT: B 274 THR cc_start: 0.7770 (OUTLIER) cc_final: 0.7464 (t) REVERT: B 278 LYS cc_start: 0.7697 (ttpp) cc_final: 0.7164 (ttpp) outliers start: 16 outliers final: 10 residues processed: 69 average time/residue: 0.1578 time to fit residues: 14.1450 Evaluate side-chains 70 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 0.0870 chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 chunk 12 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 27 optimal weight: 0.0040 overall best weight: 0.2770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.124988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.100484 restraints weight = 6316.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.103757 restraints weight = 3443.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.105979 restraints weight = 2324.980| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4229 Z= 0.146 Angle : 0.683 9.553 5770 Z= 0.338 Chirality : 0.044 0.242 647 Planarity : 0.004 0.047 721 Dihedral : 6.557 56.154 703 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 3.59 % Allowed : 17.04 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.48 (0.37), residues: 207 loop : -2.90 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.002 0.001 HIS B 69 PHE 0.022 0.002 PHE B 133 TYR 0.016 0.001 TYR B 204 ARG 0.001 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 5) link_NAG-ASN : angle 2.37515 ( 15) link_BETA1-4 : bond 0.00500 ( 2) link_BETA1-4 : angle 1.93513 ( 6) hydrogen bonds : bond 0.05413 ( 109) hydrogen bonds : angle 5.67463 ( 303) SS BOND : bond 0.00416 ( 4) SS BOND : angle 4.05545 ( 8) covalent geometry : bond 0.00339 ( 4218) covalent geometry : angle 0.65351 ( 5741) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.478 Fit side-chains REVERT: B 68 ILE cc_start: 0.7328 (OUTLIER) cc_final: 0.7039 (mp) REVERT: B 274 THR cc_start: 0.7791 (OUTLIER) cc_final: 0.7472 (t) outliers start: 16 outliers final: 9 residues processed: 66 average time/residue: 0.1820 time to fit residues: 17.7875 Evaluate side-chains 66 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 108 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 0.1980 chunk 16 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.2980 chunk 28 optimal weight: 6.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.125827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.102773 restraints weight = 6195.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.105965 restraints weight = 3309.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.107937 restraints weight = 2201.518| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4229 Z= 0.159 Angle : 0.698 9.538 5770 Z= 0.348 Chirality : 0.044 0.242 647 Planarity : 0.004 0.045 721 Dihedral : 6.534 56.174 703 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 2.47 % Allowed : 17.26 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.50 (0.37), residues: 207 loop : -2.91 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.002 0.001 HIS B 49 PHE 0.014 0.002 PHE B 59 TYR 0.017 0.001 TYR B 204 ARG 0.002 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00112 ( 5) link_NAG-ASN : angle 2.42254 ( 15) link_BETA1-4 : bond 0.00555 ( 2) link_BETA1-4 : angle 1.89294 ( 6) hydrogen bonds : bond 0.05568 ( 109) hydrogen bonds : angle 5.70695 ( 303) SS BOND : bond 0.00496 ( 4) SS BOND : angle 3.15573 ( 8) covalent geometry : bond 0.00375 ( 4218) covalent geometry : angle 0.67589 ( 5741) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: B 68 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.7051 (mp) REVERT: B 97 LYS cc_start: 0.8429 (mtmt) cc_final: 0.8013 (mtmm) REVERT: B 113 LYS cc_start: 0.8264 (mmtm) cc_final: 0.8020 (mttm) REVERT: B 274 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7497 (t) REVERT: B 278 LYS cc_start: 0.7718 (ttpp) cc_final: 0.7168 (ttpp) outliers start: 11 outliers final: 9 residues processed: 65 average time/residue: 0.1507 time to fit residues: 12.8177 Evaluate side-chains 69 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.0010 chunk 10 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 43 optimal weight: 0.8980 overall best weight: 0.1786 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.126241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.101852 restraints weight = 6306.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.105213 restraints weight = 3451.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.107423 restraints weight = 2323.291| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4229 Z= 0.116 Angle : 0.654 9.531 5770 Z= 0.318 Chirality : 0.043 0.237 647 Planarity : 0.004 0.042 721 Dihedral : 6.336 55.801 703 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.69 % Allowed : 17.26 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.96 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.57 (0.37), residues: 207 loop : -2.92 (0.29), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.002 0.001 HIS B 69 PHE 0.014 0.001 PHE B 133 TYR 0.017 0.001 TYR B 265 ARG 0.001 0.000 ARG H 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 5) link_NAG-ASN : angle 2.29686 ( 15) link_BETA1-4 : bond 0.00510 ( 2) link_BETA1-4 : angle 2.03082 ( 6) hydrogen bonds : bond 0.04441 ( 109) hydrogen bonds : angle 5.55250 ( 303) SS BOND : bond 0.00340 ( 4) SS BOND : angle 2.51223 ( 8) covalent geometry : bond 0.00261 ( 4218) covalent geometry : angle 0.63444 ( 5741) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: B 68 ILE cc_start: 0.7311 (OUTLIER) cc_final: 0.7036 (mp) REVERT: B 97 LYS cc_start: 0.8373 (mtmt) cc_final: 0.7971 (mtmm) REVERT: B 113 LYS cc_start: 0.8275 (mmtm) cc_final: 0.8030 (mttm) REVERT: B 274 THR cc_start: 0.7762 (OUTLIER) cc_final: 0.7449 (t) REVERT: B 278 LYS cc_start: 0.7692 (ttpp) cc_final: 0.7149 (ttpp) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.1402 time to fit residues: 12.1791 Evaluate side-chains 69 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 108 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.0270 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.098613 restraints weight = 6153.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.101753 restraints weight = 3352.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.103985 restraints weight = 2279.410| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 4229 Z= 0.314 Angle : 0.815 9.529 5770 Z= 0.418 Chirality : 0.049 0.247 647 Planarity : 0.005 0.052 721 Dihedral : 6.945 57.035 703 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 2.47 % Allowed : 18.39 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.45 (0.38), residues: 201 loop : -3.06 (0.29), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 64 HIS 0.004 0.001 HIS B 49 PHE 0.026 0.003 PHE B 59 TYR 0.026 0.002 TYR B 204 ARG 0.002 0.001 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 5) link_NAG-ASN : angle 2.57426 ( 15) link_BETA1-4 : bond 0.00456 ( 2) link_BETA1-4 : angle 1.78865 ( 6) hydrogen bonds : bond 0.07867 ( 109) hydrogen bonds : angle 5.95735 ( 303) SS BOND : bond 0.00880 ( 4) SS BOND : angle 3.59840 ( 8) covalent geometry : bond 0.00774 ( 4218) covalent geometry : angle 0.79324 ( 5741) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.439 Fit side-chains REVERT: B 33 THR cc_start: 0.8100 (p) cc_final: 0.7802 (p) REVERT: B 68 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7107 (mp) REVERT: B 274 THR cc_start: 0.7887 (OUTLIER) cc_final: 0.7580 (t) outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 0.1047 time to fit residues: 10.0410 Evaluate side-chains 65 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 0.0870 chunk 18 optimal weight: 0.3980 chunk 38 optimal weight: 0.4980 chunk 26 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 13 optimal weight: 0.5980 overall best weight: 0.2958 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.125816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.101494 restraints weight = 6251.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.104929 restraints weight = 3322.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.107238 restraints weight = 2204.476| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4229 Z= 0.153 Angle : 0.716 9.491 5770 Z= 0.356 Chirality : 0.044 0.235 647 Planarity : 0.004 0.044 721 Dihedral : 6.690 55.915 703 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 1.79 % Allowed : 19.28 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.46 (0.37), residues: 211 loop : -3.04 (0.29), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.002 0.001 HIS B 69 PHE 0.021 0.002 PHE B 133 TYR 0.016 0.001 TYR B 204 ARG 0.001 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 5) link_NAG-ASN : angle 2.41350 ( 15) link_BETA1-4 : bond 0.00494 ( 2) link_BETA1-4 : angle 1.92165 ( 6) hydrogen bonds : bond 0.05567 ( 109) hydrogen bonds : angle 5.74873 ( 303) SS BOND : bond 0.00446 ( 4) SS BOND : angle 3.00204 ( 8) covalent geometry : bond 0.00356 ( 4218) covalent geometry : angle 0.69513 ( 5741) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.398 Fit side-chains REVERT: B 68 ILE cc_start: 0.7328 (OUTLIER) cc_final: 0.7040 (mp) REVERT: B 274 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7511 (t) outliers start: 8 outliers final: 6 residues processed: 61 average time/residue: 0.1046 time to fit residues: 9.1805 Evaluate side-chains 62 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 0 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 44 optimal weight: 0.1980 chunk 4 optimal weight: 0.0870 chunk 46 optimal weight: 0.8980 chunk 18 optimal weight: 0.0970 chunk 43 optimal weight: 0.0970 chunk 17 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 overall best weight: 0.1554 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.127339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.104729 restraints weight = 6185.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.107966 restraints weight = 3284.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.110134 restraints weight = 2169.747| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4229 Z= 0.116 Angle : 0.673 9.531 5770 Z= 0.326 Chirality : 0.044 0.234 647 Planarity : 0.004 0.042 721 Dihedral : 6.405 55.895 703 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.02 % Allowed : 19.06 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.57 (0.36), residues: 211 loop : -2.99 (0.30), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 32 HIS 0.002 0.001 HIS B 245 PHE 0.019 0.001 PHE B 133 TYR 0.017 0.001 TYR B 265 ARG 0.001 0.000 ARG H 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 5) link_NAG-ASN : angle 2.31736 ( 15) link_BETA1-4 : bond 0.00576 ( 2) link_BETA1-4 : angle 2.03927 ( 6) hydrogen bonds : bond 0.04360 ( 109) hydrogen bonds : angle 5.55601 ( 303) SS BOND : bond 0.00325 ( 4) SS BOND : angle 2.48379 ( 8) covalent geometry : bond 0.00262 ( 4218) covalent geometry : angle 0.65456 ( 5741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2449.04 seconds wall clock time: 44 minutes 23.48 seconds (2663.48 seconds total)