Starting phenix.real_space_refine on Wed Jun 3 17:25:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21nw_67854/06_2026/21nw_67854.cif Found real_map, /net/cci-nas-00/data/ceres_data/21nw_67854/06_2026/21nw_67854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21nw_67854/06_2026/21nw_67854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21nw_67854/06_2026/21nw_67854.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21nw_67854/06_2026/21nw_67854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21nw_67854/06_2026/21nw_67854.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 48 5.16 5 C 5000 2.51 5 N 1212 2.21 5 O 1340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7604 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1852 Classifications: {'peptide': 235} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 225} Chain breaks: 2 Chain: "B" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1852 Classifications: {'peptide': 235} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 225} Chain breaks: 2 Chain: "C" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1852 Classifications: {'peptide': 235} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 225} Chain breaks: 2 Chain: "D" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1852 Classifications: {'peptide': 235} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 225} Chain breaks: 2 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'CPL': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-3': 1, 'CPL:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'CPL': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-3': 1, 'CPL:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'CPL': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-3': 1, 'CPL:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'CPL': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-3': 1, 'CPL:plan-4': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 2.08, per 1000 atoms: 0.27 Number of scatterers: 7604 At special positions: 0 Unit cell: (89.816, 89.816, 86.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 4 15.00 O 1340 8.00 N 1212 7.00 C 5000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 38 " - pdb=" SG CYS A 140 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 38 " - pdb=" SG CYS B 140 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 38 " - pdb=" SG CYS C 140 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 38 " - pdb=" SG CYS D 140 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 150 " distance=2.03 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 A 402 " - " ASN A 139 " " NAG B 402 " - " ASN B 139 " " NAG C 402 " - " ASN C 139 " " NAG D 402 " - " ASN D 139 " Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 398.1 milliseconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 75.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 removed outlier: 3.574A pdb=" N LEU A 9 " --> pdb=" O TRP A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 29 removed outlier: 3.926A pdb=" N LEU A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 44 removed outlier: 4.009A pdb=" N ILE A 43 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A 44 " --> pdb=" O ASP A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 44' Processing helix chain 'A' and resid 53 through 79 Processing helix chain 'A' and resid 88 through 121 Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 166 through 187 Processing helix chain 'A' and resid 194 through 217 removed outlier: 3.858A pdb=" N VAL A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 243 Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 19 through 29 removed outlier: 3.932A pdb=" N LEU B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 44 removed outlier: 4.013A pdb=" N ILE B 43 " --> pdb=" O ASP B 40 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG B 44 " --> pdb=" O ASP B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 44' Processing helix chain 'B' and resid 53 through 79 Processing helix chain 'B' and resid 88 through 121 Processing helix chain 'B' and resid 126 through 132 Processing helix chain 'B' and resid 153 through 161 Processing helix chain 'B' and resid 166 through 187 Processing helix chain 'B' and resid 194 through 217 removed outlier: 3.858A pdb=" N VAL B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 243 Processing helix chain 'C' and resid 6 through 19 Processing helix chain 'C' and resid 19 through 29 removed outlier: 3.911A pdb=" N LEU C 27 " --> pdb=" O ALA C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 44 removed outlier: 4.012A pdb=" N ILE C 43 " --> pdb=" O ASP C 40 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG C 44 " --> pdb=" O ASP C 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 44' Processing helix chain 'C' and resid 53 through 79 Processing helix chain 'C' and resid 88 through 121 Processing helix chain 'C' and resid 126 through 132 Processing helix chain 'C' and resid 153 through 161 Processing helix chain 'C' and resid 166 through 187 Processing helix chain 'C' and resid 194 through 217 removed outlier: 3.855A pdb=" N VAL C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 243 Processing helix chain 'D' and resid 6 through 19 Processing helix chain 'D' and resid 19 through 29 removed outlier: 3.911A pdb=" N LEU D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 44 removed outlier: 4.011A pdb=" N ILE D 43 " --> pdb=" O ASP D 40 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG D 44 " --> pdb=" O ASP D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 44' Processing helix chain 'D' and resid 53 through 79 Processing helix chain 'D' and resid 88 through 121 Processing helix chain 'D' and resid 126 through 132 Processing helix chain 'D' and resid 153 through 161 Processing helix chain 'D' and resid 166 through 187 Processing helix chain 'D' and resid 194 through 217 removed outlier: 3.596A pdb=" N ARG D 214 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 243 531 hydrogen bonds defined for protein. 1593 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: 1.21 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1124 1.31 - 1.44: 2320 1.44 - 1.56: 4272 1.56 - 1.69: 8 1.69 - 1.81: 64 Bond restraints: 7788 Sorted by residual: bond pdb=" C11 CPL D 401 " pdb=" O3 CPL D 401 " ideal model delta sigma weight residual 1.327 1.405 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C11 CPL C 401 " pdb=" O3 CPL C 401 " ideal model delta sigma weight residual 1.327 1.405 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C11 CPL A 401 " pdb=" O3 CPL A 401 " ideal model delta sigma weight residual 1.327 1.404 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C11 CPL B 401 " pdb=" O3 CPL B 401 " ideal model delta sigma weight residual 1.327 1.404 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C31 CPL B 401 " pdb=" O2 CPL B 401 " ideal model delta sigma weight residual 1.332 1.408 -0.076 2.00e-02 2.50e+03 1.46e+01 ... (remaining 7783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 10511 3.35 - 6.69: 73 6.69 - 10.04: 8 10.04 - 13.38: 4 13.38 - 16.73: 4 Bond angle restraints: 10600 Sorted by residual: angle pdb=" O3P CPL D 401 " pdb=" P CPL D 401 " pdb=" O4P CPL D 401 " ideal model delta sigma weight residual 93.29 110.02 -16.73 3.00e+00 1.11e-01 3.11e+01 angle pdb=" O3P CPL B 401 " pdb=" P CPL B 401 " pdb=" O4P CPL B 401 " ideal model delta sigma weight residual 93.29 110.00 -16.71 3.00e+00 1.11e-01 3.10e+01 angle pdb=" O3P CPL C 401 " pdb=" P CPL C 401 " pdb=" O4P CPL C 401 " ideal model delta sigma weight residual 93.29 109.99 -16.70 3.00e+00 1.11e-01 3.10e+01 angle pdb=" O3P CPL A 401 " pdb=" P CPL A 401 " pdb=" O4P CPL A 401 " ideal model delta sigma weight residual 93.29 109.25 -15.96 3.00e+00 1.11e-01 2.83e+01 angle pdb=" O1P CPL A 401 " pdb=" P CPL A 401 " pdb=" O2P CPL A 401 " ideal model delta sigma weight residual 119.55 109.12 10.43 3.00e+00 1.11e-01 1.21e+01 ... (remaining 10595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 3892 16.90 - 33.81: 461 33.81 - 50.71: 183 50.71 - 67.61: 27 67.61 - 84.51: 25 Dihedral angle restraints: 4588 sinusoidal: 1824 harmonic: 2764 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 150 " pdb=" CB CYS B 150 " ideal model delta sinusoidal sigma weight residual -86.00 -158.35 72.35 1 1.00e+01 1.00e-02 6.69e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 150 " pdb=" CB CYS C 150 " ideal model delta sinusoidal sigma weight residual -86.00 -158.34 72.34 1 1.00e+01 1.00e-02 6.69e+01 dihedral pdb=" CB CYS D 131 " pdb=" SG CYS D 131 " pdb=" SG CYS D 150 " pdb=" CB CYS D 150 " ideal model delta sinusoidal sigma weight residual -86.00 -158.29 72.29 1 1.00e+01 1.00e-02 6.68e+01 ... (remaining 4585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 867 0.037 - 0.075: 286 0.075 - 0.112: 63 0.112 - 0.149: 8 0.149 - 0.187: 4 Chirality restraints: 1228 Sorted by residual: chirality pdb=" C2 CPL D 401 " pdb=" C1 CPL D 401 " pdb=" C3 CPL D 401 " pdb=" O2 CPL D 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.50 0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" C2 CPL B 401 " pdb=" C1 CPL B 401 " pdb=" C3 CPL B 401 " pdb=" O2 CPL B 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.50 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" C2 CPL C 401 " pdb=" C1 CPL C 401 " pdb=" C3 CPL C 401 " pdb=" O2 CPL C 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.50 0.18 2.00e-01 2.50e+01 8.44e-01 ... (remaining 1225 not shown) Planarity restraints: 1292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 145 " -0.007 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" C GLN C 145 " 0.023 2.00e-02 2.50e+03 pdb=" O GLN C 145 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU C 146 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 145 " -0.006 2.00e-02 2.50e+03 1.20e-02 1.44e+00 pdb=" C GLN A 145 " 0.021 2.00e-02 2.50e+03 pdb=" O GLN A 145 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU A 146 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 20 " 0.019 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO A 21 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " 0.017 5.00e-02 4.00e+02 ... (remaining 1289 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1473 2.77 - 3.30: 7251 3.30 - 3.83: 13158 3.83 - 4.37: 14964 4.37 - 4.90: 27080 Nonbonded interactions: 63926 Sorted by model distance: nonbonded pdb=" O MET A 57 " pdb=" OG1 THR A 61 " model vdw 2.233 3.040 nonbonded pdb=" O MET C 57 " pdb=" OG1 THR C 61 " model vdw 2.239 3.040 nonbonded pdb=" O MET B 57 " pdb=" OG1 THR B 61 " model vdw 2.240 3.040 nonbonded pdb=" NH1 ARG D 122 " pdb=" OD1 ASP D 224 " model vdw 2.297 3.120 nonbonded pdb=" NH1 ARG C 122 " pdb=" OD1 ASP C 224 " model vdw 2.299 3.120 ... (remaining 63921 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.350 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.990 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:8.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.005 0.078 7800 Z= 0.229 Angle : 0.742 16.726 10628 Z= 0.315 Chirality : 0.038 0.187 1228 Planarity : 0.003 0.030 1288 Dihedral : 17.394 84.512 2796 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.79 % Allowed : 22.73 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.28), residues: 916 helix: 2.12 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.76 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 48 TYR 0.008 0.001 TYR C 165 PHE 0.007 0.001 PHE D 246 TRP 0.003 0.001 TRP C 135 HIS 0.002 0.000 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.23 ( 7788) covalent geometry : angle 0.74185 / 0.32 (10600) SS BOND : bond 0.00144 / 0.07 ( 8) SS BOND : angle 0.40323 / 0.29 ( 16) hydrogen bonds : bond 0.13984 / 9.20 ( 531) hydrogen bonds : angle 6.67452 / 4.92 ( 1593) link_NAG-ASN : bond 0.00154 / 0.08 ( 4) link_NAG-ASN : angle 0.81838 / 0.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.230 Fit side-chains outliers start: 30 outliers final: 26 residues processed: 102 average time/residue: 0.3676 time to fit residues: 40.7807 Evaluate side-chains 95 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 244 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.0070 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.144148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.114984 restraints weight = 8443.469| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.79 r_work: 0.3105 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7800 Z= 0.123 Angle : 0.445 5.097 10628 Z= 0.232 Chirality : 0.037 0.125 1228 Planarity : 0.004 0.029 1288 Dihedral : 12.511 83.013 1274 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.79 % Allowed : 20.71 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.27), residues: 916 helix: 2.51 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -0.62 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 122 TYR 0.010 0.001 TYR D 174 PHE 0.013 0.001 PHE D 246 TRP 0.002 0.001 TRP C 222 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 7788) covalent geometry : angle 0.44252 / 0.23 (10600) SS BOND : bond 0.00163 / 0.08 ( 8) SS BOND : angle 0.22340 / 0.17 ( 16) hydrogen bonds : bond 0.04221 / 2.82 ( 531) hydrogen bonds : angle 4.63389 / 3.34 ( 1593) link_NAG-ASN : bond 0.00080 / 0.04 ( 4) link_NAG-ASN : angle 1.61806 / 1.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 0.280 Fit side-chains REVERT: A 141 SER cc_start: 0.7940 (m) cc_final: 0.7530 (p) REVERT: A 217 ASP cc_start: 0.8267 (m-30) cc_final: 0.8048 (m-30) REVERT: B 141 SER cc_start: 0.7931 (m) cc_final: 0.7522 (p) REVERT: C 141 SER cc_start: 0.7905 (m) cc_final: 0.7489 (p) outliers start: 30 outliers final: 13 residues processed: 89 average time/residue: 0.2991 time to fit residues: 29.5260 Evaluate side-chains 85 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 247 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 90 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.141542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112235 restraints weight = 8477.052| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.79 r_work: 0.3069 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7800 Z= 0.161 Angle : 0.449 4.429 10628 Z= 0.237 Chirality : 0.037 0.117 1228 Planarity : 0.004 0.030 1288 Dihedral : 11.644 85.332 1245 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.04 % Allowed : 19.32 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.27), residues: 916 helix: 2.64 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.74 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 193 TYR 0.011 0.001 TYR D 174 PHE 0.015 0.002 PHE C 22 TRP 0.002 0.001 TRP C 135 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 7788) covalent geometry : angle 0.44558 / 0.24 (10600) SS BOND : bond 0.00179 / 0.09 ( 8) SS BOND : angle 0.30768 / 0.21 ( 16) hydrogen bonds : bond 0.04360 / 2.91 ( 531) hydrogen bonds : angle 4.54490 / 3.27 ( 1593) link_NAG-ASN : bond 0.00134 / 0.07 ( 4) link_NAG-ASN : angle 1.71993 / 1.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 0.197 Fit side-chains REVERT: A 141 SER cc_start: 0.7937 (m) cc_final: 0.7536 (p) REVERT: B 141 SER cc_start: 0.7934 (m) cc_final: 0.7520 (p) REVERT: C 141 SER cc_start: 0.7918 (m) cc_final: 0.7503 (p) REVERT: D 145 GLN cc_start: 0.7300 (pt0) cc_final: 0.7100 (pt0) outliers start: 32 outliers final: 17 residues processed: 89 average time/residue: 0.3561 time to fit residues: 34.7113 Evaluate side-chains 88 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 247 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 4 optimal weight: 0.4980 chunk 48 optimal weight: 0.0570 chunk 70 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 0.0970 chunk 42 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 231 GLN B 184 GLN C 184 GLN D 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.151957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124912 restraints weight = 8481.356| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.67 r_work: 0.3132 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7800 Z= 0.100 Angle : 0.415 7.379 10628 Z= 0.212 Chirality : 0.035 0.115 1228 Planarity : 0.003 0.027 1288 Dihedral : 11.185 86.645 1245 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.16 % Allowed : 20.83 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.27), residues: 916 helix: 2.85 (0.19), residues: 648 sheet: None (None), residues: 0 loop : -0.63 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 48 TYR 0.010 0.001 TYR C 174 PHE 0.014 0.001 PHE B 22 TRP 0.002 0.000 TRP C 135 HIS 0.002 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 ( 7788) covalent geometry : angle 0.41264 / 0.21 (10600) SS BOND : bond 0.00180 / 0.09 ( 8) SS BOND : angle 0.28590 / 0.20 ( 16) hydrogen bonds : bond 0.03734 / 2.52 ( 531) hydrogen bonds : angle 4.35104 / 3.14 ( 1593) link_NAG-ASN : bond 0.00021 / 0.01 ( 4) link_NAG-ASN : angle 1.35707 / 0.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.297 Fit side-chains REVERT: A 57 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.6816 (ttm) REVERT: A 141 SER cc_start: 0.7878 (m) cc_final: 0.7510 (p) REVERT: B 57 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.6274 (ttm) REVERT: B 141 SER cc_start: 0.7924 (m) cc_final: 0.7545 (p) REVERT: C 57 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6281 (ttm) REVERT: C 141 SER cc_start: 0.7892 (m) cc_final: 0.7515 (p) outliers start: 25 outliers final: 14 residues processed: 89 average time/residue: 0.3509 time to fit residues: 34.3445 Evaluate side-chains 86 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 247 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 20 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 54 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.143874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.114490 restraints weight = 8556.615| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.82 r_work: 0.3100 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7800 Z= 0.114 Angle : 0.422 8.220 10628 Z= 0.216 Chirality : 0.036 0.117 1228 Planarity : 0.003 0.027 1288 Dihedral : 10.977 89.205 1245 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.79 % Allowed : 20.20 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.27), residues: 916 helix: 2.89 (0.19), residues: 648 sheet: None (None), residues: 0 loop : -0.63 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 48 TYR 0.010 0.001 TYR C 174 PHE 0.015 0.001 PHE B 22 TRP 0.002 0.001 TRP C 135 HIS 0.003 0.001 HIS C 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 7788) covalent geometry : angle 0.42005 / 0.22 (10600) SS BOND : bond 0.00164 / 0.08 ( 8) SS BOND : angle 0.33574 / 0.24 ( 16) hydrogen bonds : bond 0.03769 / 2.54 ( 531) hydrogen bonds : angle 4.30793 / 3.10 ( 1593) link_NAG-ASN : bond 0.00023 / 0.01 ( 4) link_NAG-ASN : angle 1.33603 / 0.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.296 Fit side-chains REVERT: A 57 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.6606 (ttm) REVERT: A 141 SER cc_start: 0.7850 (m) cc_final: 0.7482 (p) REVERT: B 57 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6147 (ttm) REVERT: C 57 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6144 (ttm) outliers start: 30 outliers final: 20 residues processed: 96 average time/residue: 0.3754 time to fit residues: 39.3963 Evaluate side-chains 94 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 247 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.142683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.113216 restraints weight = 8627.169| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.82 r_work: 0.3082 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7800 Z= 0.130 Angle : 0.426 7.098 10628 Z= 0.220 Chirality : 0.036 0.113 1228 Planarity : 0.003 0.029 1288 Dihedral : 10.617 89.004 1245 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.30 % Allowed : 18.31 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.27), residues: 916 helix: 2.88 (0.19), residues: 648 sheet: None (None), residues: 0 loop : -0.64 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 193 TYR 0.010 0.001 TYR C 174 PHE 0.015 0.001 PHE D 22 TRP 0.002 0.001 TRP C 135 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 7788) covalent geometry : angle 0.42351 / 0.22 (10600) SS BOND : bond 0.00167 / 0.08 ( 8) SS BOND : angle 0.30759 / 0.22 ( 16) hydrogen bonds : bond 0.03912 / 2.62 ( 531) hydrogen bonds : angle 4.33800 / 3.12 ( 1593) link_NAG-ASN : bond 0.00027 / 0.01 ( 4) link_NAG-ASN : angle 1.47567 / 1.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 75 time to evaluate : 0.302 Fit side-chains REVERT: A 57 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.6732 (ttm) REVERT: A 141 SER cc_start: 0.7902 (m) cc_final: 0.7535 (p) REVERT: B 57 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6189 (ttm) REVERT: B 141 SER cc_start: 0.7967 (m) cc_final: 0.7605 (p) REVERT: C 57 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6200 (ttm) REVERT: C 141 SER cc_start: 0.8000 (m) cc_final: 0.7622 (p) outliers start: 42 outliers final: 28 residues processed: 106 average time/residue: 0.3507 time to fit residues: 40.6303 Evaluate side-chains 106 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 247 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 34 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.140276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.110879 restraints weight = 8567.248| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.81 r_work: 0.3112 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7800 Z= 0.171 Angle : 0.449 6.604 10628 Z= 0.236 Chirality : 0.038 0.116 1228 Planarity : 0.004 0.030 1288 Dihedral : 10.307 86.165 1245 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.30 % Allowed : 17.93 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.27), residues: 916 helix: 2.77 (0.19), residues: 648 sheet: None (None), residues: 0 loop : -0.70 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 193 TYR 0.011 0.001 TYR D 174 PHE 0.019 0.002 PHE C 22 TRP 0.002 0.001 TRP A 5 HIS 0.004 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 7788) covalent geometry : angle 0.44638 / 0.24 (10600) SS BOND : bond 0.00157 / 0.07 ( 8) SS BOND : angle 0.41536 / 0.30 ( 16) hydrogen bonds : bond 0.04292 / 2.86 ( 531) hydrogen bonds : angle 4.45309 / 3.19 ( 1593) link_NAG-ASN : bond 0.00123 / 0.06 ( 4) link_NAG-ASN : angle 1.58830 / 1.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 74 time to evaluate : 0.294 Fit side-chains REVERT: A 57 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.6960 (ttm) REVERT: A 141 SER cc_start: 0.8120 (m) cc_final: 0.7768 (p) REVERT: B 57 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.6515 (ttm) REVERT: B 141 SER cc_start: 0.8099 (m) cc_final: 0.7746 (p) REVERT: C 57 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.6527 (ttm) outliers start: 42 outliers final: 32 residues processed: 104 average time/residue: 0.3549 time to fit residues: 40.3054 Evaluate side-chains 109 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 247 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 4 optimal weight: 0.0670 chunk 12 optimal weight: 0.0170 chunk 64 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.143587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.114348 restraints weight = 8529.609| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.81 r_work: 0.3098 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7800 Z= 0.102 Angle : 0.402 6.777 10628 Z= 0.208 Chirality : 0.035 0.114 1228 Planarity : 0.003 0.028 1288 Dihedral : 9.803 81.215 1245 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.17 % Allowed : 19.07 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.27), residues: 916 helix: 3.04 (0.18), residues: 648 sheet: None (None), residues: 0 loop : -0.62 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 122 TYR 0.010 0.001 TYR D 174 PHE 0.018 0.001 PHE A 22 TRP 0.002 0.001 TRP B 222 HIS 0.002 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 7788) covalent geometry : angle 0.40026 / 0.21 (10600) SS BOND : bond 0.00164 / 0.08 ( 8) SS BOND : angle 0.28222 / 0.20 ( 16) hydrogen bonds : bond 0.03715 / 2.50 ( 531) hydrogen bonds : angle 4.30236 / 3.09 ( 1593) link_NAG-ASN : bond 0.00066 / 0.03 ( 4) link_NAG-ASN : angle 1.25681 / 0.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 0.284 Fit side-chains REVERT: A 141 SER cc_start: 0.7883 (m) cc_final: 0.7531 (p) REVERT: B 57 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.6273 (ttm) REVERT: B 141 SER cc_start: 0.7961 (m) cc_final: 0.7630 (p) REVERT: C 57 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6304 (ttm) outliers start: 33 outliers final: 28 residues processed: 100 average time/residue: 0.3759 time to fit residues: 40.9621 Evaluate side-chains 104 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 247 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 27 optimal weight: 0.2980 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 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 = 0.3559 r_free = 0.3559 target = 0.142471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.113189 restraints weight = 8491.854| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.80 r_work: 0.3084 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7800 Z= 0.122 Angle : 0.411 6.630 10628 Z= 0.214 Chirality : 0.036 0.111 1228 Planarity : 0.003 0.028 1288 Dihedral : 9.689 78.006 1245 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.29 % Allowed : 18.69 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.27), residues: 916 helix: 3.03 (0.18), residues: 648 sheet: None (None), residues: 0 loop : -0.64 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 48 TYR 0.010 0.001 TYR C 174 PHE 0.019 0.001 PHE A 22 TRP 0.002 0.000 TRP D 135 HIS 0.002 0.001 HIS C 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 7788) covalent geometry : angle 0.40830 / 0.21 (10600) SS BOND : bond 0.00159 / 0.07 ( 8) SS BOND : angle 0.31790 / 0.22 ( 16) hydrogen bonds : bond 0.03853 / 2.59 ( 531) hydrogen bonds : angle 4.31179 / 3.09 ( 1593) link_NAG-ASN : bond 0.00017 / 0.01 ( 4) link_NAG-ASN : angle 1.42023 / 0.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 74 time to evaluate : 0.298 Fit side-chains REVERT: A 57 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6773 (ttm) REVERT: A 141 SER cc_start: 0.7879 (m) cc_final: 0.7517 (p) REVERT: A 145 GLN cc_start: 0.7655 (pt0) cc_final: 0.7448 (pt0) REVERT: B 57 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6240 (ttm) REVERT: B 141 SER cc_start: 0.7982 (m) cc_final: 0.7652 (p) REVERT: C 57 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.6213 (ttm) outliers start: 34 outliers final: 31 residues processed: 101 average time/residue: 0.3924 time to fit residues: 43.1994 Evaluate side-chains 108 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 74 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 247 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.143501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.114235 restraints weight = 8513.834| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.81 r_work: 0.3098 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7800 Z= 0.105 Angle : 0.400 6.635 10628 Z= 0.208 Chirality : 0.035 0.112 1228 Planarity : 0.003 0.028 1288 Dihedral : 9.449 73.565 1245 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.67 % Allowed : 18.18 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.27), residues: 916 helix: 3.11 (0.18), residues: 648 sheet: None (None), residues: 0 loop : -0.62 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 44 TYR 0.010 0.001 TYR C 174 PHE 0.018 0.001 PHE D 22 TRP 0.002 0.000 TRP B 135 HIS 0.002 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 7788) covalent geometry : angle 0.39767 / 0.21 (10600) SS BOND : bond 0.00159 / 0.08 ( 8) SS BOND : angle 0.29195 / 0.20 ( 16) hydrogen bonds : bond 0.03686 / 2.48 ( 531) hydrogen bonds : angle 4.26047 / 3.06 ( 1593) link_NAG-ASN : bond 0.00047 / 0.02 ( 4) link_NAG-ASN : angle 1.28222 / 0.87 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.252 Fit side-chains REVERT: A 57 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.7005 (ttm) REVERT: B 57 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6238 (ttm) REVERT: C 57 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6246 (ttm) outliers start: 37 outliers final: 31 residues processed: 102 average time/residue: 0.3968 time to fit residues: 44.0219 Evaluate side-chains 106 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 22 PHE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 247 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 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 = 0.3558 r_free = 0.3558 target = 0.142394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113121 restraints weight = 8582.124| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.80 r_work: 0.3083 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7800 Z= 0.121 Angle : 0.410 6.485 10628 Z= 0.214 Chirality : 0.036 0.110 1228 Planarity : 0.003 0.028 1288 Dihedral : 9.424 71.557 1245 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 4.80 % Allowed : 18.31 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.27), residues: 916 helix: 3.05 (0.18), residues: 648 sheet: None (None), residues: 0 loop : -0.63 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 48 TYR 0.010 0.001 TYR C 174 PHE 0.019 0.001 PHE B 22 TRP 0.002 0.001 TRP D 135 HIS 0.002 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 7788) covalent geometry : angle 0.40777 / 0.21 (10600) SS BOND : bond 0.00165 / 0.08 ( 8) SS BOND : angle 0.30829 / 0.22 ( 16) hydrogen bonds : bond 0.03839 / 2.58 ( 531) hydrogen bonds : angle 4.29274 / 3.08 ( 1593) link_NAG-ASN : bond 0.00011 / 0.01 ( 4) link_NAG-ASN : angle 1.43630 / 0.98 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2311.40 seconds wall clock time: 40 minutes 20.85 seconds (2420.85 seconds total)