Starting phenix.real_space_refine on Wed Jul 1 23:00:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sof_25269/07_2026/7sof_25269.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sof_25269/07_2026/7sof_25269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sof_25269/07_2026/7sof_25269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sof_25269/07_2026/7sof_25269.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7sof_25269/07_2026/7sof_25269.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sof_25269/07_2026/7sof_25269.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sof_25269/07_2026/7sof_25269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sof_25269/07_2026/7sof_25269.cif" } resolution = 3.6 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= 0.045 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 2426 2.51 5 N 611 2.21 5 O 685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3735 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 730 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "H" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 916 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 117} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1966 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 13, 'TRANS': 244} Chain breaks: 4 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'PHE:plan': 1, 'ASP:plan': 7, 'ARG:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 0.93, per 1000 atoms: 0.25 Number of scatterers: 3735 At special positions: 0 Unit cell: (73.341, 91.044, 77.556, 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 685 8.00 N 611 7.00 C 2426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 149 " " NAG A1306 " - " ASN A 17 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 139.5 milliseconds 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 912 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 6 sheets defined 4.7% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.797A pdb=" N GLU L 82 " --> pdb=" O THR L 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'A' and resid 294 through 303 Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.529A pdb=" N VAL L 10 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 48 through 54 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 59 through 61 current: chain 'H' and resid 108 through 115 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 108 through 115 current: chain 'A' and resid 116 through 121 removed outlier: 6.601A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N PHE A 140 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLU A 156 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ASP A 142 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYS A 154 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR A 144 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TRP A 152 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.484A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.711A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) 116 hydrogen bonds defined for protein. 288 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.36 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 730 1.33 - 1.45: 971 1.45 - 1.57: 2117 1.57 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3834 Sorted by residual: bond pdb=" NE ARG A 246 " pdb=" CZ ARG A 246 " ideal model delta sigma weight residual 1.326 1.369 -0.043 1.10e-02 8.26e+03 1.50e+01 bond pdb=" NE ARG A 78 " pdb=" CZ ARG A 78 " ideal model delta sigma weight residual 1.326 1.367 -0.041 1.10e-02 8.26e+03 1.41e+01 bond pdb=" N ILE L 94 " pdb=" CA ILE L 94 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.85e+00 bond pdb=" C5 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" C5 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.17e+00 ... (remaining 3829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 4327 1.49 - 2.99: 734 2.99 - 4.48: 108 4.48 - 5.98: 52 5.98 - 7.47: 27 Bond angle restraints: 5248 Sorted by residual: angle pdb=" C GLN H 41 " pdb=" N PRO H 42 " pdb=" CA PRO H 42 " ideal model delta sigma weight residual 119.66 125.79 -6.13 7.30e-01 1.88e+00 7.05e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.20 -7.17 9.90e-01 1.02e+00 5.24e+01 angle pdb=" C GLY H 8 " pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 119.76 126.99 -7.23 1.03e+00 9.43e-01 4.93e+01 angle pdb=" C ASP A 138 " pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta sigma weight residual 119.76 126.70 -6.94 1.00e+00 1.00e+00 4.82e+01 angle pdb=" C ARG L 53 " pdb=" N PRO L 54 " pdb=" CA PRO L 54 " ideal model delta sigma weight residual 119.85 126.83 -6.98 1.01e+00 9.80e-01 4.78e+01 ... (remaining 5243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 2078 16.47 - 32.95: 52 32.95 - 49.42: 11 49.42 - 65.90: 4 65.90 - 82.37: 1 Dihedral angle restraints: 2146 sinusoidal: 729 harmonic: 1417 Sorted by residual: dihedral pdb=" C THR L 93 " pdb=" N THR L 93 " pdb=" CA THR L 93 " pdb=" CB THR L 93 " ideal model delta harmonic sigma weight residual -122.00 -132.33 10.33 0 2.50e+00 1.60e-01 1.71e+01 dihedral pdb=" CA GLY H 105 " pdb=" C GLY H 105 " pdb=" N GLU H 106 " pdb=" CA GLU H 106 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ARG L 53 " pdb=" C ARG L 53 " pdb=" N PRO L 54 " pdb=" CA PRO L 54 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 2143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 447 0.070 - 0.139: 136 0.139 - 0.209: 29 0.209 - 0.278: 4 0.278 - 0.348: 10 Chirality restraints: 626 Sorted by residual: chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.71e+01 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.13e+01 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.62 0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 623 not shown) Planarity restraints: 659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 96 " 0.034 2.00e-02 2.50e+03 1.80e-02 6.45e+00 pdb=" CG TYR H 96 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR H 96 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR H 96 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR H 96 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR H 96 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR H 96 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 96 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 105 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C GLY H 105 " -0.041 2.00e-02 2.50e+03 pdb=" O GLY H 105 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU H 106 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1303 " -0.026 2.00e-02 2.50e+03 2.12e-02 5.61e+00 pdb=" C7 NAG A1303 " -0.003 2.00e-02 2.50e+03 pdb=" C8 NAG A1303 " -0.016 2.00e-02 2.50e+03 pdb=" N2 NAG A1303 " 0.035 2.00e-02 2.50e+03 pdb=" O7 NAG A1303 " 0.010 2.00e-02 2.50e+03 ... (remaining 656 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 2165 3.03 - 3.50: 3156 3.50 - 3.97: 6049 3.97 - 4.43: 6775 4.43 - 4.90: 11258 Nonbonded interactions: 29403 Sorted by model distance: nonbonded pdb=" ND1 HIS A 146 " pdb=" N LYS A 147 " model vdw 2.563 3.200 nonbonded pdb=" O PRO H 14 " pdb=" OG1 THR H 15 " model vdw 2.593 3.040 nonbonded pdb=" N ASN A 148 " pdb=" O ASN A 148 " model vdw 2.603 2.496 nonbonded pdb=" N THR H 10 " pdb=" N LEU H 11 " model vdw 2.608 2.560 nonbonded pdb=" OD1 ASP H 113 " pdb=" N VAL H 114 " model vdw 2.625 3.120 ... (remaining 29398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 11.310 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: 0.080 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.570 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 : 0.010 0.062 3848 Z= 0.575 Angle : 1.320 7.472 5285 Z= 0.869 Chirality : 0.080 0.348 626 Planarity : 0.005 0.024 652 Dihedral : 8.494 82.371 1219 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.38), residues: 474 helix: 0.56 (1.75), residues: 11 sheet: 1.23 (0.35), residues: 207 loop : -0.24 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 40 TYR 0.034 0.005 TYR H 96 PHE 0.014 0.003 PHE A 220 TRP 0.019 0.004 TRP L 90 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.01013 / 0.56 ( 3834) covalent geometry : angle 1.30778 / 0.87 ( 5248) SS BOND : bond 0.00544 / 0.35 ( 5) SS BOND : angle 1.93358 / 1.10 ( 10) hydrogen bonds : bond 0.16819 / 11.34 ( 116) hydrogen bonds : angle 7.97272 / 5.55 ( 288) link_BETA1-4 : bond 0.05715 / 2.84 ( 2) link_BETA1-4 : angle 2.83908 / 1.61 ( 6) link_NAG-ASN : bond 0.05510 / 3.40 ( 7) link_NAG-ASN : angle 2.65280 / 1.51 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.085 Fit side-chains REVERT: L 36 GLN cc_start: 0.8889 (tt0) cc_final: 0.8627 (tt0) REVERT: H 3 THR cc_start: 0.7351 (t) cc_final: 0.7149 (m) REVERT: H 62 SER cc_start: 0.8441 (t) cc_final: 0.8090 (p) REVERT: H 124 SER cc_start: 0.6718 (p) cc_final: 0.6437 (t) REVERT: A 154 LYS cc_start: 0.8401 (ttpt) cc_final: 0.8075 (ttpp) REVERT: A 258 TRP cc_start: 0.7459 (m-90) cc_final: 0.7187 (m-90) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0482 time to fit residues: 5.2749 Evaluate side-chains 63 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 49 GLN H 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.191427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.159749 restraints weight = 4162.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.163117 restraints weight = 3141.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.164023 restraints weight = 3017.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.164791 restraints weight = 2063.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.165430 restraints weight = 1890.901| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3848 Z= 0.170 Angle : 0.616 5.999 5285 Z= 0.320 Chirality : 0.047 0.157 626 Planarity : 0.005 0.051 652 Dihedral : 4.676 17.888 517 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.69 % Favored : 98.10 % Rotamer: Outliers : 1.47 % Allowed : 7.35 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.39), residues: 474 helix: 1.71 (1.54), residues: 11 sheet: 1.36 (0.38), residues: 191 loop : -0.07 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.026 0.002 TYR L 48 PHE 0.017 0.002 PHE A 55 TRP 0.010 0.001 TRP H 103 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 3834) covalent geometry : angle 0.59780 / 0.32 ( 5248) SS BOND : bond 0.00490 / 0.25 ( 5) SS BOND : angle 1.65011 / 1.07 ( 10) hydrogen bonds : bond 0.03639 / 2.54 ( 116) hydrogen bonds : angle 6.19285 / 4.23 ( 288) link_BETA1-4 : bond 0.00495 / 0.25 ( 2) link_BETA1-4 : angle 1.70170 / 0.89 ( 6) link_NAG-ASN : bond 0.00271 / 0.16 ( 7) link_NAG-ASN : angle 1.97776 / 1.06 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.075 Fit side-chains REVERT: L 53 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7884 (mtm110) REVERT: A 108 THR cc_start: 0.8666 (p) cc_final: 0.8244 (t) REVERT: A 138 ASP cc_start: 0.7987 (t0) cc_final: 0.7742 (t0) REVERT: A 154 LYS cc_start: 0.8631 (ttpt) cc_final: 0.8276 (ttpp) REVERT: A 258 TRP cc_start: 0.8224 (m-90) cc_final: 0.7712 (m-90) outliers start: 5 outliers final: 2 residues processed: 68 average time/residue: 0.0550 time to fit residues: 4.5791 Evaluate side-chains 66 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain H residue 83 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.0570 chunk 16 optimal weight: 0.2980 chunk 37 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.184033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.151798 restraints weight = 4160.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.153189 restraints weight = 3029.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.154671 restraints weight = 3102.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.155740 restraints weight = 2258.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.158322 restraints weight = 1999.454| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3848 Z= 0.158 Angle : 0.566 6.136 5285 Z= 0.293 Chirality : 0.045 0.172 626 Planarity : 0.004 0.049 652 Dihedral : 4.397 16.602 517 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.24 % Allowed : 7.94 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.38), residues: 474 helix: 2.86 (1.64), residues: 11 sheet: 1.21 (0.35), residues: 214 loop : -0.27 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.018 0.002 TYR L 48 PHE 0.012 0.002 PHE A 168 TRP 0.007 0.001 TRP H 103 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 3834) covalent geometry : angle 0.55596 / 0.29 ( 5248) SS BOND : bond 0.00379 / 0.19 ( 5) SS BOND : angle 1.42265 / 0.91 ( 10) hydrogen bonds : bond 0.03488 / 2.45 ( 116) hydrogen bonds : angle 5.80566 / 3.92 ( 288) link_BETA1-4 : bond 0.00838 / 0.44 ( 2) link_BETA1-4 : angle 1.58273 / 0.89 ( 6) link_NAG-ASN : bond 0.00322 / 0.21 ( 7) link_NAG-ASN : angle 1.26594 / 0.68 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8172 (t0) cc_final: 0.7814 (t0) REVERT: A 154 LYS cc_start: 0.8658 (ttpt) cc_final: 0.8336 (ttpp) REVERT: A 258 TRP cc_start: 0.8229 (m-90) cc_final: 0.7614 (m-90) outliers start: 11 outliers final: 7 residues processed: 71 average time/residue: 0.0585 time to fit residues: 4.9312 Evaluate side-chains 65 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 210 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.161353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.129750 restraints weight = 4293.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.130534 restraints weight = 3692.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.132318 restraints weight = 3696.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.133109 restraints weight = 2731.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.135678 restraints weight = 2398.729| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3848 Z= 0.175 Angle : 0.574 7.693 5285 Z= 0.294 Chirality : 0.045 0.164 626 Planarity : 0.005 0.046 652 Dihedral : 4.464 17.100 517 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.41 % Allowed : 7.94 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.38), residues: 474 helix: 3.10 (1.63), residues: 11 sheet: 1.06 (0.37), residues: 190 loop : -0.40 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 246 TYR 0.016 0.002 TYR L 48 PHE 0.012 0.002 PHE A 238 TRP 0.006 0.001 TRP H 115 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 3834) covalent geometry : angle 0.56324 / 0.29 ( 5248) SS BOND : bond 0.00356 / 0.18 ( 5) SS BOND : angle 1.47260 / 0.94 ( 10) hydrogen bonds : bond 0.03396 / 2.38 ( 116) hydrogen bonds : angle 5.69206 / 3.82 ( 288) link_BETA1-4 : bond 0.00606 / 0.31 ( 2) link_BETA1-4 : angle 1.54975 / 0.86 ( 6) link_NAG-ASN : bond 0.00232 / 0.15 ( 7) link_NAG-ASN : angle 1.42514 / 0.77 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: L 2 TYR cc_start: 0.8722 (t80) cc_final: 0.8327 (t80) REVERT: A 154 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8306 (ttpp) outliers start: 15 outliers final: 12 residues processed: 63 average time/residue: 0.0612 time to fit residues: 4.6876 Evaluate side-chains 64 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.161082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.127682 restraints weight = 4321.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.129546 restraints weight = 3407.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.131017 restraints weight = 3372.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.132018 restraints weight = 2443.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134500 restraints weight = 2157.763| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3848 Z= 0.171 Angle : 0.565 7.244 5285 Z= 0.288 Chirality : 0.045 0.166 626 Planarity : 0.004 0.044 652 Dihedral : 4.411 16.422 517 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.71 % Allowed : 8.53 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.38), residues: 474 helix: 3.21 (1.64), residues: 11 sheet: 0.93 (0.36), residues: 195 loop : -0.42 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 158 TYR 0.015 0.001 TYR A 265 PHE 0.012 0.002 PHE A 238 TRP 0.007 0.001 TRP A 258 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 3834) covalent geometry : angle 0.55434 / 0.29 ( 5248) SS BOND : bond 0.00327 / 0.16 ( 5) SS BOND : angle 1.43356 / 0.91 ( 10) hydrogen bonds : bond 0.03318 / 2.33 ( 116) hydrogen bonds : angle 5.62070 / 3.76 ( 288) link_BETA1-4 : bond 0.00694 / 0.35 ( 2) link_BETA1-4 : angle 1.60135 / 0.90 ( 6) link_NAG-ASN : bond 0.00264 / 0.17 ( 7) link_NAG-ASN : angle 1.34176 / 0.73 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8304 (ttpp) outliers start: 16 outliers final: 13 residues processed: 65 average time/residue: 0.0770 time to fit residues: 6.1285 Evaluate side-chains 66 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.0870 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.159607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.127942 restraints weight = 4378.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.129117 restraints weight = 3691.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130590 restraints weight = 3680.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.131612 restraints weight = 2717.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.134079 restraints weight = 2347.151| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3848 Z= 0.140 Angle : 0.549 7.615 5285 Z= 0.278 Chirality : 0.045 0.164 626 Planarity : 0.004 0.044 652 Dihedral : 4.301 15.790 517 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.82 % Allowed : 9.71 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.39), residues: 474 helix: 3.28 (1.65), residues: 11 sheet: 0.88 (0.37), residues: 191 loop : -0.27 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 158 TYR 0.015 0.001 TYR A 265 PHE 0.012 0.002 PHE A 55 TRP 0.007 0.001 TRP A 258 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 3834) covalent geometry : angle 0.53835 / 0.28 ( 5248) SS BOND : bond 0.00297 / 0.15 ( 5) SS BOND : angle 1.32413 / 0.86 ( 10) hydrogen bonds : bond 0.03125 / 2.22 ( 116) hydrogen bonds : angle 5.47187 / 3.66 ( 288) link_BETA1-4 : bond 0.00559 / 0.28 ( 2) link_BETA1-4 : angle 1.62089 / 0.91 ( 6) link_NAG-ASN : bond 0.00271 / 0.18 ( 7) link_NAG-ASN : angle 1.36805 / 0.75 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8663 (ttpt) cc_final: 0.8295 (ttpp) REVERT: A 258 TRP cc_start: 0.8248 (m-90) cc_final: 0.7483 (m-90) outliers start: 13 outliers final: 13 residues processed: 64 average time/residue: 0.0668 time to fit residues: 5.1503 Evaluate side-chains 65 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.0570 chunk 33 optimal weight: 0.0020 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.158762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127394 restraints weight = 4440.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.127067 restraints weight = 4479.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.130305 restraints weight = 4957.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.131092 restraints weight = 3240.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.132617 restraints weight = 2742.079| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3848 Z= 0.119 Angle : 0.535 7.378 5285 Z= 0.270 Chirality : 0.044 0.165 626 Planarity : 0.004 0.043 652 Dihedral : 4.211 15.902 517 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.82 % Allowed : 10.29 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.39), residues: 474 helix: 3.17 (1.65), residues: 11 sheet: 0.88 (0.37), residues: 191 loop : -0.32 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 158 TYR 0.015 0.001 TYR A 265 PHE 0.017 0.001 PHE A 55 TRP 0.005 0.001 TRP H 103 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 3834) covalent geometry : angle 0.52513 / 0.27 ( 5248) SS BOND : bond 0.00267 / 0.13 ( 5) SS BOND : angle 1.25266 / 0.82 ( 10) hydrogen bonds : bond 0.02990 / 2.14 ( 116) hydrogen bonds : angle 5.37622 / 3.60 ( 288) link_BETA1-4 : bond 0.00627 / 0.32 ( 2) link_BETA1-4 : angle 1.59304 / 0.89 ( 6) link_NAG-ASN : bond 0.00278 / 0.18 ( 7) link_NAG-ASN : angle 1.28938 / 0.70 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8662 (ttpt) cc_final: 0.8299 (ttpp) REVERT: A 258 TRP cc_start: 0.8242 (m-90) cc_final: 0.7479 (m-90) outliers start: 13 outliers final: 12 residues processed: 64 average time/residue: 0.0708 time to fit residues: 5.4977 Evaluate side-chains 65 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 0.0980 chunk 3 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.158187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126520 restraints weight = 4383.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.125526 restraints weight = 4405.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.126545 restraints weight = 4258.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.127052 restraints weight = 3534.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.127967 restraints weight = 3278.685| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3848 Z= 0.160 Angle : 0.570 7.928 5285 Z= 0.283 Chirality : 0.045 0.167 626 Planarity : 0.004 0.043 652 Dihedral : 4.265 16.213 517 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.12 % Allowed : 10.29 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.39), residues: 474 helix: 3.53 (1.70), residues: 11 sheet: 0.80 (0.36), residues: 190 loop : -0.45 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 158 TYR 0.015 0.001 TYR A 265 PHE 0.018 0.002 PHE A 55 TRP 0.006 0.001 TRP H 115 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 3834) covalent geometry : angle 0.56017 / 0.28 ( 5248) SS BOND : bond 0.00324 / 0.16 ( 5) SS BOND : angle 1.41627 / 0.91 ( 10) hydrogen bonds : bond 0.03136 / 2.23 ( 116) hydrogen bonds : angle 5.43273 / 3.63 ( 288) link_BETA1-4 : bond 0.00601 / 0.30 ( 2) link_BETA1-4 : angle 1.51600 / 0.85 ( 6) link_NAG-ASN : bond 0.00252 / 0.17 ( 7) link_NAG-ASN : angle 1.34098 / 0.74 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8311 (ttpp) REVERT: A 258 TRP cc_start: 0.8276 (m-90) cc_final: 0.7523 (m-90) outliers start: 14 outliers final: 13 residues processed: 62 average time/residue: 0.0887 time to fit residues: 6.6109 Evaluate side-chains 65 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.165240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.133972 restraints weight = 4346.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.134872 restraints weight = 4028.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.136115 restraints weight = 4186.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.137267 restraints weight = 2992.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.138306 restraints weight = 2586.581| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3848 Z= 0.158 Angle : 0.561 7.774 5285 Z= 0.283 Chirality : 0.045 0.163 626 Planarity : 0.004 0.042 652 Dihedral : 4.278 15.897 517 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.12 % Allowed : 11.47 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.38), residues: 474 helix: 3.04 (1.65), residues: 11 sheet: 0.75 (0.36), residues: 190 loop : -0.46 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 158 TYR 0.015 0.001 TYR A 265 PHE 0.020 0.002 PHE A 55 TRP 0.006 0.001 TRP H 115 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 3834) covalent geometry : angle 0.55007 / 0.28 ( 5248) SS BOND : bond 0.00308 / 0.15 ( 5) SS BOND : angle 1.43065 / 0.92 ( 10) hydrogen bonds : bond 0.03158 / 2.25 ( 116) hydrogen bonds : angle 5.42685 / 3.62 ( 288) link_BETA1-4 : bond 0.00595 / 0.30 ( 2) link_BETA1-4 : angle 1.52864 / 0.86 ( 6) link_NAG-ASN : bond 0.00253 / 0.17 ( 7) link_NAG-ASN : angle 1.36467 / 0.76 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8658 (ttpt) cc_final: 0.8299 (ttpp) REVERT: A 258 TRP cc_start: 0.8272 (m-90) cc_final: 0.7507 (m-90) outliers start: 14 outliers final: 13 residues processed: 61 average time/residue: 0.0795 time to fit residues: 5.8143 Evaluate side-chains 63 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.0070 chunk 46 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 0.0870 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.166455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.135371 restraints weight = 4348.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134801 restraints weight = 3905.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.137168 restraints weight = 4103.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.137801 restraints weight = 2908.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.139344 restraints weight = 2611.825| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3848 Z= 0.119 Angle : 0.555 8.193 5285 Z= 0.274 Chirality : 0.044 0.159 626 Planarity : 0.004 0.041 652 Dihedral : 4.144 15.543 517 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.53 % Allowed : 12.35 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.39), residues: 474 helix: 3.44 (1.71), residues: 11 sheet: 0.79 (0.36), residues: 191 loop : -0.45 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 158 TYR 0.015 0.001 TYR A 265 PHE 0.020 0.001 PHE A 55 TRP 0.005 0.001 TRP H 103 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 3834) covalent geometry : angle 0.54567 / 0.27 ( 5248) SS BOND : bond 0.00263 / 0.13 ( 5) SS BOND : angle 1.22491 / 0.80 ( 10) hydrogen bonds : bond 0.02943 / 2.11 ( 116) hydrogen bonds : angle 5.30137 / 3.53 ( 288) link_BETA1-4 : bond 0.00564 / 0.29 ( 2) link_BETA1-4 : angle 1.56121 / 0.87 ( 6) link_NAG-ASN : bond 0.00279 / 0.18 ( 7) link_NAG-ASN : angle 1.31765 / 0.72 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8622 (ttpt) cc_final: 0.8271 (ttpp) REVERT: A 258 TRP cc_start: 0.8268 (m-90) cc_final: 0.7517 (m-90) outliers start: 12 outliers final: 11 residues processed: 62 average time/residue: 0.0817 time to fit residues: 6.0878 Evaluate side-chains 64 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 39 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 0.0870 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.161378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.129803 restraints weight = 4270.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.130871 restraints weight = 3675.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.132123 restraints weight = 3819.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.132777 restraints weight = 2758.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.133431 restraints weight = 2546.385| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3848 Z= 0.119 Angle : 0.551 7.666 5285 Z= 0.273 Chirality : 0.045 0.161 626 Planarity : 0.004 0.044 652 Dihedral : 4.105 15.402 517 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.82 % Allowed : 13.24 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.38), residues: 474 helix: 3.51 (1.73), residues: 11 sheet: 0.80 (0.36), residues: 191 loop : -0.47 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 158 TYR 0.015 0.001 TYR A 265 PHE 0.019 0.001 PHE A 55 TRP 0.005 0.001 TRP H 115 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 3834) covalent geometry : angle 0.54171 / 0.27 ( 5248) SS BOND : bond 0.00253 / 0.13 ( 5) SS BOND : angle 1.21631 / 0.80 ( 10) hydrogen bonds : bond 0.02896 / 2.07 ( 116) hydrogen bonds : angle 5.30243 / 3.52 ( 288) link_BETA1-4 : bond 0.00538 / 0.27 ( 2) link_BETA1-4 : angle 1.52385 / 0.85 ( 6) link_NAG-ASN : bond 0.00269 / 0.18 ( 7) link_NAG-ASN : angle 1.26993 / 0.70 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 864.55 seconds wall clock time: 15 minutes 35.28 seconds (935.28 seconds total)