Starting phenix.real_space_refine on Tue Aug 4 23:40:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/29km_57240/08_2026/29km_57240.cif Found real_map, /net/cci-nas-00/data/ceres_data/29km_57240/08_2026/29km_57240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/29km_57240/08_2026/29km_57240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/29km_57240/08_2026/29km_57240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/29km_57240/08_2026/29km_57240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/29km_57240/08_2026/29km_57240.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 34 5.16 5 C 4694 2.51 5 N 1230 2.21 5 O 1382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7340 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1362 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 10, 'TRANS': 154} Chain: "B" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2308 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 14, 'TRANS': 268} Chain: "C" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2308 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 14, 'TRANS': 268} Chain: "D" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1362 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 10, 'TRANS': 154} Time building chain proxies: 1.89, per 1000 atoms: 0.26 Number of scatterers: 7340 At special positions: 0 Unit cell: (89.25, 121.55, 85, 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 34 16.00 O 1382 8.00 N 1230 7.00 C 4694 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 302.7 milliseconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 8 sheets defined 58.6% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.563A pdb=" N ARG A 27 " --> pdb=" O GLN A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 39 through 60 Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 75 through 89 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.719A pdb=" N GLU A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 134 through 145 Processing helix chain 'B' and resid 23 through 39 removed outlier: 4.287A pdb=" N GLN B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 39 through 52 removed outlier: 3.563A pdb=" N PHE B 43 " --> pdb=" O GLY B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 73 Processing helix chain 'B' and resid 75 through 90 Processing helix chain 'B' and resid 115 through 122 Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.653A pdb=" N PHE B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.773A pdb=" N ALA B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 208 through 215 removed outlier: 3.511A pdb=" N PHE B 212 " --> pdb=" O ASP B 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 226 removed outlier: 3.557A pdb=" N ALA B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 242 Processing helix chain 'B' and resid 244 through 256 removed outlier: 3.631A pdb=" N ASN B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 280 Processing helix chain 'C' and resid 23 through 34 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 39 through 52 removed outlier: 3.579A pdb=" N PHE C 43 " --> pdb=" O GLY C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 73 Processing helix chain 'C' and resid 75 through 90 Processing helix chain 'C' and resid 115 through 122 Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 134 through 145 removed outlier: 3.644A pdb=" N PHE C 145 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 165 removed outlier: 3.809A pdb=" N ALA C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 208 through 215 removed outlier: 3.556A pdb=" N PHE C 212 " --> pdb=" O ASP C 208 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY C 215 " --> pdb=" O LEU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 226 removed outlier: 3.579A pdb=" N ALA C 225 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 242 Processing helix chain 'C' and resid 244 through 256 removed outlier: 3.603A pdb=" N ASN C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 279 Processing helix chain 'D' and resid 23 through 34 removed outlier: 3.596A pdb=" N ARG D 27 " --> pdb=" O GLN D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 39 Processing helix chain 'D' and resid 39 through 59 Processing helix chain 'D' and resid 65 through 73 Processing helix chain 'D' and resid 75 through 90 Processing helix chain 'D' and resid 115 through 121 removed outlier: 3.636A pdb=" N GLU D 121 " --> pdb=" O ASN D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 134 Processing helix chain 'D' and resid 134 through 145 removed outlier: 3.522A pdb=" N TYR D 138 " --> pdb=" O GLY D 134 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 64 removed outlier: 3.503A pdb=" N SER A 63 " --> pdb=" O TYR A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 148 Processing sheet with id=AA3, first strand: chain 'A' and resid 155 through 156 Processing sheet with id=AA4, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA5, first strand: chain 'C' and resid 63 through 64 Processing sheet with id=AA6, first strand: chain 'C' and resid 155 through 156 removed outlier: 3.524A pdb=" N LYS D 97 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 189 through 191 Processing sheet with id=AA8, first strand: chain 'C' and resid 285 through 288 388 hydrogen bonds defined for protein. 1098 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: 1.14 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2404 1.34 - 1.46: 1121 1.46 - 1.57: 3911 1.57 - 1.69: 0 1.69 - 1.80: 68 Bond restraints: 7504 Sorted by residual: bond pdb=" C GLY A 134 " pdb=" O GLY A 134 " ideal model delta sigma weight residual 1.235 1.225 0.009 1.35e-02 5.49e+03 4.94e-01 bond pdb=" C VAL A 133 " pdb=" N GLY A 134 " ideal model delta sigma weight residual 1.331 1.320 0.010 1.46e-02 4.69e+03 4.81e-01 bond pdb=" C ILE C 221 " pdb=" O ILE C 221 " ideal model delta sigma weight residual 1.240 1.232 0.008 1.26e-02 6.30e+03 3.85e-01 bond pdb=" N GLU C 278 " pdb=" CA GLU C 278 " ideal model delta sigma weight residual 1.463 1.457 0.006 1.08e-02 8.57e+03 3.43e-01 bond pdb=" CA VAL C 287 " pdb=" CB VAL C 287 " ideal model delta sigma weight residual 1.538 1.532 0.007 1.30e-02 5.92e+03 2.72e-01 ... (remaining 7499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.89: 9724 0.89 - 1.79: 335 1.79 - 2.68: 50 2.68 - 3.58: 32 3.58 - 4.47: 7 Bond angle restraints: 10148 Sorted by residual: angle pdb=" N LYS B 135 " pdb=" CA LYS B 135 " pdb=" C LYS B 135 " ideal model delta sigma weight residual 111.14 113.06 -1.92 1.08e+00 8.57e-01 3.17e+00 angle pdb=" C ARG A 132 " pdb=" N VAL A 133 " pdb=" CA VAL A 133 " ideal model delta sigma weight residual 121.97 119.24 2.73 1.80e+00 3.09e-01 2.30e+00 angle pdb=" C GLU C 278 " pdb=" N ARG C 279 " pdb=" CA ARG C 279 " ideal model delta sigma weight residual 122.62 119.96 2.66 1.78e+00 3.16e-01 2.23e+00 angle pdb=" N GLU B 278 " pdb=" CA GLU B 278 " pdb=" C GLU B 278 " ideal model delta sigma weight residual 111.03 112.65 -1.62 1.11e+00 8.12e-01 2.14e+00 angle pdb=" CA TRP D 50 " pdb=" CB TRP D 50 " pdb=" CG TRP D 50 " ideal model delta sigma weight residual 113.60 116.34 -2.74 1.90e+00 2.77e-01 2.08e+00 ... (remaining 10143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4301 17.79 - 35.58: 211 35.58 - 53.38: 40 53.38 - 71.17: 9 71.17 - 88.96: 5 Dihedral angle restraints: 4566 sinusoidal: 1944 harmonic: 2622 Sorted by residual: dihedral pdb=" CA MET D 96 " pdb=" CB MET D 96 " pdb=" CG MET D 96 " pdb=" SD MET D 96 " ideal model delta sinusoidal sigma weight residual 60.00 114.06 -54.06 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" N LEU B 286 " pdb=" CA LEU B 286 " pdb=" CB LEU B 286 " pdb=" CG LEU B 286 " ideal model delta sinusoidal sigma weight residual -180.00 -126.59 -53.41 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" N ASN B 126 " pdb=" CA ASN B 126 " pdb=" CB ASN B 126 " pdb=" CG ASN B 126 " ideal model delta sinusoidal sigma weight residual 180.00 127.52 52.48 3 1.50e+01 4.44e-03 9.12e+00 ... (remaining 4563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 649 0.024 - 0.047: 285 0.047 - 0.070: 88 0.070 - 0.094: 42 0.094 - 0.117: 38 Chirality restraints: 1102 Sorted by residual: chirality pdb=" CA ILE D 107 " pdb=" N ILE D 107 " pdb=" C ILE D 107 " pdb=" CB ILE D 107 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 chirality pdb=" CA VAL B 15 " pdb=" N VAL B 15 " pdb=" C VAL B 15 " pdb=" CB VAL B 15 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.40e-01 chirality pdb=" CA VAL B 287 " pdb=" N VAL B 287 " pdb=" C VAL B 287 " pdb=" CB VAL B 287 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.25e-01 ... (remaining 1099 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 30 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C ILE A 30 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 30 " 0.011 2.00e-02 2.50e+03 pdb=" N THR A 31 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 30 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C ILE D 30 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE D 30 " -0.010 2.00e-02 2.50e+03 pdb=" N THR D 31 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 30 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C ILE B 30 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE B 30 " -0.009 2.00e-02 2.50e+03 pdb=" N THR B 31 " -0.008 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 3351 2.96 - 3.45: 7541 3.45 - 3.93: 11503 3.93 - 4.42: 13409 4.42 - 4.90: 21731 Nonbonded interactions: 57535 Sorted by model distance: nonbonded pdb=" OD1 ASP C 285 " pdb=" N LEU C 286 " model vdw 2.480 3.120 nonbonded pdb=" OG1 THR C 176 " pdb=" SD MET C 179 " model vdw 2.522 3.400 nonbonded pdb=" N SER B 99 " pdb=" O SER B 99 " model vdw 2.635 2.496 nonbonded pdb=" N ASP C 7 " pdb=" N VAL C 8 " model vdw 2.635 2.560 nonbonded pdb=" C ASN B 126 " pdb=" CG ASN B 126 " model vdw 2.649 2.800 ... (remaining 57530 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.010 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 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 : 0.002 0.019 7504 Z= 0.104 Angle : 0.430 4.471 10148 Z= 0.234 Chirality : 0.036 0.117 1102 Planarity : 0.003 0.028 1316 Dihedral : 11.226 88.961 2874 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.61 % Allowed : 4.17 % Favored : 95.22 % 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: 1.36 (0.29), residues: 888 helix: 1.71 (0.26), residues: 444 sheet: -0.44 (0.52), residues: 90 loop : 0.37 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 19 TYR 0.006 0.001 TYR D 95 PHE 0.009 0.001 PHE D 43 TRP 0.006 0.001 TRP B 173 HIS 0.001 0.000 HIS C 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 7504) covalent geometry : angle 0.42999 / 0.23 (10148) hydrogen bonds : bond 0.15543 / 10.12 ( 388) hydrogen bonds : angle 6.68167 / 4.58 ( 1098) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 12 ASP cc_start: 0.8890 (m-30) cc_final: 0.8420 (m-30) REVERT: A 19 ARG cc_start: 0.9104 (mtp85) cc_final: 0.8544 (mmp80) REVERT: A 96 MET cc_start: 0.9217 (ttp) cc_final: 0.8909 (ttt) REVERT: A 122 ASP cc_start: 0.9304 (t70) cc_final: 0.9093 (t70) REVERT: B 184 ARG cc_start: 0.9346 (tmm-80) cc_final: 0.9135 (tmm-80) REVERT: B 210 ASP cc_start: 0.9509 (t0) cc_final: 0.9305 (t0) REVERT: C 56 ASN cc_start: 0.9148 (m-40) cc_final: 0.8849 (m-40) REVERT: C 124 MET cc_start: 0.9560 (ttm) cc_final: 0.9248 (ttp) REVERT: C 179 MET cc_start: 0.7832 (pmm) cc_final: 0.7576 (pmm) REVERT: C 210 ASP cc_start: 0.9494 (t0) cc_final: 0.9289 (t0) REVERT: C 216 LEU cc_start: 0.8530 (tp) cc_final: 0.8157 (tp) REVERT: D 12 ASP cc_start: 0.8696 (m-30) cc_final: 0.8268 (m-30) REVERT: D 19 ARG cc_start: 0.8977 (ptm160) cc_final: 0.8551 (ttp-110) REVERT: D 152 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8676 (tm-30) REVERT: D 153 ASP cc_start: 0.9441 (m-30) cc_final: 0.8912 (t0) outliers start: 5 outliers final: 2 residues processed: 128 average time/residue: 0.0940 time to fit residues: 15.8111 Evaluate side-chains 96 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain C residue 126 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.081684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.057665 restraints weight = 18919.250| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.98 r_work: 0.2706 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 7504 Z= 0.208 Angle : 0.535 5.924 10148 Z= 0.275 Chirality : 0.039 0.165 1102 Planarity : 0.004 0.033 1316 Dihedral : 4.260 52.595 982 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.10 % Allowed : 7.35 % Favored : 91.54 % 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: 1.30 (0.29), residues: 888 helix: 1.61 (0.26), residues: 446 sheet: -0.25 (0.52), residues: 90 loop : 0.35 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 259 TYR 0.011 0.001 TYR D 95 PHE 0.010 0.001 PHE B 144 TRP 0.006 0.001 TRP B 173 HIS 0.002 0.000 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 ( 7504) covalent geometry : angle 0.53538 / 0.27 (10148) hydrogen bonds : bond 0.04522 / 2.94 ( 388) hydrogen bonds : angle 5.33724 / 3.70 ( 1098) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 12 ASP cc_start: 0.8858 (m-30) cc_final: 0.8370 (m-30) REVERT: A 19 ARG cc_start: 0.9150 (mtp85) cc_final: 0.8644 (mmp80) REVERT: A 71 MET cc_start: 0.9122 (tpp) cc_final: 0.8781 (tpp) REVERT: A 96 MET cc_start: 0.9262 (ttp) cc_final: 0.8925 (ttt) REVERT: B 124 MET cc_start: 0.9480 (ttm) cc_final: 0.9211 (ttp) REVERT: C 69 MET cc_start: 0.9402 (mtp) cc_final: 0.9202 (mtp) REVERT: C 216 LEU cc_start: 0.8508 (tp) cc_final: 0.8067 (tp) REVERT: C 226 MET cc_start: 0.9387 (tpp) cc_final: 0.9025 (tpp) REVERT: C 288 GLU cc_start: 0.8552 (pp20) cc_final: 0.8304 (tm-30) REVERT: D 12 ASP cc_start: 0.8689 (m-30) cc_final: 0.8261 (m-30) REVERT: D 19 ARG cc_start: 0.9078 (ptm160) cc_final: 0.8658 (ttp-110) REVERT: D 152 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8754 (tm-30) outliers start: 9 outliers final: 5 residues processed: 107 average time/residue: 0.0974 time to fit residues: 13.6679 Evaluate side-chains 98 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain D residue 74 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 17 optimal weight: 3.9990 chunk 80 optimal weight: 0.2980 chunk 87 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 0.0570 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.6704 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.081142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.057191 restraints weight = 18768.537| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.95 r_work: 0.2684 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7504 Z= 0.230 Angle : 0.540 5.419 10148 Z= 0.276 Chirality : 0.039 0.132 1102 Planarity : 0.004 0.034 1316 Dihedral : 4.041 53.151 980 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.47 % Allowed : 8.33 % Favored : 90.20 % 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: 1.17 (0.29), residues: 888 helix: 1.45 (0.26), residues: 448 sheet: -0.04 (0.52), residues: 90 loop : 0.27 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 184 TYR 0.010 0.001 TYR A 95 PHE 0.011 0.001 PHE C 144 TRP 0.005 0.001 TRP B 59 HIS 0.002 0.000 HIS C 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 ( 7504) covalent geometry : angle 0.54023 / 0.28 (10148) hydrogen bonds : bond 0.04137 / 2.68 ( 388) hydrogen bonds : angle 5.12571 / 3.56 ( 1098) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 12 ASP cc_start: 0.8861 (m-30) cc_final: 0.8354 (m-30) REVERT: A 71 MET cc_start: 0.9103 (tpp) cc_final: 0.8776 (tpp) REVERT: A 96 MET cc_start: 0.9259 (ttp) cc_final: 0.8908 (ttt) REVERT: B 103 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8950 (mp0) REVERT: B 124 MET cc_start: 0.9466 (ttm) cc_final: 0.9236 (ttp) REVERT: C 69 MET cc_start: 0.9414 (mtp) cc_final: 0.9195 (mtp) REVERT: C 216 LEU cc_start: 0.8530 (tp) cc_final: 0.8170 (tp) REVERT: C 226 MET cc_start: 0.9411 (tpp) cc_final: 0.9041 (tpp) REVERT: C 253 MET cc_start: 0.9610 (mtp) cc_final: 0.9369 (mmm) REVERT: C 288 GLU cc_start: 0.8634 (pp20) cc_final: 0.8391 (tm-30) REVERT: D 12 ASP cc_start: 0.8707 (m-30) cc_final: 0.8274 (m-30) REVERT: D 19 ARG cc_start: 0.9099 (ptm160) cc_final: 0.8677 (ttp-110) REVERT: D 152 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8766 (tm-30) outliers start: 12 outliers final: 4 residues processed: 106 average time/residue: 0.0992 time to fit residues: 13.8594 Evaluate side-chains 98 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain D residue 74 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.081819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.057525 restraints weight = 18730.025| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.97 r_work: 0.2739 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7504 Z= 0.121 Angle : 0.491 5.948 10148 Z= 0.248 Chirality : 0.037 0.133 1102 Planarity : 0.003 0.032 1316 Dihedral : 3.542 12.648 978 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.10 % Allowed : 9.19 % Favored : 89.71 % 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: 1.31 (0.29), residues: 888 helix: 1.53 (0.26), residues: 448 sheet: 0.21 (0.53), residues: 90 loop : 0.33 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 259 TYR 0.009 0.001 TYR A 130 PHE 0.008 0.001 PHE D 43 TRP 0.005 0.001 TRP C 173 HIS 0.001 0.000 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 7504) covalent geometry : angle 0.49115 / 0.25 (10148) hydrogen bonds : bond 0.03264 / 2.11 ( 388) hydrogen bonds : angle 4.90322 / 3.39 ( 1098) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 12 ASP cc_start: 0.8882 (m-30) cc_final: 0.8419 (m-30) REVERT: A 19 ARG cc_start: 0.9190 (mtp85) cc_final: 0.8761 (mmp80) REVERT: A 71 MET cc_start: 0.9067 (tpp) cc_final: 0.8785 (tpp) REVERT: A 96 MET cc_start: 0.9258 (ttp) cc_final: 0.8915 (ttt) REVERT: B 103 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8943 (mp0) REVERT: B 124 MET cc_start: 0.9437 (ttm) cc_final: 0.9227 (ttp) REVERT: C 216 LEU cc_start: 0.8503 (tp) cc_final: 0.8161 (tp) REVERT: C 226 MET cc_start: 0.9408 (tpp) cc_final: 0.9055 (tpp) REVERT: C 253 MET cc_start: 0.9656 (mtp) cc_final: 0.9422 (mmm) REVERT: D 12 ASP cc_start: 0.8749 (m-30) cc_final: 0.8320 (m-30) REVERT: D 19 ARG cc_start: 0.9033 (ptm160) cc_final: 0.8636 (ttp-110) REVERT: D 152 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8653 (tm-30) REVERT: D 153 ASP cc_start: 0.9386 (m-30) cc_final: 0.8781 (t0) outliers start: 9 outliers final: 4 residues processed: 108 average time/residue: 0.1016 time to fit residues: 14.4841 Evaluate side-chains 97 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain D residue 74 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.080329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.056142 restraints weight = 19161.143| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.99 r_work: 0.2668 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 7504 Z= 0.283 Angle : 0.583 6.394 10148 Z= 0.293 Chirality : 0.040 0.191 1102 Planarity : 0.004 0.034 1316 Dihedral : 3.670 14.123 978 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.10 % Allowed : 10.42 % Favored : 88.48 % 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: 1.22 (0.29), residues: 888 helix: 1.43 (0.26), residues: 448 sheet: 0.40 (0.54), residues: 90 loop : 0.26 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 259 TYR 0.010 0.001 TYR D 95 PHE 0.012 0.001 PHE D 43 TRP 0.005 0.001 TRP B 59 HIS 0.003 0.001 HIS C 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.28 ( 7504) covalent geometry : angle 0.58292 / 0.29 (10148) hydrogen bonds : bond 0.04156 / 2.68 ( 388) hydrogen bonds : angle 5.02548 / 3.50 ( 1098) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 8 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8770 (p) REVERT: A 12 ASP cc_start: 0.8856 (m-30) cc_final: 0.8333 (m-30) REVERT: A 19 ARG cc_start: 0.9229 (mtp85) cc_final: 0.8838 (mmp80) REVERT: A 96 MET cc_start: 0.9247 (ttp) cc_final: 0.8883 (ttt) REVERT: C 216 LEU cc_start: 0.8486 (tp) cc_final: 0.8120 (tp) REVERT: C 226 MET cc_start: 0.9431 (tpp) cc_final: 0.8999 (tpp) REVERT: D 12 ASP cc_start: 0.8709 (m-30) cc_final: 0.8267 (m-30) REVERT: D 19 ARG cc_start: 0.9124 (ptm160) cc_final: 0.8703 (ttp-110) REVERT: D 152 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8742 (tm-30) REVERT: D 153 ASP cc_start: 0.9421 (m-30) cc_final: 0.8894 (t0) outliers start: 9 outliers final: 3 residues processed: 103 average time/residue: 0.0952 time to fit residues: 12.9301 Evaluate side-chains 97 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain D residue 74 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 6 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 35 optimal weight: 0.0170 chunk 83 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7020 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.082701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.058569 restraints weight = 18416.419| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.93 r_work: 0.2745 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7504 Z= 0.101 Angle : 0.510 6.783 10148 Z= 0.253 Chirality : 0.037 0.135 1102 Planarity : 0.003 0.030 1316 Dihedral : 3.507 12.729 978 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.35 % Allowed : 11.03 % Favored : 87.62 % 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: 1.40 (0.29), residues: 888 helix: 1.55 (0.26), residues: 448 sheet: 0.57 (0.54), residues: 90 loop : 0.35 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 259 TYR 0.008 0.001 TYR B 130 PHE 0.008 0.001 PHE B 161 TRP 0.007 0.001 TRP C 173 HIS 0.002 0.000 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 7504) covalent geometry : angle 0.50952 / 0.25 (10148) hydrogen bonds : bond 0.02939 / 1.90 ( 388) hydrogen bonds : angle 4.80964 / 3.32 ( 1098) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 12 ASP cc_start: 0.8893 (m-30) cc_final: 0.8428 (m-30) REVERT: A 19 ARG cc_start: 0.9192 (mtp85) cc_final: 0.8764 (mmp80) REVERT: A 96 MET cc_start: 0.9249 (ttp) cc_final: 0.8922 (ttt) REVERT: B 103 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8919 (mp0) REVERT: C 216 LEU cc_start: 0.8456 (tp) cc_final: 0.8085 (tp) REVERT: C 253 MET cc_start: 0.9641 (mtp) cc_final: 0.9416 (mmm) REVERT: D 19 ARG cc_start: 0.9030 (ptm160) cc_final: 0.8686 (ttp-110) REVERT: D 152 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8666 (tm-30) REVERT: D 153 ASP cc_start: 0.9380 (m-30) cc_final: 0.8777 (t0) outliers start: 11 outliers final: 3 residues processed: 110 average time/residue: 0.0789 time to fit residues: 11.4637 Evaluate side-chains 99 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain D residue 74 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.083140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.059061 restraints weight = 18971.443| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 4.01 r_work: 0.2720 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7504 Z= 0.151 Angle : 0.554 8.040 10148 Z= 0.272 Chirality : 0.039 0.262 1102 Planarity : 0.003 0.031 1316 Dihedral : 3.499 12.506 978 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.86 % Allowed : 12.38 % 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: 1.38 (0.29), residues: 888 helix: 1.53 (0.26), residues: 448 sheet: 0.66 (0.55), residues: 90 loop : 0.33 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 259 TYR 0.010 0.001 TYR B 191 PHE 0.008 0.001 PHE C 43 TRP 0.006 0.001 TRP C 173 HIS 0.002 0.000 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 7504) covalent geometry : angle 0.55425 / 0.27 (10148) hydrogen bonds : bond 0.03257 / 2.10 ( 388) hydrogen bonds : angle 4.80428 / 3.32 ( 1098) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.214 Fit side-chains REVERT: A 12 ASP cc_start: 0.8882 (m-30) cc_final: 0.8383 (m-30) REVERT: A 19 ARG cc_start: 0.9220 (mtp85) cc_final: 0.8762 (mmp80) REVERT: A 96 MET cc_start: 0.9219 (ttp) cc_final: 0.8895 (ttt) REVERT: B 103 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8920 (mp0) REVERT: C 216 LEU cc_start: 0.8382 (tp) cc_final: 0.8022 (tp) REVERT: C 253 MET cc_start: 0.9642 (mtp) cc_final: 0.9419 (mmm) REVERT: D 12 ASP cc_start: 0.8766 (m-30) cc_final: 0.8328 (m-30) REVERT: D 19 ARG cc_start: 0.9122 (ptm160) cc_final: 0.8713 (ttp-110) REVERT: D 152 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8689 (tm-30) REVERT: D 153 ASP cc_start: 0.9410 (m-30) cc_final: 0.8806 (t0) outliers start: 7 outliers final: 4 residues processed: 105 average time/residue: 0.0756 time to fit residues: 10.5373 Evaluate side-chains 100 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain D residue 74 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 63 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.083193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.058970 restraints weight = 18620.059| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.98 r_work: 0.2758 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7504 Z= 0.103 Angle : 0.546 7.624 10148 Z= 0.267 Chirality : 0.038 0.186 1102 Planarity : 0.003 0.029 1316 Dihedral : 3.473 12.503 978 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.10 % Allowed : 11.89 % Favored : 87.01 % 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: 1.42 (0.29), residues: 888 helix: 1.55 (0.26), residues: 448 sheet: 0.70 (0.56), residues: 90 loop : 0.35 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 259 TYR 0.008 0.001 TYR B 130 PHE 0.008 0.001 PHE C 43 TRP 0.008 0.001 TRP C 173 HIS 0.001 0.000 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 7504) covalent geometry : angle 0.54578 / 0.27 (10148) hydrogen bonds : bond 0.02828 / 1.82 ( 388) hydrogen bonds : angle 4.72301 / 3.26 ( 1098) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 12 ASP cc_start: 0.8897 (m-30) cc_final: 0.8460 (m-30) REVERT: A 19 ARG cc_start: 0.9180 (mtp85) cc_final: 0.8740 (mmp80) REVERT: A 96 MET cc_start: 0.9203 (ttp) cc_final: 0.8880 (ttt) REVERT: B 103 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8909 (mp0) REVERT: B 220 MET cc_start: 0.9113 (mtt) cc_final: 0.8903 (ptp) REVERT: C 216 LEU cc_start: 0.8414 (tp) cc_final: 0.8076 (tp) REVERT: C 265 GLU cc_start: 0.9509 (pt0) cc_final: 0.9256 (pm20) REVERT: D 19 ARG cc_start: 0.9056 (ptm160) cc_final: 0.8667 (ttp-110) REVERT: D 152 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8664 (tm-30) REVERT: D 153 ASP cc_start: 0.9397 (m-30) cc_final: 0.8742 (t0) outliers start: 9 outliers final: 5 residues processed: 108 average time/residue: 0.0832 time to fit residues: 11.8542 Evaluate side-chains 102 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain D residue 74 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 40 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 37 optimal weight: 0.0970 chunk 26 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.082788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.058642 restraints weight = 18836.749| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 4.03 r_work: 0.2711 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7504 Z= 0.177 Angle : 0.589 8.357 10148 Z= 0.291 Chirality : 0.039 0.165 1102 Planarity : 0.003 0.028 1316 Dihedral : 3.548 16.853 978 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.74 % Allowed : 12.38 % Favored : 86.89 % 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: 1.39 (0.29), residues: 888 helix: 1.51 (0.26), residues: 448 sheet: 0.76 (0.55), residues: 90 loop : 0.32 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 259 TYR 0.009 0.001 TYR B 191 PHE 0.009 0.001 PHE A 43 TRP 0.006 0.001 TRP C 173 HIS 0.002 0.000 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 7504) covalent geometry : angle 0.58901 / 0.29 (10148) hydrogen bonds : bond 0.03462 / 2.23 ( 388) hydrogen bonds : angle 4.78012 / 3.30 ( 1098) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.244 Fit side-chains REVERT: A 12 ASP cc_start: 0.8943 (m-30) cc_final: 0.8484 (m-30) REVERT: A 19 ARG cc_start: 0.9188 (mtp85) cc_final: 0.8797 (mmp80) REVERT: A 96 MET cc_start: 0.9195 (ttp) cc_final: 0.8865 (ttt) REVERT: B 103 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8925 (mp0) REVERT: B 220 MET cc_start: 0.9129 (mtt) cc_final: 0.8925 (ptp) REVERT: C 216 LEU cc_start: 0.8387 (tp) cc_final: 0.8037 (tp) REVERT: C 265 GLU cc_start: 0.9517 (pt0) cc_final: 0.9251 (pm20) REVERT: D 12 ASP cc_start: 0.8778 (m-30) cc_final: 0.8348 (m-30) REVERT: D 19 ARG cc_start: 0.9071 (ptm160) cc_final: 0.8674 (ttp-110) REVERT: D 152 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8693 (tm-30) REVERT: D 153 ASP cc_start: 0.9396 (m-30) cc_final: 0.8834 (t0) outliers start: 6 outliers final: 5 residues processed: 104 average time/residue: 0.0838 time to fit residues: 11.5028 Evaluate side-chains 99 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain D residue 74 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 0 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.083393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.059202 restraints weight = 18819.694| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 4.01 r_work: 0.2731 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7504 Z= 0.149 Angle : 0.600 9.372 10148 Z= 0.295 Chirality : 0.039 0.149 1102 Planarity : 0.003 0.033 1316 Dihedral : 3.588 23.556 978 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.86 % Allowed : 12.13 % Favored : 87.01 % 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: 1.38 (0.29), residues: 888 helix: 1.50 (0.26), residues: 448 sheet: 0.83 (0.56), residues: 90 loop : 0.32 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 259 TYR 0.008 0.001 TYR B 130 PHE 0.009 0.001 PHE C 43 TRP 0.008 0.001 TRP C 173 HIS 0.001 0.000 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 7504) covalent geometry : angle 0.60016 / 0.30 (10148) hydrogen bonds : bond 0.03217 / 2.09 ( 388) hydrogen bonds : angle 4.76411 / 3.28 ( 1098) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.224 Fit side-chains REVERT: A 12 ASP cc_start: 0.8939 (m-30) cc_final: 0.8427 (m-30) REVERT: A 19 ARG cc_start: 0.9200 (mtp85) cc_final: 0.8820 (mmp80) REVERT: A 96 MET cc_start: 0.9164 (ttp) cc_final: 0.8833 (ttt) REVERT: B 103 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8884 (mp0) REVERT: B 220 MET cc_start: 0.9132 (mtt) cc_final: 0.8904 (ptp) REVERT: C 216 LEU cc_start: 0.8376 (tp) cc_final: 0.8038 (tp) REVERT: C 226 MET cc_start: 0.9422 (tpp) cc_final: 0.9159 (mmp) REVERT: C 265 GLU cc_start: 0.9519 (pt0) cc_final: 0.9234 (pm20) REVERT: D 12 ASP cc_start: 0.8767 (m-30) cc_final: 0.8324 (m-30) REVERT: D 19 ARG cc_start: 0.9098 (ptm160) cc_final: 0.8694 (ttp-110) REVERT: D 152 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8669 (tm-30) REVERT: D 153 ASP cc_start: 0.9410 (m-30) cc_final: 0.8798 (t0) outliers start: 7 outliers final: 6 residues processed: 102 average time/residue: 0.0996 time to fit residues: 13.3807 Evaluate side-chains 102 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain D residue 74 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.082758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.058612 restraints weight = 18508.945| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.94 r_work: 0.2742 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7504 Z= 0.129 Angle : 0.578 8.328 10148 Z= 0.284 Chirality : 0.038 0.144 1102 Planarity : 0.003 0.025 1316 Dihedral : 3.536 21.594 978 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.86 % Allowed : 12.13 % Favored : 87.01 % 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: 1.42 (0.29), residues: 888 helix: 1.52 (0.26), residues: 448 sheet: 0.87 (0.56), residues: 90 loop : 0.33 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 259 TYR 0.008 0.001 TYR B 130 PHE 0.009 0.001 PHE C 43 TRP 0.008 0.001 TRP C 173 HIS 0.001 0.000 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 7504) covalent geometry : angle 0.57756 / 0.28 (10148) hydrogen bonds : bond 0.03072 / 1.99 ( 388) hydrogen bonds : angle 4.73139 / 3.26 ( 1098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1453.60 seconds wall clock time: 25 minutes 33.33 seconds (1533.33 seconds total)