Starting phenix.real_space_refine on Thu Jul 2 01:08:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lrs_23498/07_2026/7lrs_23498.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lrs_23498/07_2026/7lrs_23498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lrs_23498/07_2026/7lrs_23498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lrs_23498/07_2026/7lrs_23498.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lrs_23498/07_2026/7lrs_23498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lrs_23498/07_2026/7lrs_23498.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lrs_23498/07_2026/7lrs_23498.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lrs_23498/07_2026/7lrs_23498.cif" } resolution = 3.89 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= 0.006 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 22 5.16 5 C 3100 2.51 5 N 812 2.21 5 O 978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 4912 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "D" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1625 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1636 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 Time building chain proxies: 1.15, per 1000 atoms: 0.23 Number of scatterers: 4912 At special positions: 0 Unit cell: (79.515, 66.69, 140.22, 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 22 16.00 O 978 8.00 N 812 7.00 C 3100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 97 " - pdb=" SG CYS D 100B" distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA A 3 " - " MAN A 4 " ALPHA1-6 " BMA A 3 " - " MAN A 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 1 " - " ASN C 343 " " NAG B 1 " - " ASN D 96 " Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 170.2 milliseconds 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 16 sheets defined 3.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 4.186A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.795A pdb=" N THR D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 202 removed outlier: 3.664A pdb=" N LEU E 201 " --> pdb=" O HIS E 198 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER E 202 " --> pdb=" O GLN E 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 202' Processing sheet with id=AA1, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.768A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.749A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 5 " --> pdb=" O LYS D 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.736A pdb=" N THR D 110 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS D 12 " --> pdb=" O THR D 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 33 through 36 removed outlier: 3.786A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AA7, first strand: chain 'D' and resid 93 through 94 removed outlier: 3.505A pdb=" N ILE D 102 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 97 through 98 removed outlier: 3.631A pdb=" N VAL D 100A" --> pdb=" O SER D 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.515A pdb=" N GLY D 139 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 180 " --> pdb=" O CYS D 140 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.515A pdb=" N GLY D 139 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 180 " --> pdb=" O CYS D 140 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 151 through 152 removed outlier: 4.133A pdb=" N THR D 151 " --> pdb=" O ASN D 199 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN D 199 " --> pdb=" O THR D 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'E' and resid 20 through 22 Processing sheet with id=AB5, first strand: chain 'E' and resid 45 through 49 removed outlier: 6.681A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 85 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.594A pdb=" N PHE E 116 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL E 133 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL E 132 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 145 through 148 removed outlier: 4.106A pdb=" N LYS E 145 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR E 197 " --> pdb=" O LYS E 145 " (cutoff:3.500A) 86 hydrogen bonds defined for protein. 225 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: 0.42 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1550 1.34 - 1.46: 1294 1.46 - 1.58: 2160 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 5030 Sorted by residual: bond pdb=" C1 MAN A 4 " pdb=" C2 MAN A 4 " ideal model delta sigma weight residual 1.526 1.580 -0.054 2.00e-02 2.50e+03 7.27e+00 bond pdb=" C1 MAN A 5 " pdb=" C2 MAN A 5 " ideal model delta sigma weight residual 1.526 1.567 -0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C1 MAN A 4 " pdb=" O5 MAN A 4 " ideal model delta sigma weight residual 1.399 1.437 -0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" C5 MAN A 5 " pdb=" O5 MAN A 5 " ideal model delta sigma weight residual 1.418 1.455 -0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" C1 BMA A 3 " pdb=" C2 BMA A 3 " ideal model delta sigma weight residual 1.519 1.556 -0.037 2.00e-02 2.50e+03 3.40e+00 ... (remaining 5025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 6592 1.66 - 3.31: 200 3.31 - 4.97: 43 4.97 - 6.63: 10 6.63 - 8.28: 2 Bond angle restraints: 6847 Sorted by residual: angle pdb=" CA GLY C 502 " pdb=" C GLY C 502 " pdb=" N VAL C 503 " ideal model delta sigma weight residual 114.23 116.84 -2.61 8.80e-01 1.29e+00 8.77e+00 angle pdb=" C PHE C 486 " pdb=" N ASN C 487 " pdb=" CA ASN C 487 " ideal model delta sigma weight residual 122.08 126.25 -4.17 1.47e+00 4.63e-01 8.06e+00 angle pdb=" C THR E 109 " pdb=" N VAL E 110 " pdb=" CA VAL E 110 " ideal model delta sigma weight residual 121.97 126.69 -4.72 1.80e+00 3.09e-01 6.87e+00 angle pdb=" N LYS D 201 " pdb=" CA LYS D 201 " pdb=" C LYS D 201 " ideal model delta sigma weight residual 109.81 115.60 -5.79 2.21e+00 2.05e-01 6.87e+00 angle pdb=" CA ASP E 185 " pdb=" C ASP E 185 " pdb=" N TYR E 186 " ideal model delta sigma weight residual 119.71 116.70 3.01 1.17e+00 7.31e-01 6.64e+00 ... (remaining 6842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 2601 15.99 - 31.97: 268 31.97 - 47.96: 61 47.96 - 63.95: 6 63.95 - 79.93: 8 Dihedral angle restraints: 2944 sinusoidal: 1131 harmonic: 1813 Sorted by residual: dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 88 " pdb=" CB CYS E 88 " ideal model delta sinusoidal sigma weight residual 93.00 163.08 -70.08 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 143.13 -50.13 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -133.21 47.21 1 1.00e+01 1.00e-02 3.08e+01 ... (remaining 2941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 638 0.055 - 0.110: 121 0.110 - 0.165: 22 0.165 - 0.220: 2 0.220 - 0.276: 3 Chirality restraints: 786 Sorted by residual: 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 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB ILE C 468 " pdb=" CA ILE C 468 " pdb=" CG1 ILE C 468 " pdb=" CG2 ILE C 468 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 783 not shown) Planarity restraints: 871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 146 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO D 147 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 147 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 147 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 79 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.10e+00 pdb=" N PRO E 80 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 80 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 80 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO C 521 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " -0.020 5.00e-02 4.00e+02 ... (remaining 868 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 297 2.72 - 3.27: 4858 3.27 - 3.81: 7198 3.81 - 4.36: 8340 4.36 - 4.90: 14373 Nonbonded interactions: 35066 Sorted by model distance: nonbonded pdb=" OD2 ASP E 82 " pdb=" OH TYR E 86 " model vdw 2.181 3.040 nonbonded pdb=" O SER E 171 " pdb=" OG SER E 171 " model vdw 2.240 3.040 nonbonded pdb=" OG SER E 182 " pdb=" NZ LYS E 188 " model vdw 2.245 3.120 nonbonded pdb=" O4 MAN A 5 " pdb=" O6 MAN A 5 " model vdw 2.266 3.040 nonbonded pdb=" OE2 GLU E 105 " pdb=" NE2 GLN E 166 " model vdw 2.302 3.120 ... (remaining 35061 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: 13.160 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.540 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 : 0.003 0.054 5047 Z= 0.168 Angle : 0.728 8.282 6889 Z= 0.353 Chirality : 0.048 0.276 786 Planarity : 0.005 0.043 869 Dihedral : 13.273 79.934 1757 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.70 % Favored : 88.65 % Rotamer: Outliers : 0.19 % Allowed : 0.37 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.85 (0.33), residues: 617 helix: -4.54 (0.94), residues: 13 sheet: -1.37 (0.38), residues: 207 loop : -2.18 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 44 TYR 0.011 0.001 TYR D 145 PHE 0.013 0.001 PHE E 118 TRP 0.020 0.001 TRP C 353 HIS 0.003 0.001 HIS D 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 ( 5030) covalent geometry : angle 0.71932 / 0.35 ( 6847) SS BOND : bond 0.00288 / 0.16 ( 9) SS BOND : angle 1.46575 / 0.78 ( 18) hydrogen bonds : bond 0.29489 / 18.65 ( 75) hydrogen bonds : angle 10.62608 / 7.60 ( 225) link_ALPHA1-3 : bond 0.00729 / 0.38 ( 1) link_ALPHA1-3 : angle 1.09259 / 0.54 ( 3) link_ALPHA1-6 : bond 0.00969 / 0.51 ( 1) link_ALPHA1-6 : angle 1.52289 / 0.71 ( 3) link_BETA1-4 : bond 0.00370 / 0.18 ( 4) link_BETA1-4 : angle 2.05235 / 1.03 ( 12) link_NAG-ASN : bond 0.00285 / 0.15 ( 2) link_NAG-ASN : angle 0.99703 / 0.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.163 Fit side-chains REVERT: D 82 LEU cc_start: 0.8695 (mt) cc_final: 0.8348 (mm) REVERT: D 90 TYR cc_start: 0.8121 (m-10) cc_final: 0.7531 (m-80) REVERT: D 155 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8180 (t0) REVERT: D 201 LYS cc_start: 0.8906 (pptt) cc_final: 0.8631 (pptt) REVERT: E 82 ASP cc_start: 0.8046 (t70) cc_final: 0.7828 (t0) REVERT: E 123 GLU cc_start: 0.8605 (tp30) cc_final: 0.8373 (tp30) outliers start: 1 outliers final: 0 residues processed: 103 average time/residue: 0.0645 time to fit residues: 8.4357 Evaluate side-chains 82 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 155 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.0010 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.0030 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN D 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.067484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.058429 restraints weight = 19650.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.060272 restraints weight = 10659.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.061533 restraints weight = 6668.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.062356 restraints weight = 4586.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.062943 restraints weight = 3417.539| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5047 Z= 0.132 Angle : 0.717 10.318 6889 Z= 0.348 Chirality : 0.046 0.164 786 Planarity : 0.005 0.042 869 Dihedral : 4.718 39.374 679 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.21 % Favored : 88.98 % Rotamer: Outliers : 0.74 % Allowed : 10.76 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.80 (0.33), residues: 617 helix: -4.00 (1.15), residues: 13 sheet: -1.05 (0.38), residues: 200 loop : -2.34 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 41 TYR 0.020 0.001 TYR C 380 PHE 0.012 0.001 PHE E 118 TRP 0.014 0.001 TRP C 436 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 5030) covalent geometry : angle 0.70662 / 0.35 ( 6847) SS BOND : bond 0.00456 / 0.29 ( 9) SS BOND : angle 1.58769 / 0.85 ( 18) hydrogen bonds : bond 0.03986 / 2.50 ( 75) hydrogen bonds : angle 7.42807 / 5.14 ( 225) link_ALPHA1-3 : bond 0.00826 / 0.43 ( 1) link_ALPHA1-3 : angle 2.00868 / 1.06 ( 3) link_ALPHA1-6 : bond 0.00909 / 0.48 ( 1) link_ALPHA1-6 : angle 1.65154 / 0.72 ( 3) link_BETA1-4 : bond 0.00509 / 0.25 ( 4) link_BETA1-4 : angle 2.07538 / 1.07 ( 12) link_NAG-ASN : bond 0.00290 / 0.15 ( 2) link_NAG-ASN : angle 1.14617 / 0.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: C 389 ASP cc_start: 0.8434 (p0) cc_final: 0.8169 (p0) REVERT: D 155 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8311 (t0) REVERT: D 176 TYR cc_start: 0.7977 (m-10) cc_final: 0.7700 (m-10) REVERT: E 123 GLU cc_start: 0.8696 (tp30) cc_final: 0.8403 (tp30) outliers start: 4 outliers final: 1 residues processed: 91 average time/residue: 0.0578 time to fit residues: 6.8969 Evaluate side-chains 83 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 198 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.064904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.055936 restraints weight = 19609.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.057760 restraints weight = 10542.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.058977 restraints weight = 6574.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.059795 restraints weight = 4528.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.060354 restraints weight = 3359.057| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5047 Z= 0.174 Angle : 0.704 11.184 6889 Z= 0.344 Chirality : 0.045 0.158 786 Planarity : 0.005 0.050 869 Dihedral : 4.852 37.839 679 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.86 % Favored : 88.33 % Rotamer: Outliers : 1.86 % Allowed : 13.17 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.68 (0.33), residues: 617 helix: -2.04 (2.23), residues: 7 sheet: -0.92 (0.40), residues: 188 loop : -2.34 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 454 TYR 0.024 0.001 TYR C 380 PHE 0.013 0.001 PHE D 146 TRP 0.015 0.001 TRP C 436 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 5030) covalent geometry : angle 0.69241 / 0.34 ( 6847) SS BOND : bond 0.00366 / 0.15 ( 9) SS BOND : angle 1.36277 / 0.76 ( 18) hydrogen bonds : bond 0.03574 / 2.26 ( 75) hydrogen bonds : angle 6.83099 / 4.73 ( 225) link_ALPHA1-3 : bond 0.01185 / 0.62 ( 1) link_ALPHA1-3 : angle 1.71942 / 0.94 ( 3) link_ALPHA1-6 : bond 0.01307 / 0.69 ( 1) link_ALPHA1-6 : angle 2.02095 / 0.96 ( 3) link_BETA1-4 : bond 0.00550 / 0.27 ( 4) link_BETA1-4 : angle 2.12711 / 1.09 ( 12) link_NAG-ASN : bond 0.00415 / 0.20 ( 2) link_NAG-ASN : angle 1.83503 / 0.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: D 155 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8308 (t0) REVERT: D 176 TYR cc_start: 0.8034 (m-10) cc_final: 0.7646 (m-10) REVERT: E 82 ASP cc_start: 0.8845 (t0) cc_final: 0.8585 (t0) REVERT: E 123 GLU cc_start: 0.8722 (tp30) cc_final: 0.8502 (tp30) outliers start: 10 outliers final: 4 residues processed: 91 average time/residue: 0.0606 time to fit residues: 7.1071 Evaluate side-chains 83 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.063695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.054798 restraints weight = 19701.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.056615 restraints weight = 10680.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.057829 restraints weight = 6662.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058602 restraints weight = 4578.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.059205 restraints weight = 3420.096| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5047 Z= 0.177 Angle : 0.711 12.074 6889 Z= 0.349 Chirality : 0.045 0.155 786 Planarity : 0.005 0.047 869 Dihedral : 4.985 37.322 679 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.97 % Allowed : 10.70 % Favored : 88.33 % Rotamer: Outliers : 2.97 % Allowed : 15.77 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.67 (0.33), residues: 617 helix: -1.90 (2.25), residues: 7 sheet: -0.88 (0.40), residues: 188 loop : -2.35 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 83 TYR 0.027 0.001 TYR C 380 PHE 0.009 0.001 PHE C 486 TRP 0.016 0.001 TRP C 436 HIS 0.004 0.002 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 ( 5030) covalent geometry : angle 0.70011 / 0.35 ( 6847) SS BOND : bond 0.00559 / 0.29 ( 9) SS BOND : angle 1.27337 / 0.71 ( 18) hydrogen bonds : bond 0.03001 / 1.88 ( 75) hydrogen bonds : angle 6.43442 / 4.45 ( 225) link_ALPHA1-3 : bond 0.01212 / 0.64 ( 1) link_ALPHA1-3 : angle 1.88157 / 1.01 ( 3) link_ALPHA1-6 : bond 0.01267 / 0.67 ( 1) link_ALPHA1-6 : angle 2.06105 / 0.98 ( 3) link_BETA1-4 : bond 0.00528 / 0.26 ( 4) link_BETA1-4 : angle 2.27865 / 1.18 ( 12) link_NAG-ASN : bond 0.00346 / 0.17 ( 2) link_NAG-ASN : angle 1.60750 / 0.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: D 155 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8197 (t0) REVERT: D 176 TYR cc_start: 0.8120 (m-10) cc_final: 0.7723 (m-10) REVERT: E 82 ASP cc_start: 0.8876 (t0) cc_final: 0.8507 (t0) REVERT: E 123 GLU cc_start: 0.8699 (tp30) cc_final: 0.8479 (tp30) outliers start: 16 outliers final: 10 residues processed: 90 average time/residue: 0.0518 time to fit residues: 6.0363 Evaluate side-chains 92 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 53 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.063445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.054422 restraints weight = 19872.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.056263 restraints weight = 10747.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.057485 restraints weight = 6687.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.058342 restraints weight = 4602.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.058913 restraints weight = 3391.142| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5047 Z= 0.176 Angle : 0.713 12.279 6889 Z= 0.350 Chirality : 0.045 0.165 786 Planarity : 0.005 0.048 869 Dihedral : 5.038 36.112 679 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.97 % Allowed : 11.35 % Favored : 87.68 % Rotamer: Outliers : 2.41 % Allowed : 17.07 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.79 (0.32), residues: 617 helix: -3.51 (1.29), residues: 13 sheet: -0.91 (0.40), residues: 186 loop : -2.40 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 41 TYR 0.022 0.001 TYR C 380 PHE 0.014 0.001 PHE D 146 TRP 0.014 0.001 TRP C 436 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 5030) covalent geometry : angle 0.70115 / 0.35 ( 6847) SS BOND : bond 0.00305 / 0.13 ( 9) SS BOND : angle 1.44482 / 0.82 ( 18) hydrogen bonds : bond 0.02936 / 1.85 ( 75) hydrogen bonds : angle 6.40203 / 4.44 ( 225) link_ALPHA1-3 : bond 0.01184 / 0.62 ( 1) link_ALPHA1-3 : angle 1.83936 / 0.98 ( 3) link_ALPHA1-6 : bond 0.01296 / 0.68 ( 1) link_ALPHA1-6 : angle 2.02580 / 0.96 ( 3) link_BETA1-4 : bond 0.00490 / 0.24 ( 4) link_BETA1-4 : angle 2.24720 / 1.16 ( 12) link_NAG-ASN : bond 0.00395 / 0.19 ( 2) link_NAG-ASN : angle 1.57790 / 0.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 82 ASP cc_start: 0.8931 (t0) cc_final: 0.8517 (t0) REVERT: E 118 PHE cc_start: 0.7608 (m-10) cc_final: 0.7362 (m-10) REVERT: E 169 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8592 (mmmm) outliers start: 13 outliers final: 10 residues processed: 87 average time/residue: 0.0546 time to fit residues: 6.1675 Evaluate side-chains 84 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 519 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.063780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.054868 restraints weight = 19893.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.056689 restraints weight = 10793.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.057903 restraints weight = 6724.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.058741 restraints weight = 4629.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.059293 restraints weight = 3421.219| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5047 Z= 0.157 Angle : 0.715 12.332 6889 Z= 0.350 Chirality : 0.044 0.174 786 Planarity : 0.005 0.048 869 Dihedral : 4.782 24.133 677 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.97 % Allowed : 10.37 % Favored : 88.65 % Rotamer: Outliers : 2.60 % Allowed : 18.18 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.79 (0.32), residues: 617 helix: -3.52 (1.27), residues: 13 sheet: -0.96 (0.39), residues: 186 loop : -2.37 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 142 TYR 0.017 0.001 TYR D 194 PHE 0.007 0.001 PHE C 486 TRP 0.013 0.001 TRP C 436 HIS 0.007 0.002 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 5030) covalent geometry : angle 0.70298 / 0.35 ( 6847) SS BOND : bond 0.00268 / 0.11 ( 9) SS BOND : angle 1.49563 / 0.85 ( 18) hydrogen bonds : bond 0.02795 / 1.74 ( 75) hydrogen bonds : angle 5.96776 / 4.00 ( 225) link_ALPHA1-3 : bond 0.01258 / 0.66 ( 1) link_ALPHA1-3 : angle 1.88059 / 0.99 ( 3) link_ALPHA1-6 : bond 0.01219 / 0.64 ( 1) link_ALPHA1-6 : angle 1.88945 / 0.88 ( 3) link_BETA1-4 : bond 0.00458 / 0.22 ( 4) link_BETA1-4 : angle 2.23135 / 1.15 ( 12) link_NAG-ASN : bond 0.00350 / 0.17 ( 2) link_NAG-ASN : angle 1.49332 / 0.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: D 176 TYR cc_start: 0.8133 (m-10) cc_final: 0.7820 (m-10) REVERT: E 82 ASP cc_start: 0.8924 (t0) cc_final: 0.8525 (t0) REVERT: E 169 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8590 (mmmm) outliers start: 14 outliers final: 11 residues processed: 83 average time/residue: 0.0548 time to fit residues: 6.0584 Evaluate side-chains 86 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 0.0770 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 519 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.063672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.054732 restraints weight = 19656.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.056596 restraints weight = 10593.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.057845 restraints weight = 6582.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.058649 restraints weight = 4491.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.059247 restraints weight = 3332.385| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5047 Z= 0.162 Angle : 0.719 12.417 6889 Z= 0.352 Chirality : 0.045 0.184 786 Planarity : 0.005 0.048 869 Dihedral : 4.784 22.755 677 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.51 % Favored : 87.68 % Rotamer: Outliers : 2.04 % Allowed : 19.29 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.81 (0.32), residues: 617 helix: -3.51 (1.27), residues: 13 sheet: -0.99 (0.39), residues: 186 loop : -2.39 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 41 TYR 0.019 0.001 TYR C 380 PHE 0.010 0.001 PHE D 146 TRP 0.013 0.001 TRP C 436 HIS 0.006 0.002 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 5030) covalent geometry : angle 0.70757 / 0.35 ( 6847) SS BOND : bond 0.00347 / 0.16 ( 9) SS BOND : angle 1.47769 / 0.84 ( 18) hydrogen bonds : bond 0.02703 / 1.68 ( 75) hydrogen bonds : angle 5.83284 / 3.90 ( 225) link_ALPHA1-3 : bond 0.01173 / 0.62 ( 1) link_ALPHA1-3 : angle 1.81293 / 0.96 ( 3) link_ALPHA1-6 : bond 0.01184 / 0.62 ( 1) link_ALPHA1-6 : angle 1.90244 / 0.90 ( 3) link_BETA1-4 : bond 0.00477 / 0.23 ( 4) link_BETA1-4 : angle 2.23521 / 1.15 ( 12) link_NAG-ASN : bond 0.00360 / 0.17 ( 2) link_NAG-ASN : angle 1.46338 / 0.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 176 TYR cc_start: 0.8126 (m-10) cc_final: 0.7797 (m-10) REVERT: E 82 ASP cc_start: 0.8950 (t0) cc_final: 0.8556 (t0) REVERT: E 169 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8600 (mmmm) REVERT: E 192 TYR cc_start: 0.5164 (p90) cc_final: 0.4760 (p90) outliers start: 11 outliers final: 10 residues processed: 82 average time/residue: 0.0638 time to fit residues: 6.6899 Evaluate side-chains 86 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 388 ASN C 519 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.064072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.055111 restraints weight = 19866.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.056975 restraints weight = 10706.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.058221 restraints weight = 6647.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059015 restraints weight = 4546.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059624 restraints weight = 3384.896| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5047 Z= 0.148 Angle : 0.723 12.358 6889 Z= 0.354 Chirality : 0.044 0.177 786 Planarity : 0.005 0.048 869 Dihedral : 4.738 23.732 677 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.81 % Allowed : 9.89 % Favored : 89.30 % Rotamer: Outliers : 2.41 % Allowed : 19.48 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.82 (0.32), residues: 617 helix: -3.52 (1.25), residues: 13 sheet: -1.03 (0.39), residues: 186 loop : -2.37 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 142 TYR 0.027 0.001 TYR C 380 PHE 0.009 0.001 PHE D 146 TRP 0.013 0.001 TRP C 436 HIS 0.007 0.002 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 5030) covalent geometry : angle 0.71169 / 0.35 ( 6847) SS BOND : bond 0.00327 / 0.13 ( 9) SS BOND : angle 1.51829 / 0.86 ( 18) hydrogen bonds : bond 0.02647 / 1.60 ( 75) hydrogen bonds : angle 5.70880 / 3.80 ( 225) link_ALPHA1-3 : bond 0.01152 / 0.61 ( 1) link_ALPHA1-3 : angle 1.77273 / 0.93 ( 3) link_ALPHA1-6 : bond 0.01117 / 0.59 ( 1) link_ALPHA1-6 : angle 1.81185 / 0.84 ( 3) link_BETA1-4 : bond 0.00442 / 0.21 ( 4) link_BETA1-4 : angle 2.20956 / 1.14 ( 12) link_NAG-ASN : bond 0.00308 / 0.15 ( 2) link_NAG-ASN : angle 1.36019 / 0.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: D 155 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.7812 (p0) REVERT: D 175 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7771 (pp) REVERT: D 176 TYR cc_start: 0.8103 (m-10) cc_final: 0.7797 (m-10) REVERT: E 82 ASP cc_start: 0.8928 (t0) cc_final: 0.8524 (t0) REVERT: E 169 LYS cc_start: 0.8856 (mmmt) cc_final: 0.8585 (mmmm) REVERT: E 192 TYR cc_start: 0.5179 (p90) cc_final: 0.4801 (p90) outliers start: 13 outliers final: 10 residues processed: 82 average time/residue: 0.0724 time to fit residues: 7.5658 Evaluate side-chains 87 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 55 optimal weight: 0.0070 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.064299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.055436 restraints weight = 19479.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.057283 restraints weight = 10476.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.058487 restraints weight = 6491.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.059349 restraints weight = 4461.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059942 restraints weight = 3287.683| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5047 Z= 0.139 Angle : 0.716 12.233 6889 Z= 0.353 Chirality : 0.044 0.188 786 Planarity : 0.005 0.048 869 Dihedral : 4.698 25.897 677 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.70 % Favored : 88.49 % Rotamer: Outliers : 2.41 % Allowed : 20.41 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.80 (0.32), residues: 617 helix: -3.55 (1.24), residues: 13 sheet: -1.03 (0.39), residues: 186 loop : -2.34 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 41 TYR 0.033 0.001 TYR C 380 PHE 0.006 0.001 PHE D 146 TRP 0.012 0.001 TRP C 436 HIS 0.003 0.001 HIS D 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 5030) covalent geometry : angle 0.70639 / 0.35 ( 6847) SS BOND : bond 0.00275 / 0.12 ( 9) SS BOND : angle 1.42623 / 0.81 ( 18) hydrogen bonds : bond 0.02595 / 1.57 ( 75) hydrogen bonds : angle 5.64459 / 3.76 ( 225) link_ALPHA1-3 : bond 0.01189 / 0.63 ( 1) link_ALPHA1-3 : angle 1.71591 / 0.90 ( 3) link_ALPHA1-6 : bond 0.01074 / 0.57 ( 1) link_ALPHA1-6 : angle 1.73024 / 0.80 ( 3) link_BETA1-4 : bond 0.00447 / 0.22 ( 4) link_BETA1-4 : angle 2.15926 / 1.11 ( 12) link_NAG-ASN : bond 0.00279 / 0.14 ( 2) link_NAG-ASN : angle 1.23008 / 0.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 388 ASN cc_start: 0.7856 (m-40) cc_final: 0.7622 (m110) REVERT: C 465 GLU cc_start: 0.8752 (tp30) cc_final: 0.8451 (tp30) REVERT: D 175 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7770 (pp) REVERT: D 176 TYR cc_start: 0.8096 (m-10) cc_final: 0.7765 (m-10) REVERT: E 82 ASP cc_start: 0.8944 (t0) cc_final: 0.8547 (t0) REVERT: E 169 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8579 (mmmm) REVERT: E 192 TYR cc_start: 0.5129 (p90) cc_final: 0.4748 (p90) outliers start: 13 outliers final: 10 residues processed: 85 average time/residue: 0.0674 time to fit residues: 7.3381 Evaluate side-chains 87 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 23 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.063912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.055018 restraints weight = 19688.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.056867 restraints weight = 10636.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.058081 restraints weight = 6604.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.058924 restraints weight = 4536.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.059508 restraints weight = 3358.570| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5047 Z= 0.153 Angle : 0.739 12.340 6889 Z= 0.363 Chirality : 0.045 0.190 786 Planarity : 0.005 0.048 869 Dihedral : 4.714 25.164 677 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.18 % Favored : 88.01 % Rotamer: Outliers : 2.04 % Allowed : 21.15 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.87 (0.32), residues: 617 helix: -3.51 (1.26), residues: 13 sheet: -1.21 (0.38), residues: 190 loop : -2.33 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 142 TYR 0.028 0.001 TYR C 380 PHE 0.008 0.001 PHE D 146 TRP 0.012 0.001 TRP C 436 HIS 0.004 0.001 HIS D 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 5030) covalent geometry : angle 0.72896 / 0.36 ( 6847) SS BOND : bond 0.00258 / 0.10 ( 9) SS BOND : angle 1.53968 / 0.87 ( 18) hydrogen bonds : bond 0.02674 / 1.65 ( 75) hydrogen bonds : angle 5.71809 / 3.81 ( 225) link_ALPHA1-3 : bond 0.01150 / 0.61 ( 1) link_ALPHA1-3 : angle 1.69319 / 0.89 ( 3) link_ALPHA1-6 : bond 0.01152 / 0.61 ( 1) link_ALPHA1-6 : angle 1.83059 / 0.86 ( 3) link_BETA1-4 : bond 0.00453 / 0.22 ( 4) link_BETA1-4 : angle 2.18010 / 1.13 ( 12) link_NAG-ASN : bond 0.00315 / 0.15 ( 2) link_NAG-ASN : angle 1.31040 / 0.57 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: C 388 ASN cc_start: 0.7848 (m-40) cc_final: 0.7498 (m-40) REVERT: C 406 GLU cc_start: 0.8742 (tt0) cc_final: 0.8378 (tp30) REVERT: C 465 GLU cc_start: 0.8764 (tp30) cc_final: 0.8472 (tp30) REVERT: D 175 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7781 (pp) REVERT: D 176 TYR cc_start: 0.8099 (m-10) cc_final: 0.7784 (m-10) REVERT: E 82 ASP cc_start: 0.8959 (t0) cc_final: 0.8564 (t0) REVERT: E 169 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8581 (mmmm) REVERT: E 192 TYR cc_start: 0.5192 (p90) cc_final: 0.4795 (p90) outliers start: 11 outliers final: 10 residues processed: 85 average time/residue: 0.0668 time to fit residues: 7.3306 Evaluate side-chains 90 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.0030 chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 0.0470 chunk 42 optimal weight: 2.9990 overall best weight: 0.4488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.064614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.055629 restraints weight = 19692.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.057528 restraints weight = 10510.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.058794 restraints weight = 6471.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.059665 restraints weight = 4395.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060217 restraints weight = 3232.277| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5047 Z= 0.131 Angle : 0.724 12.121 6889 Z= 0.354 Chirality : 0.045 0.192 786 Planarity : 0.005 0.047 869 Dihedral : 4.616 26.010 677 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.81 % Allowed : 9.89 % Favored : 89.30 % Rotamer: Outliers : 2.04 % Allowed : 21.15 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.81 (0.33), residues: 617 helix: -3.61 (1.20), residues: 13 sheet: -1.20 (0.39), residues: 190 loop : -2.26 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 41 TYR 0.028 0.001 TYR C 380 PHE 0.011 0.001 PHE E 62 TRP 0.012 0.001 TRP C 436 HIS 0.003 0.001 HIS D 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 5030) covalent geometry : angle 0.71530 / 0.35 ( 6847) SS BOND : bond 0.00269 / 0.13 ( 9) SS BOND : angle 1.38040 / 0.78 ( 18) hydrogen bonds : bond 0.02442 / 1.49 ( 75) hydrogen bonds : angle 5.50835 / 3.65 ( 225) link_ALPHA1-3 : bond 0.01061 / 0.56 ( 1) link_ALPHA1-3 : angle 1.64995 / 0.86 ( 3) link_ALPHA1-6 : bond 0.00968 / 0.51 ( 1) link_ALPHA1-6 : angle 1.64864 / 0.76 ( 3) link_BETA1-4 : bond 0.00409 / 0.20 ( 4) link_BETA1-4 : angle 2.10582 / 1.08 ( 12) link_NAG-ASN : bond 0.00260 / 0.13 ( 2) link_NAG-ASN : angle 1.13559 / 0.49 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 977.45 seconds wall clock time: 17 minutes 34.52 seconds (1054.52 seconds total)