Starting phenix.real_space_refine on Thu Jul 2 01:49:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ul3_26590/07_2026/7ul3_26590.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ul3_26590/07_2026/7ul3_26590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ul3_26590/07_2026/7ul3_26590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ul3_26590/07_2026/7ul3_26590.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ul3_26590/07_2026/7ul3_26590.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ul3_26590/07_2026/7ul3_26590.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ul3_26590/07_2026/7ul3_26590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ul3_26590/07_2026/7ul3_26590.cif" } resolution = 3.0 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= 0.019 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 31 5.16 5 C 3570 2.51 5 N 910 2.21 5 O 973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s 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: 5484 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1944 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 7, 'TRANS': 260} Chain breaks: 2 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 9, 'ASP:plan': 4, 'HIS:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "C" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 807 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 52 Chain: "H" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1300 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 9 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 3, 'GLN:plan1': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "L" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1413 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 189} Chain breaks: 4 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 46 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'FO9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.44, per 1000 atoms: 0.26 Number of scatterers: 5484 At special positions: 0 Unit cell: (65.9452, 80.6961, 157.921, 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 31 16.00 O 973 8.00 N 910 7.00 C 3570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 91 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 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 Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 208.5 milliseconds 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 12 sheets defined 35.2% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 16 through 46 Processing helix chain 'A' and resid 53 through 70 removed outlier: 3.828A pdb=" N ILE A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 removed outlier: 4.011A pdb=" N PHE A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 104 removed outlier: 3.632A pdb=" N ILE A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 131 through 153 Processing helix chain 'A' and resid 181 through 191 removed outlier: 3.590A pdb=" N GLY A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 212 removed outlier: 3.541A pdb=" N LEU A 196 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 261 Proline residue: A 249 - end of helix removed outlier: 3.527A pdb=" N GLY A 258 " --> pdb=" O PHE A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 292 removed outlier: 3.746A pdb=" N VAL A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N SER A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 292 through 303 Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 98 through 100C Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.523A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 5 through 9 removed outlier: 3.596A pdb=" N GLN C 5 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER C 27 " --> pdb=" O GLN C 5 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER C 23 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR C 81 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 72 " --> pdb=" O TYR C 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 59 through 61 removed outlier: 5.752A pdb=" N GLY C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG C 40 " --> pdb=" O GLY C 49 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU C 33 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ARG C 102 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 35 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 41 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 59 through 61 removed outlier: 5.752A pdb=" N GLY C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG C 40 " --> pdb=" O GLY C 49 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU C 33 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ARG C 102 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 35 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 41 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.699A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 58 through 59 removed outlier: 4.155A pdb=" N SER H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR H 50 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.509A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 151 through 153 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.581A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB1, first strand: chain 'L' and resid 22 through 24 removed outlier: 4.046A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.790A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.824A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS L 194 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 894 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: 0.66 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 860 1.29 - 1.42: 1508 1.42 - 1.56: 3189 1.56 - 1.69: 3 1.69 - 1.83: 38 Bond restraints: 5598 Sorted by residual: bond pdb=" C5 FO9 A 401 " pdb=" S1 FO9 A 401 " ideal model delta sigma weight residual 1.802 1.541 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C6 FO9 A 401 " pdb=" S1 FO9 A 401 " ideal model delta sigma weight residual 1.771 1.550 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C4 FO9 A 401 " pdb=" N4 FO9 A 401 " ideal model delta sigma weight residual 1.284 1.452 -0.168 2.00e-02 2.50e+03 7.02e+01 bond pdb=" C4 FO9 A 401 " pdb=" C5 FO9 A 401 " ideal model delta sigma weight residual 1.516 1.377 0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" C THR L 74 " pdb=" O THR L 74 " ideal model delta sigma weight residual 1.234 1.154 0.080 1.22e-02 6.72e+03 4.30e+01 ... (remaining 5593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 7602 3.58 - 7.16: 53 7.16 - 10.74: 10 10.74 - 14.32: 2 14.32 - 17.89: 2 Bond angle restraints: 7669 Sorted by residual: angle pdb=" CA LEU L 73 " pdb=" C LEU L 73 " pdb=" N THR L 74 " ideal model delta sigma weight residual 115.51 123.82 -8.31 1.24e+00 6.50e-01 4.49e+01 angle pdb=" C THR L 22 " pdb=" CA THR L 22 " pdb=" CB THR L 22 " ideal model delta sigma weight residual 109.65 99.01 10.64 1.75e+00 3.27e-01 3.70e+01 angle pdb=" C2 FO9 A 401 " pdb=" S FO9 A 401 " pdb=" C3 FO9 A 401 " ideal model delta sigma weight residual 97.71 115.60 -17.89 3.00e+00 1.11e-01 3.56e+01 angle pdb=" CA THR L 74 " pdb=" C THR L 74 " pdb=" O THR L 74 " ideal model delta sigma weight residual 120.99 114.46 6.53 1.12e+00 7.97e-01 3.40e+01 angle pdb=" O FO9 A 401 " pdb=" S2 FO9 A 401 " pdb=" O1 FO9 A 401 " ideal model delta sigma weight residual 116.54 99.19 17.35 3.00e+00 1.11e-01 3.35e+01 ... (remaining 7664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 3018 17.79 - 35.58: 160 35.58 - 53.37: 26 53.37 - 71.15: 7 71.15 - 88.94: 1 Dihedral angle restraints: 3212 sinusoidal: 993 harmonic: 2219 Sorted by residual: dihedral pdb=" CB CYS A 91 " pdb=" SG CYS A 91 " pdb=" SG CYS A 174 " pdb=" CB CYS A 174 " ideal model delta sinusoidal sigma weight residual -86.00 -156.31 70.31 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" C THR L 22 " pdb=" N THR L 22 " pdb=" CA THR L 22 " pdb=" CB THR L 22 " ideal model delta harmonic sigma weight residual -122.00 -108.53 -13.47 0 2.50e+00 1.60e-01 2.90e+01 dihedral pdb=" C THR L 20 " pdb=" N THR L 20 " pdb=" CA THR L 20 " pdb=" CB THR L 20 " ideal model delta harmonic sigma weight residual -122.00 -111.45 -10.55 0 2.50e+00 1.60e-01 1.78e+01 ... (remaining 3209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 700 0.047 - 0.093: 174 0.093 - 0.140: 47 0.140 - 0.187: 2 0.187 - 0.233: 5 Chirality restraints: 928 Sorted by residual: chirality pdb=" CA THR L 22 " pdb=" N THR L 22 " pdb=" C THR L 22 " pdb=" CB THR L 22 " both_signs ideal model delta sigma weight residual False 2.53 2.76 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA LEU L 73 " pdb=" N LEU L 73 " pdb=" C LEU L 73 " pdb=" CB LEU L 73 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA THR L 74 " pdb=" N THR L 74 " pdb=" C THR L 74 " pdb=" CB THR L 74 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.93e-01 ... (remaining 925 not shown) Planarity restraints: 952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 284 " 0.076 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO A 285 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR L 72 " 0.023 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" C THR L 72 " -0.076 2.00e-02 2.50e+03 pdb=" O THR L 72 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU L 73 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 FO9 A 401 " -0.038 2.00e-02 2.50e+03 3.01e-02 1.81e+01 pdb=" C6 FO9 A 401 " 0.028 2.00e-02 2.50e+03 pdb=" C7 FO9 A 401 " -0.002 2.00e-02 2.50e+03 pdb=" N1 FO9 A 401 " 0.019 2.00e-02 2.50e+03 pdb=" N2 FO9 A 401 " -0.050 2.00e-02 2.50e+03 pdb=" N3 FO9 A 401 " 0.039 2.00e-02 2.50e+03 pdb=" N4 FO9 A 401 " -0.015 2.00e-02 2.50e+03 pdb=" S1 FO9 A 401 " 0.019 2.00e-02 2.50e+03 ... (remaining 949 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 503 2.75 - 3.29: 5099 3.29 - 3.82: 8519 3.82 - 4.36: 9597 4.36 - 4.90: 17572 Nonbonded interactions: 41290 Sorted by model distance: nonbonded pdb=" N PHE C 31 " pdb=" O ARG C 102 " model vdw 2.211 3.120 nonbonded pdb=" O ARG A 213 " pdb=" NH2 ARG C 102 " model vdw 2.324 3.120 nonbonded pdb=" OD1 ASP H 101 " pdb=" N TYR H 102 " model vdw 2.355 3.120 nonbonded pdb=" O ASN A 280 " pdb=" OD1 ASN A 280 " model vdw 2.364 3.040 nonbonded pdb=" NH1 ARG A 230 " pdb=" O ILE C 105 " model vdw 2.388 3.120 ... (remaining 41285 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 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: 4.450 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.450 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5600 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 : 0.007 0.261 5604 Z= 0.366 Angle : 0.877 17.894 7681 Z= 0.483 Chirality : 0.046 0.233 928 Planarity : 0.007 0.114 952 Dihedral : 11.435 88.942 1764 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 3.57 % 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: 1.41 (0.30), residues: 727 helix: 2.31 (0.32), residues: 228 sheet: 1.24 (0.36), residues: 198 loop : -0.34 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 94 TYR 0.028 0.002 TYR C 81 PHE 0.019 0.002 PHE A 191 TRP 0.015 0.001 TRP H 100G HIS 0.010 0.002 HIS H 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.37 ( 5598) covalent geometry : angle 0.87636 / 0.48 ( 7669) SS BOND : bond 0.00348 / 0.22 ( 6) SS BOND : angle 1.40079 / 1.13 ( 12) hydrogen bonds : bond 0.19189 / 13.40 ( 313) hydrogen bonds : angle 7.15023 / 5.28 ( 894) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.121 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3024 time to fit residues: 20.9965 Evaluate side-chains 41 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.0470 chunk 61 optimal weight: 0.0040 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.4890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN A 292 ASN H 200 HIS L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.252024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.176023 restraints weight = 7282.587| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 3.87 r_work: 0.3994 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5604 Z= 0.123 Angle : 0.554 6.589 7681 Z= 0.295 Chirality : 0.041 0.137 928 Planarity : 0.005 0.068 952 Dihedral : 4.611 54.217 817 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.25 % Allowed : 9.61 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.93 (0.31), residues: 727 helix: 2.56 (0.32), residues: 243 sheet: 1.78 (0.36), residues: 206 loop : -0.30 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 73 TYR 0.017 0.002 TYR A 78 PHE 0.014 0.001 PHE H 27 TRP 0.012 0.001 TRP A 275 HIS 0.002 0.001 HIS H 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 5598) covalent geometry : angle 0.55452 / 0.29 ( 7669) SS BOND : bond 0.00306 / 0.18 ( 6) SS BOND : angle 0.52593 / 0.36 ( 12) hydrogen bonds : bond 0.04016 / 2.86 ( 313) hydrogen bonds : angle 5.02495 / 3.77 ( 894) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.197 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 46 average time/residue: 0.3144 time to fit residues: 15.7289 Evaluate side-chains 42 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 68 optimal weight: 30.0000 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 30.0000 chunk 2 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4797 r_free = 0.4797 target = 0.246393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.168054 restraints weight = 7050.474| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 3.83 r_work: 0.3901 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 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 : 0.004 0.037 5604 Z= 0.155 Angle : 0.565 6.540 7681 Z= 0.301 Chirality : 0.042 0.145 928 Planarity : 0.005 0.054 952 Dihedral : 4.645 48.473 817 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.68 % Allowed : 10.02 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.68 (0.31), residues: 727 helix: 2.22 (0.33), residues: 243 sheet: 1.86 (0.36), residues: 200 loop : -0.45 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 47 TYR 0.018 0.002 TYR A 94 PHE 0.018 0.002 PHE H 27 TRP 0.012 0.002 TRP A 275 HIS 0.003 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 5598) covalent geometry : angle 0.56489 / 0.30 ( 7669) SS BOND : bond 0.00225 / 0.15 ( 6) SS BOND : angle 0.57701 / 0.41 ( 12) hydrogen bonds : bond 0.04909 / 3.53 ( 313) hydrogen bonds : angle 4.69021 / 3.46 ( 894) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.212 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 48 average time/residue: 0.2908 time to fit residues: 15.1571 Evaluate side-chains 43 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 30 optimal weight: 0.2980 chunk 68 optimal weight: 30.0000 chunk 73 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.247152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.168438 restraints weight = 7081.748| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 3.90 r_work: 0.3860 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5604 Z= 0.122 Angle : 0.509 7.948 7681 Z= 0.267 Chirality : 0.040 0.150 928 Planarity : 0.004 0.045 952 Dihedral : 4.372 43.673 817 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.07 % Allowed : 12.07 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.77 (0.31), residues: 727 helix: 2.31 (0.33), residues: 242 sheet: 2.00 (0.35), residues: 208 loop : -0.57 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.015 0.001 TYR A 78 PHE 0.013 0.001 PHE H 27 TRP 0.009 0.001 TRP A 143 HIS 0.002 0.001 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 5598) covalent geometry : angle 0.50950 / 0.27 ( 7669) SS BOND : bond 0.00231 / 0.14 ( 6) SS BOND : angle 0.44607 / 0.30 ( 12) hydrogen bonds : bond 0.04000 / 2.90 ( 313) hydrogen bonds : angle 4.40871 / 3.26 ( 894) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.229 Fit side-chains REVERT: A 115 ASP cc_start: 0.7560 (t0) cc_final: 0.7299 (t0) REVERT: H 20 LEU cc_start: 0.6177 (pt) cc_final: 0.5885 (tp) REVERT: H 82 MET cc_start: 0.2460 (OUTLIER) cc_final: 0.2044 (mpp) outliers start: 15 outliers final: 10 residues processed: 44 average time/residue: 0.2682 time to fit residues: 12.9982 Evaluate side-chains 46 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 71 optimal weight: 50.0000 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 42 optimal weight: 6.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- 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 = 0.4792 r_free = 0.4792 target = 0.245105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.164884 restraints weight = 7143.698| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 4.04 r_work: 0.3821 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5604 Z= 0.161 Angle : 0.557 6.886 7681 Z= 0.295 Chirality : 0.042 0.150 928 Planarity : 0.004 0.040 952 Dihedral : 4.579 45.656 817 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.66 % Allowed : 13.50 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.54 (0.31), residues: 727 helix: 2.05 (0.33), residues: 242 sheet: 1.99 (0.36), residues: 206 loop : -0.72 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.016 0.002 TYR A 126 PHE 0.017 0.002 PHE H 27 TRP 0.011 0.001 TRP A 275 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 5598) covalent geometry : angle 0.55691 / 0.29 ( 7669) SS BOND : bond 0.00292 / 0.17 ( 6) SS BOND : angle 0.47707 / 0.32 ( 12) hydrogen bonds : bond 0.04994 / 3.61 ( 313) hydrogen bonds : angle 4.53524 / 3.34 ( 894) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 115 ASP cc_start: 0.7544 (t0) cc_final: 0.7259 (t0) outliers start: 13 outliers final: 10 residues processed: 43 average time/residue: 0.2638 time to fit residues: 12.3724 Evaluate side-chains 45 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 57 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 73 optimal weight: 50.0000 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 35 HIS H 39 GLN L 38 GLN L 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.244322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.162651 restraints weight = 7019.202| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.94 r_work: 0.3819 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5604 Z= 0.146 Angle : 0.527 6.699 7681 Z= 0.278 Chirality : 0.040 0.143 928 Planarity : 0.004 0.036 952 Dihedral : 4.444 44.009 817 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.86 % Allowed : 13.50 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.47 (0.31), residues: 727 helix: 2.06 (0.33), residues: 242 sheet: 1.70 (0.37), residues: 214 loop : -0.67 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 18 TYR 0.015 0.002 TYR A 78 PHE 0.013 0.001 PHE H 27 TRP 0.008 0.001 TRP A 275 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 5598) covalent geometry : angle 0.52717 / 0.28 ( 7669) SS BOND : bond 0.00283 / 0.17 ( 6) SS BOND : angle 0.47568 / 0.32 ( 12) hydrogen bonds : bond 0.04400 / 3.19 ( 313) hydrogen bonds : angle 4.39200 / 3.23 ( 894) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.6295 (OUTLIER) cc_final: 0.5059 (t80) REVERT: A 115 ASP cc_start: 0.7845 (t0) cc_final: 0.7610 (t0) REVERT: C 117 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7849 (p) REVERT: H 4 LEU cc_start: 0.4265 (OUTLIER) cc_final: 0.4028 (mt) outliers start: 14 outliers final: 10 residues processed: 48 average time/residue: 0.3157 time to fit residues: 16.5095 Evaluate side-chains 52 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 12 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4785 r_free = 0.4785 target = 0.244623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.164520 restraints weight = 7130.581| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 3.95 r_work: 0.3819 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5604 Z= 0.153 Angle : 0.542 6.365 7681 Z= 0.287 Chirality : 0.041 0.145 928 Planarity : 0.004 0.034 952 Dihedral : 4.450 44.497 817 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.48 % Allowed : 13.50 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.31), residues: 727 helix: 2.03 (0.33), residues: 242 sheet: 1.66 (0.37), residues: 214 loop : -0.74 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 94 TYR 0.015 0.002 TYR A 250 PHE 0.013 0.001 PHE H 27 TRP 0.009 0.001 TRP A 275 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 5598) covalent geometry : angle 0.54206 / 0.29 ( 7669) SS BOND : bond 0.00298 / 0.18 ( 6) SS BOND : angle 0.49375 / 0.33 ( 12) hydrogen bonds : bond 0.04652 / 3.37 ( 313) hydrogen bonds : angle 4.41462 / 3.25 ( 894) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.6096 (OUTLIER) cc_final: 0.5019 (t80) REVERT: A 115 ASP cc_start: 0.7716 (t0) cc_final: 0.7474 (t0) REVERT: C 117 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7854 (p) REVERT: H 4 LEU cc_start: 0.4114 (OUTLIER) cc_final: 0.3914 (mt) outliers start: 17 outliers final: 11 residues processed: 50 average time/residue: 0.2845 time to fit residues: 15.5561 Evaluate side-chains 53 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 4 optimal weight: 0.5980 chunk 61 optimal weight: 0.0040 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 = 0.4765 r_free = 0.4765 target = 0.244902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.163994 restraints weight = 7045.502| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 3.95 r_work: 0.3842 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5604 Z= 0.117 Angle : 0.501 6.334 7681 Z= 0.263 Chirality : 0.039 0.139 928 Planarity : 0.004 0.034 952 Dihedral : 4.248 41.871 817 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.27 % Allowed : 13.70 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.54 (0.32), residues: 727 helix: 2.22 (0.33), residues: 242 sheet: 1.70 (0.37), residues: 214 loop : -0.71 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.016 0.001 TYR A 78 PHE 0.011 0.001 PHE H 27 TRP 0.009 0.001 TRP A 275 HIS 0.001 0.000 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 5598) covalent geometry : angle 0.50096 / 0.26 ( 7669) SS BOND : bond 0.00263 / 0.15 ( 6) SS BOND : angle 0.47085 / 0.31 ( 12) hydrogen bonds : bond 0.03946 / 2.87 ( 313) hydrogen bonds : angle 4.21832 / 3.11 ( 894) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.6303 (OUTLIER) cc_final: 0.5166 (t80) REVERT: A 115 ASP cc_start: 0.7925 (t0) cc_final: 0.7680 (t0) REVERT: C 32 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7909 (ttp80) REVERT: C 117 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7842 (p) REVERT: H 4 LEU cc_start: 0.4272 (OUTLIER) cc_final: 0.4067 (mt) outliers start: 16 outliers final: 10 residues processed: 50 average time/residue: 0.2882 time to fit residues: 15.6568 Evaluate side-chains 52 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 0.0040 chunk 62 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.244943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.165659 restraints weight = 7029.198| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 3.87 r_work: 0.3836 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5604 Z= 0.126 Angle : 0.513 7.139 7681 Z= 0.269 Chirality : 0.040 0.143 928 Planarity : 0.004 0.035 952 Dihedral : 4.219 41.357 817 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.07 % Allowed : 13.70 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.54 (0.32), residues: 727 helix: 2.25 (0.33), residues: 242 sheet: 1.66 (0.37), residues: 214 loop : -0.70 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 94 TYR 0.013 0.001 TYR A 250 PHE 0.010 0.001 PHE A 243 TRP 0.010 0.001 TRP A 275 HIS 0.001 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 5598) covalent geometry : angle 0.51339 / 0.27 ( 7669) SS BOND : bond 0.00277 / 0.17 ( 6) SS BOND : angle 0.45666 / 0.30 ( 12) hydrogen bonds : bond 0.04108 / 2.99 ( 313) hydrogen bonds : angle 4.20985 / 3.10 ( 894) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.6033 (OUTLIER) cc_final: 0.4914 (t80) REVERT: A 115 ASP cc_start: 0.7830 (t0) cc_final: 0.7569 (t0) REVERT: C 117 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7823 (p) outliers start: 15 outliers final: 11 residues processed: 49 average time/residue: 0.2722 time to fit residues: 14.5574 Evaluate side-chains 51 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 51 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 56 optimal weight: 0.4980 chunk 71 optimal weight: 9.9990 chunk 73 optimal weight: 50.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4777 r_free = 0.4777 target = 0.243912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.164025 restraints weight = 7100.134| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 3.88 r_work: 0.3820 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5604 Z= 0.165 Angle : 0.552 6.931 7681 Z= 0.292 Chirality : 0.041 0.150 928 Planarity : 0.004 0.035 952 Dihedral : 4.451 45.143 817 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.07 % Allowed : 13.91 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.28 (0.31), residues: 727 helix: 2.05 (0.34), residues: 236 sheet: 1.58 (0.37), residues: 214 loop : -0.85 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 94 TYR 0.016 0.002 TYR A 250 PHE 0.013 0.002 PHE A 243 TRP 0.009 0.001 TRP A 275 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 ( 5598) covalent geometry : angle 0.55216 / 0.29 ( 7669) SS BOND : bond 0.00332 / 0.20 ( 6) SS BOND : angle 0.54113 / 0.34 ( 12) hydrogen bonds : bond 0.04808 / 3.49 ( 313) hydrogen bonds : angle 4.40888 / 3.25 ( 894) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.5864 (OUTLIER) cc_final: 0.4806 (t80) REVERT: A 115 ASP cc_start: 0.7547 (t0) cc_final: 0.7246 (t0) REVERT: C 117 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7809 (p) outliers start: 15 outliers final: 11 residues processed: 49 average time/residue: 0.2700 time to fit residues: 14.4605 Evaluate side-chains 50 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4787 r_free = 0.4787 target = 0.245214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.165471 restraints weight = 7117.767| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 4.01 r_work: 0.3834 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5604 Z= 0.130 Angle : 0.514 6.828 7681 Z= 0.270 Chirality : 0.040 0.141 928 Planarity : 0.004 0.035 952 Dihedral : 4.275 42.959 817 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.86 % Allowed : 14.72 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.44 (0.32), residues: 727 helix: 2.18 (0.33), residues: 242 sheet: 1.62 (0.37), residues: 213 loop : -0.76 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 94 TYR 0.015 0.001 TYR A 250 PHE 0.010 0.001 PHE H 27 TRP 0.009 0.001 TRP H 100E HIS 0.001 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 5598) covalent geometry : angle 0.51449 / 0.27 ( 7669) SS BOND : bond 0.00276 / 0.16 ( 6) SS BOND : angle 0.45552 / 0.30 ( 12) hydrogen bonds : bond 0.04120 / 3.00 ( 313) hydrogen bonds : angle 4.23130 / 3.12 ( 894) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2040.70 seconds wall clock time: 35 minutes 31.11 seconds (2131.11 seconds total)