Starting phenix.real_space_refine on Tue Mar 3 13:47:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ul3_26590/03_2026/7ul3_26590.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ul3_26590/03_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_26590/03_2026/7ul3_26590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ul3_26590/03_2026/7ul3_26590.map" model { file = "/net/cci-nas-00/data/ceres_data/7ul3_26590/03_2026/7ul3_26590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ul3_26590/03_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 1.11, per 1000 atoms: 0.20 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: 0.35 Conformation dependent library (CDL) restraints added in 275.4 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: 0.24 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: 0.88 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: 1.15 - 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: 3020 17.79 - 35.58: 161 35.58 - 53.37: 27 53.37 - 71.15: 7 71.15 - 88.94: 1 Dihedral angle restraints: 3216 sinusoidal: 997 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 3213 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.200 Find NCS groups from input model: 0.010 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5341 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 : 11.481 88.942 1768 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 covalent geometry : bond 0.00693 ( 5598) covalent geometry : angle 0.87636 ( 7669) SS BOND : bond 0.00348 ( 6) SS BOND : angle 1.40079 ( 12) hydrogen bonds : bond 0.19189 ( 313) hydrogen bonds : angle 7.15023 ( 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 : 0.207 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3215 time to fit residues: 22.1948 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 : 0.200 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4845 r_free = 0.4845 target = 0.251916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.175656 restraints weight = 7286.800| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 3.92 r_work: 0.3990 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5604 Z= 0.130 Angle : 0.559 6.447 7681 Z= 0.296 Chirality : 0.041 0.138 928 Planarity : 0.005 0.068 952 Dihedral : 4.947 55.582 821 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.25 % Allowed : 9.00 % Favored : 88.75 % 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: 1.79 (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 68 TYR 0.017 0.002 TYR A 78 PHE 0.013 0.001 PHE H 27 TRP 0.012 0.001 TRP A 275 HIS 0.002 0.001 HIS H 100B Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5598) covalent geometry : angle 0.55882 ( 7669) SS BOND : bond 0.00339 ( 6) SS BOND : angle 0.50048 ( 12) hydrogen bonds : bond 0.03982 ( 313) hydrogen bonds : angle 4.97092 ( 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 52 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.192 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 47 average time/residue: 0.3302 time to fit residues: 16.8464 Evaluate side-chains 40 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 51 optimal weight: 30.0000 chunk 2 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.246292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.167792 restraints weight = 7054.658| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 3.81 r_work: 0.3900 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.2766 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= 0.172 Angle : 0.577 5.680 7681 Z= 0.307 Chirality : 0.042 0.161 928 Planarity : 0.005 0.056 952 Dihedral : 4.853 46.657 821 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.27 % Allowed : 10.63 % Favored : 86.09 % 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: 1.64 (0.31), residues: 727 helix: 2.18 (0.32), residues: 243 sheet: 1.83 (0.36), residues: 200 loop : -0.45 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 68 TYR 0.017 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 H 35 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 5598) covalent geometry : angle 0.57750 ( 7669) SS BOND : bond 0.00284 ( 6) SS BOND : angle 0.54257 ( 12) hydrogen bonds : bond 0.04966 ( 313) hydrogen bonds : angle 4.78896 ( 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 53 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.224 Fit side-chains REVERT: H 20 LEU cc_start: 0.5246 (pt) cc_final: 0.5005 (tp) outliers start: 16 outliers final: 8 residues processed: 45 average time/residue: 0.3565 time to fit residues: 17.2890 Evaluate side-chains 44 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 54 LEU 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: 0.6980 chunk 68 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.244403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.163114 restraints weight = 7042.580| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 3.91 r_work: 0.3820 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5604 Z= 0.168 Angle : 0.556 5.547 7681 Z= 0.298 Chirality : 0.042 0.155 928 Planarity : 0.004 0.047 952 Dihedral : 4.787 41.050 821 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.68 % Allowed : 11.45 % 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: 1.51 (0.31), residues: 727 helix: 2.01 (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 0.003 0.000 ARG C 68 TYR 0.016 0.002 TYR A 94 PHE 0.016 0.002 PHE H 27 TRP 0.009 0.002 TRP A 275 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 5598) covalent geometry : angle 0.55575 ( 7669) SS BOND : bond 0.00312 ( 6) SS BOND : angle 0.50558 ( 12) hydrogen bonds : bond 0.04829 ( 313) hydrogen bonds : angle 4.62011 ( 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 54 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.207 Fit side-chains REVERT: A 115 ASP cc_start: 0.7799 (t0) cc_final: 0.7558 (t0) REVERT: H 20 LEU cc_start: 0.5319 (pt) cc_final: 0.5056 (tp) outliers start: 18 outliers final: 12 residues processed: 47 average time/residue: 0.3119 time to fit residues: 16.0313 Evaluate side-chains 48 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 54 LEU Chi-restraints excluded: chain L residue 74 THR 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: 0.5980 chunk 28 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 59 optimal weight: 0.0770 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.246656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.167947 restraints weight = 7172.881| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 3.92 r_work: 0.3852 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5604 Z= 0.118 Angle : 0.500 5.474 7681 Z= 0.263 Chirality : 0.040 0.140 928 Planarity : 0.004 0.040 952 Dihedral : 4.425 36.121 821 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.66 % Allowed : 13.91 % Favored : 83.44 % 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: 1.59 (0.31), residues: 727 helix: 2.22 (0.33), residues: 242 sheet: 1.99 (0.37), residues: 201 loop : -0.73 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 18 TYR 0.013 0.001 TYR A 94 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 covalent geometry : bond 0.00265 ( 5598) covalent geometry : angle 0.49977 ( 7669) SS BOND : bond 0.00252 ( 6) SS BOND : angle 0.46372 ( 12) hydrogen bonds : bond 0.03958 ( 313) hydrogen bonds : angle 4.33121 ( 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 52 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 115 ASP cc_start: 0.7668 (t0) cc_final: 0.7415 (t0) REVERT: H 20 LEU cc_start: 0.5429 (pt) cc_final: 0.5185 (tp) REVERT: H 82 MET cc_start: 0.2583 (OUTLIER) cc_final: 0.2258 (mpp) outliers start: 13 outliers final: 8 residues processed: 47 average time/residue: 0.3199 time to fit residues: 16.2979 Evaluate side-chains 48 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 82 MET Chi-restraints excluded: chain L residue 74 THR 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: 0.0570 chunk 36 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 73 optimal weight: 50.0000 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 68 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.247025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.168653 restraints weight = 7049.101| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 3.89 r_work: 0.3868 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5604 Z= 0.106 Angle : 0.487 5.677 7681 Z= 0.255 Chirality : 0.039 0.136 928 Planarity : 0.004 0.036 952 Dihedral : 4.265 34.497 821 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.86 % Allowed : 13.70 % Favored : 83.44 % 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: 1.72 (0.31), residues: 727 helix: 2.36 (0.33), residues: 242 sheet: 1.77 (0.37), residues: 214 loop : -0.56 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 18 TYR 0.016 0.001 TYR A 78 PHE 0.011 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 covalent geometry : bond 0.00232 ( 5598) covalent geometry : angle 0.48676 ( 7669) SS BOND : bond 0.00248 ( 6) SS BOND : angle 0.40630 ( 12) hydrogen bonds : bond 0.03713 ( 313) hydrogen bonds : angle 4.17218 ( 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 58 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 117 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7708 (p) REVERT: H 20 LEU cc_start: 0.5368 (pt) cc_final: 0.5113 (tp) REVERT: H 82 MET cc_start: 0.2491 (OUTLIER) cc_final: 0.2193 (mpp) REVERT: L 145 LYS cc_start: 0.6144 (tttp) cc_final: 0.5940 (ptmt) outliers start: 14 outliers final: 7 residues processed: 53 average time/residue: 0.3748 time to fit residues: 21.2667 Evaluate side-chains 51 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.8980 chunk 54 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.244904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.165276 restraints weight = 7177.110| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 3.97 r_work: 0.3822 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5604 Z= 0.154 Angle : 0.541 5.588 7681 Z= 0.287 Chirality : 0.041 0.148 928 Planarity : 0.004 0.035 952 Dihedral : 4.505 37.988 821 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.66 % Allowed : 14.52 % Favored : 82.82 % 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: 2.15 (0.33), residues: 242 sheet: 1.71 (0.37), residues: 214 loop : -0.64 (0.36), 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 0.015 0.001 PHE H 27 TRP 0.009 0.001 TRP A 275 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5598) covalent geometry : angle 0.54126 ( 7669) SS BOND : bond 0.00293 ( 6) SS BOND : angle 0.46297 ( 12) hydrogen bonds : bond 0.04630 ( 313) hydrogen bonds : angle 4.32323 ( 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 58 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: C 117 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7809 (p) REVERT: H 20 LEU cc_start: 0.5367 (pt) cc_final: 0.5124 (tp) REVERT: H 82 MET cc_start: 0.2493 (OUTLIER) cc_final: 0.2176 (mpp) outliers start: 13 outliers final: 8 residues processed: 54 average time/residue: 0.3718 time to fit residues: 21.4986 Evaluate side-chains 53 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 82 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 4 optimal weight: 0.5980 chunk 61 optimal weight: 0.0870 chunk 28 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 46 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 198 HIS ** 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 = 0.4768 r_free = 0.4768 target = 0.244781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.164645 restraints weight = 7091.803| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 4.00 r_work: 0.3841 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5604 Z= 0.113 Angle : 0.510 6.105 7681 Z= 0.268 Chirality : 0.039 0.137 928 Planarity : 0.004 0.034 952 Dihedral : 4.312 35.940 821 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.45 % Allowed : 16.16 % Favored : 81.39 % 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: 1.66 (0.32), residues: 727 helix: 2.33 (0.33), residues: 242 sheet: 1.68 (0.37), residues: 214 loop : -0.58 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 94 TYR 0.015 0.001 TYR A 78 PHE 0.011 0.001 PHE H 27 TRP 0.009 0.001 TRP A 143 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 5598) covalent geometry : angle 0.51023 ( 7669) SS BOND : bond 0.00251 ( 6) SS BOND : angle 0.39147 ( 12) hydrogen bonds : bond 0.03859 ( 313) hydrogen bonds : angle 4.14496 ( 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 57 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.6236 (OUTLIER) cc_final: 0.5137 (t80) REVERT: C 117 THR cc_start: 0.8118 (OUTLIER) cc_final: 0.7807 (p) REVERT: H 20 LEU cc_start: 0.5391 (pt) cc_final: 0.5143 (tp) REVERT: H 82 MET cc_start: 0.2500 (OUTLIER) cc_final: 0.2184 (mpp) outliers start: 12 outliers final: 7 residues processed: 53 average time/residue: 0.4074 time to fit residues: 23.1115 Evaluate side-chains 54 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 82 MET Chi-restraints excluded: chain H residue 100 LEU 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: 0.8980 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS L 38 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.243253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.163691 restraints weight = 7117.693| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 3.91 r_work: 0.3815 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5604 Z= 0.178 Angle : 0.584 8.017 7681 Z= 0.309 Chirality : 0.042 0.149 928 Planarity : 0.004 0.035 952 Dihedral : 4.605 39.737 821 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.45 % Allowed : 15.95 % Favored : 81.60 % 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: 1.27 (0.31), residues: 727 helix: 2.04 (0.34), residues: 236 sheet: 1.51 (0.37), residues: 214 loop : -0.80 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 94 TYR 0.017 0.002 TYR A 250 PHE 0.014 0.002 PHE A 243 TRP 0.009 0.001 TRP H 100E HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 5598) covalent geometry : angle 0.58376 ( 7669) SS BOND : bond 0.00328 ( 6) SS BOND : angle 0.49855 ( 12) hydrogen bonds : bond 0.04983 ( 313) hydrogen bonds : angle 4.43340 ( 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 57 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.5937 (OUTLIER) cc_final: 0.4873 (t80) REVERT: C 117 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7802 (p) REVERT: H 20 LEU cc_start: 0.5363 (pt) cc_final: 0.5123 (tp) REVERT: H 82 MET cc_start: 0.2463 (OUTLIER) cc_final: 0.2139 (mpp) REVERT: L 145 LYS cc_start: 0.3219 (pttt) cc_final: 0.2118 (mmtm) outliers start: 12 outliers final: 8 residues processed: 54 average time/residue: 0.4044 time to fit residues: 23.2176 Evaluate side-chains 55 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 82 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 51 optimal weight: 8.9990 chunk 6 optimal weight: 0.4980 chunk 7 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 198 HIS ** 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 = 0.4786 r_free = 0.4786 target = 0.244803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.165828 restraints weight = 7128.195| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 3.97 r_work: 0.3835 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5604 Z= 0.130 Angle : 0.539 8.916 7681 Z= 0.283 Chirality : 0.040 0.139 928 Planarity : 0.004 0.036 952 Dihedral : 4.400 37.361 821 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.66 % Allowed : 16.16 % Favored : 81.19 % 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: 1.33 (0.32), residues: 727 helix: 2.18 (0.34), residues: 236 sheet: 1.53 (0.37), residues: 213 loop : -0.82 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 32 TYR 0.015 0.001 TYR A 78 PHE 0.010 0.001 PHE A 254 TRP 0.009 0.001 TRP H 100E HIS 0.001 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5598) covalent geometry : angle 0.53910 ( 7669) SS BOND : bond 0.00278 ( 6) SS BOND : angle 0.42950 ( 12) hydrogen bonds : bond 0.04135 ( 313) hydrogen bonds : angle 4.23205 ( 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 59 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.6025 (OUTLIER) cc_final: 0.4874 (t80) REVERT: C 117 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7811 (p) REVERT: H 20 LEU cc_start: 0.5555 (pt) cc_final: 0.5268 (tp) REVERT: H 82 MET cc_start: 0.2489 (OUTLIER) cc_final: 0.2191 (mpp) REVERT: L 145 LYS cc_start: 0.3354 (pttt) cc_final: 0.2253 (mmtm) outliers start: 13 outliers final: 9 residues processed: 55 average time/residue: 0.3918 time to fit residues: 22.9092 Evaluate side-chains 57 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 82 MET 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: 0.5980 chunk 33 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 0.0000 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 198 HIS ** 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 = 0.4775 r_free = 0.4775 target = 0.243344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.164613 restraints weight = 7091.338| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 3.84 r_work: 0.3824 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5604 Z= 0.154 Angle : 0.556 6.987 7681 Z= 0.294 Chirality : 0.041 0.146 928 Planarity : 0.004 0.036 952 Dihedral : 4.492 38.561 821 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.86 % Allowed : 15.95 % Favored : 81.19 % 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: 1.23 (0.32), residues: 727 helix: 2.07 (0.34), residues: 236 sheet: 1.50 (0.37), residues: 213 loop : -0.88 (0.35), residues: 278 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 0.012 0.001 PHE A 243 TRP 0.009 0.001 TRP H 100E HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 5598) covalent geometry : angle 0.55641 ( 7669) SS BOND : bond 0.00318 ( 6) SS BOND : angle 0.45494 ( 12) hydrogen bonds : bond 0.04591 ( 313) hydrogen bonds : angle 4.33448 ( 894) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2308.94 seconds wall clock time: 39 minutes 52.17 seconds (2392.17 seconds total)