Starting phenix.real_space_refine on Thu Jul 24 06:52:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ul3_26590/07_2025/7ul3_26590.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ul3_26590/07_2025/7ul3_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_2025/7ul3_26590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ul3_26590/07_2025/7ul3_26590.map" model { file = "/net/cci-nas-00/data/ceres_data/7ul3_26590/07_2025/7ul3_26590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ul3_26590/07_2025/7ul3_26590.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 3, 'ARG:plan': 9, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 4} 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: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} 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: {'GLN:plan1': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} 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: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3} 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: 5.29, per 1000 atoms: 0.96 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: 1.62 Conformation dependent library (CDL) restraints added in 720.6 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: 0.79 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: 1.73 Time building geometry restraints manager: 1.86 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: 2.980 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.940 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:14.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.630 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.001 TRP H 100G HIS 0.010 0.002 HIS H 200 PHE 0.019 0.002 PHE A 191 TYR 0.028 0.002 TYR C 81 ARG 0.005 0.001 ARG H 94 Details of bonding type rmsd hydrogen bonds : bond 0.19189 ( 313) hydrogen bonds : angle 7.15023 ( 894) SS BOND : bond 0.00348 ( 6) SS BOND : angle 1.40079 ( 12) covalent geometry : bond 0.00693 ( 5598) covalent geometry : angle 0.87636 ( 7669) *********************** 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 : 0.627 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.6769 time to fit residues: 47.1328 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 : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 0.0670 chunk 67 optimal weight: 20.0000 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.252942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.177655 restraints weight = 7144.586| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 3.84 r_work: 0.4010 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5604 Z= 0.118 Angle : 0.548 6.319 7681 Z= 0.291 Chirality : 0.041 0.138 928 Planarity : 0.005 0.068 952 Dihedral : 4.900 55.074 821 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.25 % Allowed : 8.59 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.31), residues: 727 helix: 2.60 (0.32), residues: 244 sheet: 1.80 (0.36), residues: 206 loop : -0.25 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 275 HIS 0.002 0.001 HIS H 100B PHE 0.012 0.001 PHE H 27 TYR 0.016 0.002 TYR A 78 ARG 0.005 0.001 ARG C 73 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 313) hydrogen bonds : angle 5.02023 ( 894) SS BOND : bond 0.00329 ( 6) SS BOND : angle 0.49827 ( 12) covalent geometry : bond 0.00244 ( 5598) covalent geometry : angle 0.54813 ( 7669) *********************** 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 : 0.547 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 46 average time/residue: 0.6906 time to fit residues: 34.6060 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 : 0.596 ------------------------------------------------------------------------------- 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 103 THR Chi-restraints excluded: chain C residue 120 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 73 optimal weight: 40.0000 chunk 36 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 64 optimal weight: 40.0000 chunk 50 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.246390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.168165 restraints weight = 7120.825| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 3.82 r_work: 0.3899 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5604 Z= 0.158 Angle : 0.571 6.623 7681 Z= 0.304 Chirality : 0.042 0.151 928 Planarity : 0.004 0.055 952 Dihedral : 4.815 44.452 821 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.68 % Allowed : 10.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.31), residues: 727 helix: 2.27 (0.33), residues: 242 sheet: 1.90 (0.36), residues: 199 loop : -0.46 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 275 HIS 0.003 0.001 HIS L 189 PHE 0.018 0.002 PHE H 27 TYR 0.018 0.002 TYR A 94 ARG 0.004 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.04896 ( 313) hydrogen bonds : angle 4.68789 ( 894) SS BOND : bond 0.00250 ( 6) SS BOND : angle 0.54471 ( 12) covalent geometry : bond 0.00355 ( 5598) covalent geometry : angle 0.57105 ( 7669) *********************** 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 : 0.519 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 47 average time/residue: 0.6558 time to fit residues: 33.8810 Evaluate side-chains 42 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain H residue 57 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 3 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4787 r_free = 0.4787 target = 0.243682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.165465 restraints weight = 7219.375| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 3.79 r_work: 0.3844 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5604 Z= 0.172 Angle : 0.563 8.160 7681 Z= 0.299 Chirality : 0.042 0.160 928 Planarity : 0.004 0.047 952 Dihedral : 4.786 40.920 821 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.48 % Allowed : 12.07 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.31), residues: 727 helix: 2.00 (0.33), residues: 242 sheet: 1.92 (0.36), residues: 200 loop : -0.74 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 35 HIS 0.003 0.001 HIS H 35 PHE 0.017 0.002 PHE H 27 TYR 0.017 0.002 TYR A 126 ARG 0.003 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.04880 ( 313) hydrogen bonds : angle 4.62835 ( 894) SS BOND : bond 0.00264 ( 6) SS BOND : angle 0.52532 ( 12) covalent geometry : bond 0.00407 ( 5598) covalent geometry : angle 0.56351 ( 7669) *********************** 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 50 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 0.613 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 44 average time/residue: 0.5603 time to fit residues: 27.7783 Evaluate side-chains 45 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 2 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 65 optimal weight: 30.0000 chunk 68 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN H 35 HIS L 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.244887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.167648 restraints weight = 7058.511| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 3.75 r_work: 0.3900 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5604 Z= 0.129 Angle : 0.512 6.806 7681 Z= 0.268 Chirality : 0.040 0.147 928 Planarity : 0.004 0.040 952 Dihedral : 4.434 36.084 821 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.04 % Allowed : 13.70 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.31), residues: 727 helix: 2.15 (0.33), residues: 242 sheet: 1.64 (0.37), residues: 208 loop : -0.61 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.002 0.001 HIS H 35 PHE 0.015 0.001 PHE H 27 TYR 0.013 0.001 TYR A 94 ARG 0.002 0.000 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 313) hydrogen bonds : angle 4.34977 ( 894) SS BOND : bond 0.00253 ( 6) SS BOND : angle 0.48881 ( 12) covalent geometry : bond 0.00295 ( 5598) covalent geometry : angle 0.51163 ( 7669) *********************** 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: 10 poor density : 38 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 115 ASP cc_start: 0.7974 (t0) cc_final: 0.7753 (t0) REVERT: C 117 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7782 (p) REVERT: H 4 LEU cc_start: 0.4510 (OUTLIER) cc_final: 0.4186 (mt) outliers start: 10 outliers final: 8 residues processed: 46 average time/residue: 0.6017 time to fit residues: 30.5063 Evaluate side-chains 47 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 4 LEU 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 1 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 70 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4791 r_free = 0.4791 target = 0.244166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.166880 restraints weight = 7009.437| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 3.72 r_work: 0.3856 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5604 Z= 0.129 Angle : 0.515 6.593 7681 Z= 0.270 Chirality : 0.040 0.141 928 Planarity : 0.004 0.036 952 Dihedral : 4.411 36.553 821 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.66 % Allowed : 13.09 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.31), residues: 727 helix: 2.19 (0.33), residues: 242 sheet: 1.70 (0.36), residues: 214 loop : -0.65 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.002 0.000 HIS L 189 PHE 0.011 0.001 PHE H 27 TYR 0.015 0.001 TYR A 78 ARG 0.002 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 313) hydrogen bonds : angle 4.29329 ( 894) SS BOND : bond 0.00263 ( 6) SS BOND : angle 0.43256 ( 12) covalent geometry : bond 0.00294 ( 5598) covalent geometry : angle 0.51477 ( 7669) *********************** 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 50 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.6409 (OUTLIER) cc_final: 0.5269 (t80) REVERT: A 115 ASP cc_start: 0.7965 (t0) cc_final: 0.7720 (t0) REVERT: C 117 THR cc_start: 0.8090 (OUTLIER) cc_final: 0.7764 (p) REVERT: H 4 LEU cc_start: 0.4305 (OUTLIER) cc_final: 0.4065 (mt) outliers start: 13 outliers final: 8 residues processed: 46 average time/residue: 0.7114 time to fit residues: 35.7592 Evaluate side-chains 47 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 0.5980 chunk 49 optimal weight: 40.0000 chunk 51 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.4770 r_free = 0.4770 target = 0.241660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.163607 restraints weight = 6978.288| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 3.71 r_work: 0.3827 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5604 Z= 0.186 Angle : 0.574 6.311 7681 Z= 0.306 Chirality : 0.042 0.150 928 Planarity : 0.004 0.035 952 Dihedral : 4.713 40.522 821 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.07 % Allowed : 13.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.31), residues: 727 helix: 1.89 (0.33), residues: 242 sheet: 1.54 (0.36), residues: 214 loop : -0.82 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.015 0.002 PHE H 27 TYR 0.017 0.002 TYR A 250 ARG 0.002 0.000 ARG H 94 Details of bonding type rmsd hydrogen bonds : bond 0.05163 ( 313) hydrogen bonds : angle 4.55477 ( 894) SS BOND : bond 0.00329 ( 6) SS BOND : angle 0.53358 ( 12) covalent geometry : bond 0.00445 ( 5598) covalent geometry : angle 0.57432 ( 7669) *********************** 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 54 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.6140 (OUTLIER) cc_final: 0.5035 (t80) REVERT: A 115 ASP cc_start: 0.7722 (t0) cc_final: 0.7417 (t0) REVERT: C 117 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7818 (p) outliers start: 15 outliers final: 11 residues processed: 51 average time/residue: 0.6414 time to fit residues: 35.9064 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 : 0.589 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 53 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4787 r_free = 0.4787 target = 0.243844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.166217 restraints weight = 7035.212| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 3.77 r_work: 0.3854 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5604 Z= 0.125 Angle : 0.511 6.214 7681 Z= 0.269 Chirality : 0.040 0.140 928 Planarity : 0.004 0.035 952 Dihedral : 4.433 37.291 821 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.86 % Allowed : 13.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.31), residues: 727 helix: 2.12 (0.34), residues: 242 sheet: 1.60 (0.37), residues: 214 loop : -0.79 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.001 0.000 HIS L 189 PHE 0.012 0.001 PHE H 27 TYR 0.015 0.001 TYR A 78 ARG 0.002 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 313) hydrogen bonds : angle 4.29855 ( 894) SS BOND : bond 0.00274 ( 6) SS BOND : angle 0.48184 ( 12) covalent geometry : bond 0.00282 ( 5598) covalent geometry : angle 0.51110 ( 7669) *********************** 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 53 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.6409 (OUTLIER) cc_final: 0.5152 (t80) REVERT: A 115 ASP cc_start: 0.7952 (t0) cc_final: 0.7689 (t0) REVERT: C 32 ARG cc_start: 0.8185 (ttp80) cc_final: 0.7916 (ttp80) REVERT: C 117 THR cc_start: 0.8141 (OUTLIER) cc_final: 0.7832 (p) outliers start: 14 outliers final: 10 residues processed: 49 average time/residue: 0.7039 time to fit residues: 37.7463 Evaluate side-chains 51 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 0.0570 chunk 38 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.4788 r_free = 0.4788 target = 0.243948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.166467 restraints weight = 7028.109| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 3.77 r_work: 0.3855 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5604 Z= 0.124 Angle : 0.510 7.201 7681 Z= 0.267 Chirality : 0.040 0.140 928 Planarity : 0.004 0.035 952 Dihedral : 4.322 36.320 821 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.45 % Allowed : 14.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.31), residues: 727 helix: 2.21 (0.33), residues: 242 sheet: 1.56 (0.36), residues: 214 loop : -0.75 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 275 HIS 0.001 0.000 HIS L 189 PHE 0.010 0.001 PHE A 243 TYR 0.014 0.001 TYR A 250 ARG 0.002 0.000 ARG H 94 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 313) hydrogen bonds : angle 4.21154 ( 894) SS BOND : bond 0.00272 ( 6) SS BOND : angle 0.43409 ( 12) covalent geometry : bond 0.00282 ( 5598) covalent geometry : angle 0.51016 ( 7669) *********************** 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 51 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.6266 (OUTLIER) cc_final: 0.5123 (t80) REVERT: A 115 ASP cc_start: 0.7838 (t0) cc_final: 0.7591 (t0) REVERT: C 117 THR cc_start: 0.8125 (OUTLIER) cc_final: 0.7804 (p) outliers start: 12 outliers final: 9 residues processed: 48 average time/residue: 0.6911 time to fit residues: 36.2937 Evaluate side-chains 50 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 73 optimal weight: 50.0000 chunk 22 optimal weight: 0.0770 chunk 60 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.244645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.166738 restraints weight = 7108.672| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 3.81 r_work: 0.3853 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.4319 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= 0.125 Angle : 0.510 6.994 7681 Z= 0.267 Chirality : 0.040 0.141 928 Planarity : 0.004 0.035 952 Dihedral : 4.333 36.753 821 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.86 % Allowed : 14.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.31), residues: 727 helix: 2.24 (0.33), residues: 242 sheet: 1.55 (0.36), residues: 214 loop : -0.71 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.001 0.000 HIS L 189 PHE 0.010 0.001 PHE A 243 TYR 0.017 0.001 TYR A 78 ARG 0.002 0.000 ARG C 32 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 313) hydrogen bonds : angle 4.20154 ( 894) SS BOND : bond 0.00273 ( 6) SS BOND : angle 0.45275 ( 12) covalent geometry : bond 0.00286 ( 5598) covalent geometry : angle 0.51031 ( 7669) ********************** 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: 14 poor density : 39 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.6141 (OUTLIER) cc_final: 0.5027 (t80) REVERT: A 115 ASP cc_start: 0.7774 (t0) cc_final: 0.7498 (t0) REVERT: C 117 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7792 (p) outliers start: 14 outliers final: 11 residues processed: 49 average time/residue: 0.6514 time to fit residues: 35.0454 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 : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR 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 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 68 optimal weight: 7.9990 chunk 61 optimal weight: 0.0670 chunk 38 optimal weight: 20.0000 chunk 2 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 62 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.4808 r_free = 0.4808 target = 0.245566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.168175 restraints weight = 7095.955| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 3.84 r_work: 0.3867 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5604 Z= 0.112 Angle : 0.497 6.775 7681 Z= 0.258 Chirality : 0.039 0.136 928 Planarity : 0.004 0.036 952 Dihedral : 4.211 35.533 821 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.66 % Allowed : 14.72 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.32), residues: 727 helix: 2.34 (0.33), residues: 242 sheet: 1.58 (0.36), residues: 214 loop : -0.65 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.001 0.000 HIS H 35 PHE 0.010 0.001 PHE A 254 TYR 0.012 0.001 TYR A 250 ARG 0.002 0.000 ARG H 94 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 313) hydrogen bonds : angle 4.09708 ( 894) SS BOND : bond 0.00265 ( 6) SS BOND : angle 0.43436 ( 12) covalent geometry : bond 0.00249 ( 5598) covalent geometry : angle 0.49678 ( 7669) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4609.71 seconds wall clock time: 79 minutes 13.12 seconds (4753.12 seconds total)