Starting phenix.real_space_refine on Tue Feb 11 11:49:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ul3_26590/02_2025/7ul3_26590.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ul3_26590/02_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_26590/02_2025/7ul3_26590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ul3_26590/02_2025/7ul3_26590.map" model { file = "/net/cci-nas-00/data/ceres_data/7ul3_26590/02_2025/7ul3_26590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ul3_26590/02_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-5592/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: 4.48, per 1000 atoms: 0.82 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: 1.68 Conformation dependent library (CDL) restraints added in 662.2 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: 0.70 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: 1.52 Time building geometry restraints manager: 1.62 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: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.190 Find NCS groups from input model: 0.060 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:14.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.750 ------------------------------------------------------------------------------- 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 5598 Z= 0.496 Angle : 0.876 17.894 7669 Z= 0.482 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 *********************** 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 : 0.580 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.6862 time to fit residues: 47.6311 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 : 0.611 ------------------------------------------------------------------------------- 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: 5.9990 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 = 72)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.177652 restraints weight = 7144.586| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 3.84 r_work: 0.4010 rms_B_bonded: 4.31 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 5598 Z= 0.162 Angle : 0.548 6.319 7669 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 *********************** 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 : 0.601 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 46 average time/residue: 0.7560 time to fit residues: 37.7246 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 : 0.485 ------------------------------------------------------------------------------- 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: 30.0000 chunk 63 optimal weight: 0.9990 chunk 64 optimal weight: 0.0170 chunk 50 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 = 0.4816 r_free = 0.4816 target = 0.248608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.171125 restraints weight = 7143.800| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 3.82 r_work: 0.3930 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5598 Z= 0.184 Angle : 0.530 7.107 7669 Z= 0.280 Chirality : 0.041 0.144 928 Planarity : 0.004 0.054 952 Dihedral : 4.575 42.217 821 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.48 % Allowed : 10.63 % Favored : 85.89 % 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: 1.91 (0.31), residues: 727 helix: 2.46 (0.33), residues: 243 sheet: 1.93 (0.34), residues: 207 loop : -0.40 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 275 HIS 0.002 0.001 HIS L 189 PHE 0.015 0.001 PHE H 27 TYR 0.016 0.002 TYR A 94 ARG 0.002 0.000 ARG C 68 *********************** 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 55 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 0.591 Fit side-chains REVERT: C 36 MET cc_start: 0.7162 (mmm) cc_final: 0.6961 (mmm) outliers start: 17 outliers final: 7 residues processed: 47 average time/residue: 0.5824 time to fit residues: 30.6018 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 : 0.584 ------------------------------------------------------------------------------- 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: 0.9980 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 50.0000 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN L 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.245253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.166891 restraints weight = 7226.731| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 3.86 r_work: 0.3848 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5598 Z= 0.248 Angle : 0.550 5.551 7669 Z= 0.294 Chirality : 0.042 0.163 928 Planarity : 0.004 0.046 952 Dihedral : 4.698 40.572 821 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.27 % Allowed : 11.45 % Favored : 85.28 % 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: 1.58 (0.31), residues: 727 helix: 2.17 (0.33), residues: 242 sheet: 1.95 (0.36), residues: 200 loop : -0.66 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 35 HIS 0.003 0.001 HIS H 35 PHE 0.017 0.002 PHE H 27 TYR 0.016 0.002 TYR A 94 ARG 0.002 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.536 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 45 average time/residue: 0.6159 time to fit residues: 30.6166 Evaluate side-chains 46 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 43 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 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 = 0.4803 r_free = 0.4803 target = 0.245476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.168626 restraints weight = 7072.497| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 3.76 r_work: 0.3850 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5598 Z= 0.178 Angle : 0.495 5.462 7669 Z= 0.261 Chirality : 0.040 0.142 928 Planarity : 0.004 0.041 952 Dihedral : 4.377 36.095 821 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.25 % Allowed : 13.91 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.69 (0.31), residues: 727 helix: 2.32 (0.33), residues: 242 sheet: 2.01 (0.37), residues: 201 loop : -0.66 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.002 0.001 HIS L 189 PHE 0.013 0.001 PHE H 27 TYR 0.013 0.001 TYR A 94 ARG 0.001 0.000 ARG A 230 *********************** 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: 11 poor density : 37 time to evaluate : 0.614 Fit side-chains REVERT: A 115 ASP cc_start: 0.7507 (t0) cc_final: 0.7249 (t0) REVERT: C 117 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7720 (p) REVERT: H 20 LEU cc_start: 0.5536 (pt) cc_final: 0.5288 (tp) outliers start: 11 outliers final: 7 residues processed: 45 average time/residue: 0.5942 time to fit residues: 29.6695 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 : 0.559 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 70 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.244674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.167190 restraints weight = 7046.238| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 3.77 r_work: 0.3892 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5598 Z= 0.192 Angle : 0.505 5.513 7669 Z= 0.266 Chirality : 0.040 0.143 928 Planarity : 0.004 0.037 952 Dihedral : 4.388 36.504 821 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.45 % Allowed : 13.50 % Favored : 84.05 % 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: 1.64 (0.31), residues: 727 helix: 2.28 (0.33), residues: 242 sheet: 1.71 (0.37), residues: 208 loop : -0.52 (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 0.016 0.001 TYR A 78 ARG 0.002 0.000 ARG C 68 *********************** 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 49 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.547 Fit side-chains REVERT: A 115 ASP cc_start: 0.7986 (t0) cc_final: 0.7734 (OUTLIER) REVERT: C 117 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7793 (p) REVERT: H 4 LEU cc_start: 0.4446 (OUTLIER) cc_final: 0.4124 (mt) REVERT: H 20 LEU cc_start: 0.5610 (pt) cc_final: 0.5316 (tp) outliers start: 12 outliers final: 8 residues processed: 45 average time/residue: 0.6268 time to fit residues: 31.1334 Evaluate side-chains 46 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 49 optimal weight: 40.0000 chunk 51 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 30.0000 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 37 GLN L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.242101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.163131 restraints weight = 6975.563| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 3.77 r_work: 0.3811 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5598 Z= 0.329 Angle : 0.595 5.655 7669 Z= 0.319 Chirality : 0.043 0.154 928 Planarity : 0.004 0.037 952 Dihedral : 4.812 42.020 821 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.07 % Allowed : 13.29 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.25 (0.31), residues: 727 helix: 1.87 (0.33), residues: 242 sheet: 1.54 (0.36), residues: 214 loop : -0.74 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 35 HIS 0.003 0.001 HIS H 35 PHE 0.015 0.002 PHE H 27 TYR 0.019 0.002 TYR A 250 ARG 0.002 0.000 ARG H 94 *********************** 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 : 0.523 Fit side-chains REVERT: A 94 TYR cc_start: 0.6487 (OUTLIER) cc_final: 0.5349 (t80) REVERT: A 115 ASP cc_start: 0.7917 (t0) cc_final: 0.7694 (t0) REVERT: H 3 GLN cc_start: 0.6800 (pm20) cc_final: 0.6226 (mm-40) REVERT: H 20 LEU cc_start: 0.5588 (pt) cc_final: 0.5328 (tp) outliers start: 15 outliers final: 12 residues processed: 50 average time/residue: 0.7036 time to fit residues: 38.3632 Evaluate side-chains 51 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 7 optimal weight: 0.1980 chunk 53 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 59 optimal weight: 0.0970 chunk 29 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.4795 r_free = 0.4795 target = 0.244939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.168258 restraints weight = 7054.667| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 3.73 r_work: 0.3880 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5598 Z= 0.146 Angle : 0.480 5.408 7669 Z= 0.252 Chirality : 0.039 0.135 928 Planarity : 0.004 0.034 952 Dihedral : 4.276 35.102 821 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.86 % Allowed : 14.72 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.29 (0.33), residues: 242 sheet: 1.67 (0.37), residues: 214 loop : -0.69 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 143 HIS 0.001 0.000 HIS L 189 PHE 0.010 0.001 PHE A 254 TYR 0.015 0.001 TYR A 78 ARG 0.002 0.000 ARG H 94 *********************** 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 54 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.523 Fit side-chains REVERT: A 115 ASP cc_start: 0.7988 (t0) cc_final: 0.7783 (t0) REVERT: C 117 THR cc_start: 0.8090 (OUTLIER) cc_final: 0.7777 (p) REVERT: H 4 LEU cc_start: 0.4455 (OUTLIER) cc_final: 0.4230 (mt) REVERT: H 20 LEU cc_start: 0.5541 (pt) cc_final: 0.5304 (tp) outliers start: 14 outliers final: 8 residues processed: 49 average time/residue: 0.6932 time to fit residues: 37.1198 Evaluate side-chains 49 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4769 r_free = 0.4769 target = 0.241755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.163768 restraints weight = 7007.731| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 3.70 r_work: 0.3839 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5598 Z= 0.271 Angle : 0.559 6.921 7669 Z= 0.298 Chirality : 0.042 0.151 928 Planarity : 0.004 0.035 952 Dihedral : 4.602 40.300 821 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.86 % Allowed : 15.13 % Favored : 82.00 % 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: 1.26 (0.31), residues: 727 helix: 2.00 (0.34), residues: 236 sheet: 1.54 (0.37), residues: 214 loop : -0.81 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 275 HIS 0.002 0.001 HIS H 35 PHE 0.014 0.002 PHE H 27 TYR 0.017 0.002 TYR A 250 ARG 0.002 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1454 Ramachandran restraints generated. 727 Oldfield, 0 Emsley, 727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.556 Fit side-chains REVERT: A 94 TYR cc_start: 0.6396 (OUTLIER) cc_final: 0.5294 (t80) REVERT: A 115 ASP cc_start: 0.7879 (t0) cc_final: 0.7597 (t0) REVERT: C 32 ARG cc_start: 0.8166 (ttp80) cc_final: 0.7836 (ttp80) REVERT: C 117 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7847 (p) REVERT: H 4 LEU cc_start: 0.4224 (OUTLIER) cc_final: 0.4012 (mt) REVERT: H 20 LEU cc_start: 0.5641 (pt) cc_final: 0.5357 (tp) outliers start: 14 outliers final: 9 residues processed: 49 average time/residue: 0.6972 time to fit residues: 37.3521 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 : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 33 VAL 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: 0.0670 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 73 optimal weight: 50.0000 chunk 22 optimal weight: 0.0170 chunk 60 optimal weight: 0.8980 overall best weight: 0.5556 ------------------------------------------------------------------------------- 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 = 0.4791 r_free = 0.4791 target = 0.244446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.167582 restraints weight = 7074.769| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 3.73 r_work: 0.3871 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5598 Z= 0.168 Angle : 0.497 7.790 7669 Z= 0.261 Chirality : 0.039 0.135 928 Planarity : 0.004 0.036 952 Dihedral : 4.284 35.898 821 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.45 % Allowed : 15.54 % Favored : 82.00 % 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: 1.52 (0.32), residues: 727 helix: 2.25 (0.33), residues: 242 sheet: 1.62 (0.37), residues: 214 loop : -0.70 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 143 HIS 0.001 0.000 HIS L 189 PHE 0.011 0.001 PHE A 254 TYR 0.015 0.001 TYR A 78 ARG 0.001 0.000 ARG C 32 ********************** 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 51 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.538 Fit side-chains REVERT: A 115 ASP cc_start: 0.7985 (t0) cc_final: 0.7777 (t0) REVERT: C 117 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7800 (p) REVERT: H 4 LEU cc_start: 0.4337 (OUTLIER) cc_final: 0.4080 (mt) REVERT: H 20 LEU cc_start: 0.5571 (pt) cc_final: 0.5325 (tp) outliers start: 12 outliers final: 9 residues processed: 47 average time/residue: 0.7129 time to fit residues: 36.5201 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 : 0.624 ------------------------------------------------------------------------------- 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 4 LEU 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 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 68 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 0.0040 chunk 42 optimal weight: 0.0270 chunk 69 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 73 optimal weight: 30.0000 chunk 62 optimal weight: 0.6980 overall best weight: 0.4650 ------------------------------------------------------------------------------- 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 = 0.4799 r_free = 0.4799 target = 0.245375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.168332 restraints weight = 7079.022| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.79 r_work: 0.3882 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5598 Z= 0.151 Angle : 0.483 6.582 7669 Z= 0.252 Chirality : 0.039 0.136 928 Planarity : 0.004 0.035 952 Dihedral : 4.095 34.096 821 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.45 % Allowed : 15.34 % Favored : 82.21 % 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: 1.69 (0.32), residues: 727 helix: 2.43 (0.33), residues: 242 sheet: 1.68 (0.37), residues: 214 loop : -0.60 (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 L 189 PHE 0.010 0.001 PHE A 254 TYR 0.012 0.001 TYR A 250 ARG 0.001 0.000 ARG H 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4298.90 seconds wall clock time: 76 minutes 19.56 seconds (4579.56 seconds total)