Starting phenix.real_space_refine on Thu Mar 6 08:28:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hc8_34655/03_2025/8hc8_34655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hc8_34655/03_2025/8hc8_34655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hc8_34655/03_2025/8hc8_34655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hc8_34655/03_2025/8hc8_34655.map" model { file = "/net/cci-nas-00/data/ceres_data/8hc8_34655/03_2025/8hc8_34655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hc8_34655/03_2025/8hc8_34655.cif" } resolution = 3.95 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= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 809 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 3056 2.51 5 N 811 2.21 5 O 943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4832 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1508 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain: "H" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1734 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 220} Chain: "L" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1576 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.64, per 1000 atoms: 0.75 Number of scatterers: 4832 At special positions: 0 Unit cell: (80.85, 90.75, 113.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 943 8.00 N 811 7.00 C 3056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 111 " - pdb=" SG CYS H 116 " distance=2.03 Simple disulfide: pdb=" SG CYS H 161 " - pdb=" SG CYS H 217 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 601.7 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 14 sheets defined 7.0% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.833A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.526A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.885A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'H' and resid 78 through 80 No H-bonds generated for 'chain 'H' and resid 78 through 80' Processing helix chain 'H' and resid 177 through 179 No H-bonds generated for 'chain 'H' and resid 177 through 179' Processing helix chain 'H' and resid 208 through 210 No H-bonds generated for 'chain 'H' and resid 208 through 210' Processing helix chain 'L' and resid 126 through 131 removed outlier: 3.753A pdb=" N LYS L 131 " --> pdb=" O ASP L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 193 removed outlier: 3.679A pdb=" N LYS L 193 " --> pdb=" O ALA L 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.727A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.244A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.508A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU H 20 " --> pdb=" O LEU H 85 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER H 82 " --> pdb=" O ASP H 77 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER H 75 " --> pdb=" O PHE H 84 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR H 73 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.563A pdb=" N TYR H 98 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL H 130 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA H 96 " --> pdb=" O VAL H 130 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN H 35 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.563A pdb=" N TYR H 98 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL H 130 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA H 96 " --> pdb=" O VAL H 130 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG H 102 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU H 123 " --> pdb=" O ARG H 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 141 through 144 removed outlier: 3.546A pdb=" N SER H 141 " --> pdb=" O LYS H 164 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU H 162 " --> pdb=" O PHE H 143 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL H 205 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU H 159 " --> pdb=" O VAL H 203 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP H 165 " --> pdb=" O TYR H 197 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR H 197 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL H 202 " --> pdb=" O HIS H 185 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 141 through 144 removed outlier: 3.546A pdb=" N SER H 141 " --> pdb=" O LYS H 164 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU H 162 " --> pdb=" O PHE H 143 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL H 205 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU H 159 " --> pdb=" O VAL H 203 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP H 165 " --> pdb=" O TYR H 197 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR H 197 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER H 198 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL H 190 " --> pdb=" O SER H 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 172 through 175 removed outlier: 3.706A pdb=" N CYS H 217 " --> pdb=" O LYS H 230 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS H 230 " --> pdb=" O CYS H 217 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 219 " --> pdb=" O VAL H 228 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL H 228 " --> pdb=" O VAL H 219 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS H 221 " --> pdb=" O THR H 226 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 226 " --> pdb=" O HIS H 221 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.897A pdb=" N CYS L 23 " --> pdb=" O PHE L 76 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE L 76 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER L 70 " --> pdb=" O THR L 77 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AB3, first strand: chain 'L' and resid 50 through 53 removed outlier: 5.748A pdb=" N LEU L 51 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU L 42 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE L 53 " --> pdb=" O TRP L 40 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL L 90 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 121 through 123 removed outlier: 3.555A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER L 182 " --> pdb=" O CYS L 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 152 through 155 removed outlier: 3.861A pdb=" N GLN L 152 " --> pdb=" O GLU L 200 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS L 212 " --> pdb=" O CYS L 199 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL L 201 " --> pdb=" O VAL L 210 " (cutoff:3.500A) 92 hydrogen bonds defined for protein. 237 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: 1.22 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1552 1.35 - 1.46: 1248 1.46 - 1.58: 2124 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 4950 Sorted by residual: bond pdb=" C ALA C 372 " pdb=" N PRO C 373 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.23e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.47e+00 bond pdb=" CB PRO H 144 " pdb=" CG PRO H 144 " ideal model delta sigma weight residual 1.492 1.562 -0.070 5.00e-02 4.00e+02 1.96e+00 bond pdb=" CB GLU L 200 " pdb=" CG GLU L 200 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.73e+00 ... (remaining 4945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 6581 1.97 - 3.93: 128 3.93 - 5.90: 20 5.90 - 7.86: 9 7.86 - 9.83: 5 Bond angle restraints: 6743 Sorted by residual: angle pdb=" C TYR L 145 " pdb=" N PRO L 146 " pdb=" CA PRO L 146 " ideal model delta sigma weight residual 119.84 115.17 4.67 1.25e+00 6.40e-01 1.39e+01 angle pdb=" C PHE C 377 " pdb=" N LYS C 378 " pdb=" CA LYS C 378 " ideal model delta sigma weight residual 122.46 127.37 -4.91 1.41e+00 5.03e-01 1.21e+01 angle pdb=" CA PRO H 144 " pdb=" N PRO H 144 " pdb=" CD PRO H 144 " ideal model delta sigma weight residual 112.00 107.57 4.43 1.40e+00 5.10e-01 1.00e+01 angle pdb=" C SER C 359 " pdb=" N ASN C 360 " pdb=" CA ASN C 360 " ideal model delta sigma weight residual 122.46 126.85 -4.39 1.41e+00 5.03e-01 9.69e+00 angle pdb=" N ILE L 111 " pdb=" CA ILE L 111 " pdb=" C ILE L 111 " ideal model delta sigma weight residual 109.12 113.87 -4.75 1.58e+00 4.01e-01 9.05e+00 ... (remaining 6738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 2518 17.19 - 34.39: 332 34.39 - 51.58: 97 51.58 - 68.77: 10 68.77 - 85.97: 5 Dihedral angle restraints: 2962 sinusoidal: 1137 harmonic: 1825 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -32.64 -53.36 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 100 " pdb=" CB CYS H 100 " ideal model delta sinusoidal sigma weight residual -86.00 -126.30 40.30 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA LEU L 141 " pdb=" C LEU L 141 " pdb=" N ASN L 142 " pdb=" CA ASN L 142 " ideal model delta harmonic sigma weight residual -180.00 -162.58 -17.42 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 2959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 481 0.037 - 0.074: 184 0.074 - 0.111: 70 0.111 - 0.148: 14 0.148 - 0.185: 5 Chirality restraints: 754 Sorted by residual: chirality pdb=" CA THR L 99 " pdb=" N THR L 99 " pdb=" C THR L 99 " pdb=" CB THR L 99 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CG LEU L 186 " pdb=" CB LEU L 186 " pdb=" CD1 LEU L 186 " pdb=" CD2 LEU L 186 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CB ILE H 216 " pdb=" CA ILE H 216 " pdb=" CG1 ILE H 216 " pdb=" CG2 ILE H 216 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.25e-01 ... (remaining 751 not shown) Planarity restraints: 872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 134 " 0.027 2.00e-02 2.50e+03 5.30e-02 2.81e+01 pdb=" C SER H 134 " -0.092 2.00e-02 2.50e+03 pdb=" O SER H 134 " 0.034 2.00e-02 2.50e+03 pdb=" N ALA H 135 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE H 143 " -0.082 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO H 144 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO H 144 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO H 144 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 369 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C TYR C 369 " 0.056 2.00e-02 2.50e+03 pdb=" O TYR C 369 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN C 370 " -0.019 2.00e-02 2.50e+03 ... (remaining 869 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1580 2.83 - 3.35: 3756 3.35 - 3.87: 7648 3.87 - 4.38: 7956 4.38 - 4.90: 14303 Nonbonded interactions: 35243 Sorted by model distance: nonbonded pdb=" OG1 THR C 430 " pdb=" O PHE C 515 " model vdw 2.317 3.040 nonbonded pdb=" OG SER L 70 " pdb=" O THR L 77 " model vdw 2.371 3.040 nonbonded pdb=" OG SER L 187 " pdb=" OD2 ASP L 190 " model vdw 2.375 3.040 nonbonded pdb=" OH TYR H 63 " pdb=" O THR H 112 " model vdw 2.410 3.040 nonbonded pdb=" N ASN C 354 " pdb=" OD1 ASN C 354 " model vdw 2.415 3.120 ... (remaining 35238 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.970 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 4950 Z= 0.207 Angle : 0.712 9.829 6743 Z= 0.363 Chirality : 0.046 0.185 754 Planarity : 0.007 0.122 871 Dihedral : 16.598 85.966 1772 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.56 % Allowed : 33.02 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.17 (0.32), residues: 620 helix: -4.33 (0.50), residues: 20 sheet: 1.02 (0.43), residues: 161 loop : -1.42 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 175 HIS 0.002 0.001 HIS L 203 PHE 0.023 0.001 PHE C 456 TYR 0.031 0.001 TYR H 215 ARG 0.002 0.000 ARG L 113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.519 Fit side-chains REVERT: H 129 MET cc_start: 0.7128 (mmm) cc_final: 0.6401 (ppp) REVERT: H 177 SER cc_start: 0.6814 (m) cc_final: 0.6313 (t) outliers start: 3 outliers final: 1 residues processed: 82 average time/residue: 0.1430 time to fit residues: 15.6789 Evaluate side-chains 74 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 210 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 HIS H 218 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 GLN L 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.186616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.159398 restraints weight = 63119.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.160995 restraints weight = 38824.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.160043 restraints weight = 33600.655| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4950 Z= 0.418 Angle : 0.726 9.736 6743 Z= 0.374 Chirality : 0.047 0.171 754 Planarity : 0.006 0.078 871 Dihedral : 4.804 26.633 708 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 6.86 % Allowed : 26.72 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.48 (0.32), residues: 620 helix: -4.36 (0.43), residues: 41 sheet: 0.73 (0.42), residues: 160 loop : -1.41 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 436 HIS 0.003 0.001 HIS L 203 PHE 0.020 0.003 PHE H 121 TYR 0.038 0.003 TYR L 101 ARG 0.004 0.001 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.535 Fit side-chains REVERT: C 332 ILE cc_start: 0.6276 (OUTLIER) cc_final: 0.6041 (tt) REVERT: C 378 LYS cc_start: 0.8614 (pttt) cc_final: 0.8255 (pttt) REVERT: H 113 SER cc_start: 0.7968 (OUTLIER) cc_final: 0.7668 (p) REVERT: H 123 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8976 (tt) REVERT: L 138 VAL cc_start: 0.6707 (t) cc_final: 0.6473 (m) REVERT: L 154 LYS cc_start: 0.8687 (ptmt) cc_final: 0.8132 (pttm) outliers start: 37 outliers final: 22 residues processed: 107 average time/residue: 0.1613 time to fit residues: 22.2478 Evaluate side-chains 95 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 210 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 15 optimal weight: 0.0980 chunk 55 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 0.0770 chunk 54 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.192831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.165415 restraints weight = 63612.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.168107 restraints weight = 38189.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.166277 restraints weight = 32698.360| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4950 Z= 0.166 Angle : 0.542 6.982 6743 Z= 0.270 Chirality : 0.042 0.143 754 Planarity : 0.004 0.064 871 Dihedral : 3.887 18.614 708 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.75 % Allowed : 27.46 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.20 (0.32), residues: 620 helix: -4.27 (0.49), residues: 38 sheet: 0.77 (0.42), residues: 162 loop : -1.17 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.002 0.001 HIS C 505 PHE 0.010 0.001 PHE C 342 TYR 0.008 0.001 TYR L 101 ARG 0.004 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.504 Fit side-chains REVERT: H 215 TYR cc_start: 0.5016 (m-10) cc_final: 0.4787 (m-10) REVERT: L 138 VAL cc_start: 0.6944 (t) cc_final: 0.6649 (m) REVERT: L 154 LYS cc_start: 0.8595 (ptmt) cc_final: 0.8090 (pttt) outliers start: 31 outliers final: 19 residues processed: 103 average time/residue: 0.1434 time to fit residues: 19.7655 Evaluate side-chains 89 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.0470 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 218 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.182342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.172550 restraints weight = 6285.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.171788 restraints weight = 16641.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.171376 restraints weight = 16731.841| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4950 Z= 0.193 Angle : 0.548 7.433 6743 Z= 0.273 Chirality : 0.043 0.168 754 Planarity : 0.004 0.055 871 Dihedral : 3.754 18.710 707 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.68 % Allowed : 27.27 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.16 (0.32), residues: 620 helix: -4.17 (0.53), residues: 38 sheet: 0.72 (0.41), residues: 162 loop : -1.10 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 153 HIS 0.001 0.000 HIS L 203 PHE 0.011 0.001 PHE C 342 TYR 0.009 0.001 TYR L 101 ARG 0.004 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.500 Fit side-chains REVERT: H 215 TYR cc_start: 0.4711 (m-10) cc_final: 0.4456 (m-10) outliers start: 36 outliers final: 24 residues processed: 102 average time/residue: 0.1594 time to fit residues: 21.1880 Evaluate side-chains 95 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 13 optimal weight: 0.3980 chunk 37 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 HIS H 218 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.189614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.183159 restraints weight = 6308.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.164352 restraints weight = 13463.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.161629 restraints weight = 13292.195| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4950 Z= 0.178 Angle : 0.539 7.159 6743 Z= 0.269 Chirality : 0.042 0.162 754 Planarity : 0.004 0.049 871 Dihedral : 3.655 17.696 707 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 7.42 % Allowed : 26.53 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.05 (0.32), residues: 620 helix: -3.68 (0.76), residues: 26 sheet: 0.72 (0.41), residues: 159 loop : -1.12 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 153 HIS 0.001 0.000 HIS L 203 PHE 0.010 0.001 PHE C 342 TYR 0.008 0.001 TYR L 101 ARG 0.004 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 75 time to evaluate : 0.524 Fit side-chains REVERT: H 123 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8929 (tt) REVERT: H 215 TYR cc_start: 0.5554 (m-10) cc_final: 0.5153 (m-10) outliers start: 40 outliers final: 27 residues processed: 106 average time/residue: 0.1509 time to fit residues: 21.0090 Evaluate side-chains 102 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 42 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 HIS H 218 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.179546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.170163 restraints weight = 6414.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.169089 restraints weight = 16063.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.154691 restraints weight = 12620.948| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4950 Z= 0.198 Angle : 0.550 7.277 6743 Z= 0.275 Chirality : 0.043 0.175 754 Planarity : 0.004 0.047 871 Dihedral : 3.690 18.492 707 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 8.91 % Allowed : 25.23 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.14 (0.32), residues: 620 helix: -3.61 (0.76), residues: 27 sheet: 0.57 (0.41), residues: 165 loop : -1.17 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.001 0.000 HIS H 185 PHE 0.011 0.001 PHE C 342 TYR 0.011 0.001 TYR L 101 ARG 0.005 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 80 time to evaluate : 0.496 Fit side-chains REVERT: C 355 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8443 (ttm-80) REVERT: H 123 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8959 (tt) REVERT: H 215 TYR cc_start: 0.5678 (m-80) cc_final: 0.5221 (m-10) outliers start: 48 outliers final: 32 residues processed: 119 average time/residue: 0.1662 time to fit residues: 25.2666 Evaluate side-chains 111 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.0030 chunk 54 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 HIS H 218 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.188861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.182166 restraints weight = 6341.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.163416 restraints weight = 13217.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.160459 restraints weight = 12600.280| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4950 Z= 0.177 Angle : 0.547 7.486 6743 Z= 0.273 Chirality : 0.043 0.179 754 Planarity : 0.004 0.046 871 Dihedral : 3.661 18.007 707 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 7.61 % Allowed : 26.16 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.20 (0.33), residues: 620 helix: -3.89 (0.56), residues: 39 sheet: 0.55 (0.41), residues: 162 loop : -1.08 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.001 0.000 HIS H 221 PHE 0.010 0.001 PHE C 342 TYR 0.011 0.001 TYR L 91 ARG 0.005 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 79 time to evaluate : 0.552 Fit side-chains REVERT: H 123 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8880 (tt) REVERT: H 215 TYR cc_start: 0.5722 (m-80) cc_final: 0.5249 (m-10) outliers start: 41 outliers final: 31 residues processed: 113 average time/residue: 0.1739 time to fit residues: 25.1010 Evaluate side-chains 109 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 59 optimal weight: 7.9990 chunk 8 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 HIS H 218 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.184754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.177113 restraints weight = 6359.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.176532 restraints weight = 16821.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.158502 restraints weight = 14968.355| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4950 Z= 0.270 Angle : 0.602 8.224 6743 Z= 0.305 Chirality : 0.044 0.198 754 Planarity : 0.004 0.045 871 Dihedral : 4.053 19.955 707 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 7.79 % Allowed : 25.97 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.32), residues: 620 helix: -3.82 (0.57), residues: 40 sheet: 0.42 (0.40), residues: 165 loop : -1.25 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 153 HIS 0.001 0.000 HIS C 505 PHE 0.014 0.002 PHE L 103 TYR 0.015 0.002 TYR L 101 ARG 0.007 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 77 time to evaluate : 0.503 Fit side-chains REVERT: C 355 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8734 (ttm-80) REVERT: C 378 LYS cc_start: 0.8640 (pttt) cc_final: 0.8067 (pttp) REVERT: C 392 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7853 (p90) REVERT: H 123 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9088 (tt) REVERT: H 215 TYR cc_start: 0.6078 (m-80) cc_final: 0.5632 (m-10) outliers start: 42 outliers final: 32 residues processed: 114 average time/residue: 0.1714 time to fit residues: 24.7785 Evaluate side-chains 106 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 71 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 0.0470 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 0.1980 chunk 22 optimal weight: 0.0770 chunk 32 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 HIS H 218 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.180050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.171373 restraints weight = 6330.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.170201 restraints weight = 16292.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.156978 restraints weight = 15432.235| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4950 Z= 0.150 Angle : 0.545 7.223 6743 Z= 0.271 Chirality : 0.043 0.205 754 Planarity : 0.004 0.047 871 Dihedral : 3.672 18.734 707 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 5.01 % Allowed : 28.76 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.32), residues: 620 helix: -3.76 (0.57), residues: 40 sheet: 0.46 (0.40), residues: 165 loop : -1.13 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 153 HIS 0.001 0.000 HIS H 221 PHE 0.009 0.001 PHE H 29 TYR 0.008 0.001 TYR L 91 ARG 0.004 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.484 Fit side-chains REVERT: C 392 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7899 (p90) REVERT: H 215 TYR cc_start: 0.6024 (m-80) cc_final: 0.5636 (m-10) outliers start: 27 outliers final: 20 residues processed: 97 average time/residue: 0.1642 time to fit residues: 20.6009 Evaluate side-chains 93 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 60 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 36 optimal weight: 0.2980 chunk 55 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 HIS H 218 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.187877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.161250 restraints weight = 62483.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.164244 restraints weight = 38182.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.162173 restraints weight = 31708.148| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4950 Z= 0.203 Angle : 0.569 7.594 6743 Z= 0.285 Chirality : 0.043 0.213 754 Planarity : 0.004 0.046 871 Dihedral : 3.759 19.121 707 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 5.01 % Allowed : 28.94 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.20 (0.33), residues: 620 helix: -3.77 (0.57), residues: 40 sheet: 0.53 (0.41), residues: 161 loop : -1.08 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP H 175 HIS 0.001 0.000 HIS H 221 PHE 0.012 0.001 PHE C 342 TYR 0.010 0.001 TYR H 166 ARG 0.005 0.000 ARG H 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.540 Fit side-chains REVERT: C 355 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8738 (ttm-80) REVERT: C 392 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7831 (p90) REVERT: H 215 TYR cc_start: 0.6169 (m-80) cc_final: 0.5766 (m-10) REVERT: H 227 LYS cc_start: 0.8526 (mmtm) cc_final: 0.7602 (mmmt) outliers start: 27 outliers final: 24 residues processed: 97 average time/residue: 0.1925 time to fit residues: 23.4046 Evaluate side-chains 99 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 42 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.0470 chunk 56 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 HIS H 218 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.187648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.164825 restraints weight = 6329.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.163991 restraints weight = 12234.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.164144 restraints weight = 11227.171| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4950 Z= 0.187 Angle : 0.560 7.668 6743 Z= 0.280 Chirality : 0.043 0.211 754 Planarity : 0.004 0.045 871 Dihedral : 3.721 19.118 707 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 5.38 % Allowed : 28.20 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.19 (0.32), residues: 620 helix: -3.73 (0.62), residues: 38 sheet: 0.45 (0.40), residues: 164 loop : -1.06 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 153 HIS 0.001 0.000 HIS H 221 PHE 0.010 0.001 PHE C 342 TYR 0.008 0.001 TYR L 91 ARG 0.004 0.000 ARG H 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1790.46 seconds wall clock time: 31 minutes 44.47 seconds (1904.47 seconds total)