Starting phenix.real_space_refine on Fri Dec 27 17:27:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dl6_27497/12_2024/8dl6_27497.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dl6_27497/12_2024/8dl6_27497.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/8dl6_27497/12_2024/8dl6_27497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dl6_27497/12_2024/8dl6_27497.map" model { file = "/net/cci-nas-00/data/ceres_data/8dl6_27497/12_2024/8dl6_27497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dl6_27497/12_2024/8dl6_27497.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= 0.014 sd= 0.076 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 34 5.16 5 C 3944 2.51 5 N 1045 2.21 5 O 1147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6171 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3384 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 442, 3377 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 442, 3377 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 3439 Chain: "C" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1348 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 177 Chain: "D" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1437 Classifications: {'peptide': 219} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 81} Link IDs: {'PTRANS': 14, 'TRANS': 204} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 91 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATHR A 334 " occ=0.71 ... (12 atoms not shown) pdb=" CG2BTHR A 334 " occ=0.29 Time building chain proxies: 5.39, per 1000 atoms: 0.87 Number of scatterers: 6171 At special positions: 0 Unit cell: (75.9, 72.6, 141.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 34 16.00 O 1147 8.00 N 1045 7.00 C 3944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 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: 1.75 Conformation dependent library (CDL) restraints added in 1.5 seconds 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 9 sheets defined 49.9% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 15 through 23 Processing helix chain 'A' and resid 24 through 55 removed outlier: 4.066A pdb=" N LEU A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 85 removed outlier: 3.882A pdb=" N VAL A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASP A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 Processing helix chain 'A' and resid 116 through 124 removed outlier: 4.664A pdb=" N TYR A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 163 removed outlier: 4.387A pdb=" N THR A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 197 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 200 through 228 removed outlier: 3.911A pdb=" N GLY A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 6.527A pdb=" N ALA A 232 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 305 Processing helix chain 'A' and resid 307 through 317 removed outlier: 3.523A pdb=" N ALA A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 335 Processing helix chain 'A' and resid 340 through 368 removed outlier: 3.628A pdb=" N ILE A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 393 removed outlier: 3.583A pdb=" N THR A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 484 removed outlier: 3.550A pdb=" N VAL A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 490 through 514 removed outlier: 3.919A pdb=" N ALA A 514 " --> pdb=" O MET A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 544 Processing helix chain 'C' and resid 141 through 147 Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.570A pdb=" N GLN D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLY D 85 " --> pdb=" O LYS D 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 81 through 85' Processing helix chain 'D' and resid 106 through 110 removed outlier: 3.876A pdb=" N THR D 110 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 removed outlier: 3.653A pdb=" N GLY D 182 " --> pdb=" O TRP D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 213 Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 25 removed outlier: 3.683A pdb=" N ASP C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.697A pdb=" N MET C 31 " --> pdb=" O GLU C 125 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE C 68 " --> pdb=" O TRP C 55 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN C 57 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU C 66 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 137 through 138 removed outlier: 3.567A pdb=" N VAL C 153 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER C 151 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU C 201 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL C 153 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU C 199 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N PHE C 155 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N SER C 197 " --> pdb=" O PHE C 155 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN C 157 " --> pdb=" O MET C 195 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N MET C 195 " --> pdb=" O ASN C 157 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 165 through 170 removed outlier: 3.512A pdb=" N CYS C 214 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 225 " --> pdb=" O ALA C 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 22 through 25 removed outlier: 3.812A pdb=" N VAL D 37 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 102 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.636A pdb=" N MET D 53 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TRP D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 145 through 146 removed outlier: 4.951A pdb=" N GLY D 164 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL D 206 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU D 166 " --> pdb=" O SER D 204 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N SER D 204 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYS D 168 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU D 202 " --> pdb=" O LYS D 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 145 through 146 removed outlier: 4.951A pdb=" N GLY D 164 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL D 206 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU D 166 " --> pdb=" O SER D 204 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N SER D 204 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYS D 168 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU D 202 " --> pdb=" O LYS D 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 219 through 222 414 hydrogen bonds defined for protein. 1165 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: 2.10 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1254 1.33 - 1.45: 1461 1.45 - 1.57: 3512 1.57 - 1.69: 0 1.69 - 1.82: 55 Bond restraints: 6282 Sorted by residual: bond pdb=" C LEU A 213 " pdb=" O LEU A 213 " ideal model delta sigma weight residual 1.236 1.303 -0.066 1.15e-02 7.56e+03 3.34e+01 bond pdb=" C ALA A 379 " pdb=" O ALA A 379 " ideal model delta sigma weight residual 1.236 1.298 -0.061 1.15e-02 7.56e+03 2.85e+01 bond pdb=" C SER A 382 " pdb=" O SER A 382 " ideal model delta sigma weight residual 1.236 1.297 -0.061 1.15e-02 7.56e+03 2.78e+01 bond pdb=" C ASP A 166 " pdb=" O ASP A 166 " ideal model delta sigma weight residual 1.235 1.294 -0.058 1.22e-02 6.72e+03 2.28e+01 bond pdb=" C CYS A 217 " pdb=" O CYS A 217 " ideal model delta sigma weight residual 1.236 1.289 -0.053 1.15e-02 7.56e+03 2.14e+01 ... (remaining 6277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 8185 2.46 - 4.91: 346 4.91 - 7.37: 29 7.37 - 9.82: 6 9.82 - 12.28: 3 Bond angle restraints: 8569 Sorted by residual: angle pdb=" N PRO A 397 " pdb=" CA PRO A 397 " pdb=" C PRO A 397 " ideal model delta sigma weight residual 113.47 101.19 12.28 1.43e+00 4.89e-01 7.37e+01 angle pdb=" N PRO D 192 " pdb=" CA PRO D 192 " pdb=" CB PRO D 192 " ideal model delta sigma weight residual 103.31 110.26 -6.95 8.90e-01 1.26e+00 6.11e+01 angle pdb=" N PRO D 148 " pdb=" CA PRO D 148 " pdb=" CB PRO D 148 " ideal model delta sigma weight residual 103.25 111.41 -8.16 1.05e+00 9.07e-01 6.04e+01 angle pdb=" N PRO D 174 " pdb=" CA PRO D 174 " pdb=" CB PRO D 174 " ideal model delta sigma weight residual 103.25 111.13 -7.88 1.05e+00 9.07e-01 5.64e+01 angle pdb=" N PRO D 151 " pdb=" CA PRO D 151 " pdb=" CB PRO D 151 " ideal model delta sigma weight residual 103.25 110.81 -7.56 1.05e+00 9.07e-01 5.19e+01 ... (remaining 8564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 3291 17.11 - 34.22: 269 34.22 - 51.33: 73 51.33 - 68.44: 19 68.44 - 85.55: 5 Dihedral angle restraints: 3657 sinusoidal: 1157 harmonic: 2500 Sorted by residual: dihedral pdb=" CB CYS A 367 " pdb=" SG CYS A 367 " pdb=" SG CYS A 553 " pdb=" CB CYS A 553 " ideal model delta sinusoidal sigma weight residual 93.00 148.53 -55.53 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CA ASP C 102 " pdb=" CB ASP C 102 " pdb=" CG ASP C 102 " pdb=" OD1 ASP C 102 " ideal model delta sinusoidal sigma weight residual -30.00 -89.93 59.93 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA GLU D 108 " pdb=" C GLU D 108 " pdb=" N ASP D 109 " pdb=" CA ASP D 109 " ideal model delta harmonic sigma weight residual -180.00 -164.09 -15.91 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 3654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 652 0.047 - 0.093: 209 0.093 - 0.139: 123 0.139 - 0.185: 27 0.185 - 0.232: 14 Chirality restraints: 1025 Sorted by residual: chirality pdb=" CA PRO D 225 " pdb=" N PRO D 225 " pdb=" C PRO D 225 " pdb=" CB PRO D 225 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA VAL A 192 " pdb=" N VAL A 192 " pdb=" C VAL A 192 " pdb=" CB VAL A 192 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE A 385 " pdb=" CA ILE A 385 " pdb=" CG1 ILE A 385 " pdb=" CG2 ILE A 385 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1022 not shown) Planarity restraints: 1088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 86 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.19e+00 pdb=" C ASN A 86 " -0.050 2.00e-02 2.50e+03 pdb=" O ASN A 86 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 87 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 165 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.23e+00 pdb=" C GLU A 165 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU A 165 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP A 166 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 515 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C PRO A 515 " 0.039 2.00e-02 2.50e+03 pdb=" O PRO A 515 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN A 516 " -0.013 2.00e-02 2.50e+03 ... (remaining 1085 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 232 2.71 - 3.26: 6318 3.26 - 3.81: 9660 3.81 - 4.35: 10689 4.35 - 4.90: 19124 Nonbonded interactions: 46023 Sorted by model distance: nonbonded pdb=" N GLU C 101 " pdb=" OE1 GLU C 101 " model vdw 2.169 3.120 nonbonded pdb=" N ALA C 131 " pdb=" CB TYR C 160 " model vdw 2.175 3.520 nonbonded pdb=" OD1 ASN A 100 " pdb="CA CA A 601 " model vdw 2.220 2.510 nonbonded pdb=" O SER D 26 " pdb=" OG1 THR D 133 " model vdw 2.265 3.040 nonbonded pdb=" OE1 GLU A 165 " pdb=" OH TYR D 51 " model vdw 2.311 3.040 ... (remaining 46018 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=0.29 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.360 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.008 0.066 6282 Z= 0.523 Angle : 1.089 12.276 8569 Z= 0.788 Chirality : 0.063 0.232 1025 Planarity : 0.004 0.042 1088 Dihedral : 14.534 85.547 2050 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.93 % Allowed : 6.94 % Favored : 92.13 % Rotamer: Outliers : 3.22 % Allowed : 20.93 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.55 (0.28), residues: 867 helix: 0.61 (0.25), residues: 393 sheet: -0.13 (0.39), residues: 185 loop : -1.81 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 127 HIS 0.004 0.001 HIS A 535 PHE 0.014 0.002 PHE C 91 TYR 0.012 0.001 TYR D 51 ARG 0.005 0.001 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9258 (mm) REVERT: A 112 MET cc_start: 0.8870 (ttt) cc_final: 0.8639 (tmm) outliers start: 18 outliers final: 5 residues processed: 54 average time/residue: 1.1740 time to fit residues: 67.1572 Evaluate side-chains 40 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 553 CYS Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 78 optimal weight: 30.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN A 516 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6282 Z= 0.314 Angle : 0.661 8.126 8569 Z= 0.350 Chirality : 0.044 0.152 1025 Planarity : 0.005 0.056 1088 Dihedral : 5.500 58.905 934 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.32 % Favored : 94.21 % Rotamer: Outliers : 3.40 % Allowed : 21.82 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.82 (0.29), residues: 867 helix: 2.19 (0.25), residues: 388 sheet: 0.49 (0.40), residues: 179 loop : -1.72 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 127 HIS 0.004 0.001 HIS A 125 PHE 0.012 0.001 PHE C 91 TYR 0.012 0.001 TYR A 538 ARG 0.004 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 33 time to evaluate : 0.705 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 47 average time/residue: 1.1733 time to fit residues: 58.5965 Evaluate side-chains 37 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain C residue 57 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.0570 chunk 24 optimal weight: 0.8980 chunk 64 optimal weight: 0.0870 chunk 53 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 30.0000 chunk 84 optimal weight: 30.0000 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 overall best weight: 0.8678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6282 Z= 0.151 Angle : 0.568 8.518 8569 Z= 0.294 Chirality : 0.041 0.146 1025 Planarity : 0.004 0.047 1088 Dihedral : 5.059 59.216 932 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.21 % Favored : 94.44 % Rotamer: Outliers : 3.40 % Allowed : 21.82 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.54 (0.30), residues: 867 helix: 3.00 (0.25), residues: 386 sheet: 0.61 (0.40), residues: 183 loop : -1.51 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 127 HIS 0.002 0.001 HIS A 535 PHE 0.010 0.001 PHE A 360 TYR 0.008 0.001 TYR C 111 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.742 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 5 residues processed: 57 average time/residue: 1.2593 time to fit residues: 75.7142 Evaluate side-chains 40 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 498 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 78 optimal weight: 40.0000 chunk 83 optimal weight: 50.0000 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 22 optimal weight: 0.0050 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6282 Z= 0.263 Angle : 0.618 8.969 8569 Z= 0.321 Chirality : 0.042 0.162 1025 Planarity : 0.004 0.045 1088 Dihedral : 4.697 58.958 930 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.67 % Favored : 93.98 % Rotamer: Outliers : 2.86 % Allowed : 24.33 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.59 (0.30), residues: 867 helix: 2.90 (0.25), residues: 389 sheet: 0.77 (0.40), residues: 184 loop : -1.41 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 127 HIS 0.002 0.001 HIS A 32 PHE 0.010 0.001 PHE A 360 TYR 0.010 0.001 TYR A 538 ARG 0.005 0.001 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 132 CYS cc_start: 0.9142 (m) cc_final: 0.8905 (m) REVERT: A 507 HIS cc_start: 0.8865 (OUTLIER) cc_final: 0.8617 (t-90) REVERT: C 51 THR cc_start: 0.9528 (OUTLIER) cc_final: 0.9311 (m) outliers start: 16 outliers final: 8 residues processed: 49 average time/residue: 1.1724 time to fit residues: 61.1382 Evaluate side-chains 45 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 66 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 30.0000 chunk 0 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6282 Z= 0.202 Angle : 0.599 9.412 8569 Z= 0.307 Chirality : 0.041 0.157 1025 Planarity : 0.004 0.046 1088 Dihedral : 4.614 59.873 930 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.32 % Favored : 94.33 % Rotamer: Outliers : 3.22 % Allowed : 23.97 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.79 (0.30), residues: 867 helix: 3.08 (0.25), residues: 386 sheet: 0.86 (0.40), residues: 185 loop : -1.29 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 127 HIS 0.002 0.001 HIS A 535 PHE 0.009 0.001 PHE A 360 TYR 0.008 0.001 TYR A 538 ARG 0.003 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 132 CYS cc_start: 0.9173 (m) cc_final: 0.8905 (m) REVERT: A 165 GLU cc_start: 0.8940 (mp0) cc_final: 0.8738 (mt-10) REVERT: C 51 THR cc_start: 0.9543 (OUTLIER) cc_final: 0.9313 (m) REVERT: D 29 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7752 (mm-30) outliers start: 18 outliers final: 7 residues processed: 55 average time/residue: 1.0434 time to fit residues: 60.4694 Evaluate side-chains 47 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 66 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 83 optimal weight: 20.0000 chunk 69 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6282 Z= 0.159 Angle : 0.585 9.520 8569 Z= 0.293 Chirality : 0.041 0.153 1025 Planarity : 0.004 0.048 1088 Dihedral : 4.473 58.567 930 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.86 % Favored : 94.79 % Rotamer: Outliers : 2.33 % Allowed : 23.97 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.03 (0.30), residues: 867 helix: 3.27 (0.25), residues: 386 sheet: 1.03 (0.41), residues: 179 loop : -1.16 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 127 HIS 0.002 0.000 HIS A 535 PHE 0.009 0.001 PHE A 360 TYR 0.006 0.001 TYR A 501 ARG 0.004 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 CYS cc_start: 0.9167 (m) cc_final: 0.8835 (m) REVERT: D 29 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7599 (mm-30) REVERT: D 59 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8754 (tpp80) outliers start: 13 outliers final: 7 residues processed: 56 average time/residue: 1.1026 time to fit residues: 65.4811 Evaluate side-chains 48 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 553 CYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 59 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 60 optimal weight: 40.0000 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6282 Z= 0.207 Angle : 0.620 9.894 8569 Z= 0.314 Chirality : 0.041 0.181 1025 Planarity : 0.004 0.056 1088 Dihedral : 4.451 57.532 930 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.44 % Favored : 94.21 % Rotamer: Outliers : 2.68 % Allowed : 24.15 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.04 (0.30), residues: 867 helix: 3.20 (0.25), residues: 386 sheet: 1.09 (0.41), residues: 179 loop : -1.07 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 127 HIS 0.002 0.001 HIS A 535 PHE 0.009 0.001 PHE A 360 TYR 0.008 0.001 TYR A 538 ARG 0.004 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 CYS cc_start: 0.9185 (m) cc_final: 0.8836 (m) REVERT: D 29 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7613 (mm-30) REVERT: D 59 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8674 (tpp80) outliers start: 15 outliers final: 7 residues processed: 55 average time/residue: 1.2362 time to fit residues: 71.7951 Evaluate side-chains 47 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 553 CYS Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 59 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6282 Z= 0.317 Angle : 0.674 10.625 8569 Z= 0.347 Chirality : 0.043 0.162 1025 Planarity : 0.004 0.053 1088 Dihedral : 4.602 56.292 930 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.79 % Favored : 93.87 % Rotamer: Outliers : 2.68 % Allowed : 23.97 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.85 (0.30), residues: 867 helix: 2.95 (0.25), residues: 388 sheet: 1.05 (0.41), residues: 179 loop : -1.08 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 299 HIS 0.003 0.001 HIS A 535 PHE 0.009 0.001 PHE A 360 TYR 0.011 0.001 TYR A 501 ARG 0.004 0.001 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.876 Fit side-chains REVERT: D 29 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7610 (mm-30) REVERT: D 59 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8698 (tpp80) outliers start: 15 outliers final: 6 residues processed: 51 average time/residue: 1.2831 time to fit residues: 69.1492 Evaluate side-chains 44 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 59 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 50.0000 chunk 46 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 60 optimal weight: 50.0000 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 81 optimal weight: 40.0000 chunk 49 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 6282 Z= 0.412 Angle : 0.742 12.646 8569 Z= 0.384 Chirality : 0.044 0.166 1025 Planarity : 0.004 0.054 1088 Dihedral : 4.401 48.012 927 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.02 % Favored : 93.63 % Rotamer: Outliers : 2.33 % Allowed : 24.15 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.30), residues: 867 helix: 2.65 (0.25), residues: 387 sheet: 1.03 (0.40), residues: 179 loop : -1.04 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 299 HIS 0.006 0.001 HIS A 118 PHE 0.007 0.001 PHE A 308 TYR 0.014 0.001 TYR A 501 ARG 0.004 0.001 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 132 CYS cc_start: 0.9176 (m) cc_final: 0.8863 (m) REVERT: D 29 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7627 (mm-30) REVERT: D 59 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8763 (tpp80) REVERT: D 65 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8028 (mp0) outliers start: 13 outliers final: 7 residues processed: 50 average time/residue: 1.3415 time to fit residues: 70.6787 Evaluate side-chains 45 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 59 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 85 optimal weight: 50.0000 chunk 78 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6282 Z= 0.189 Angle : 0.674 13.346 8569 Z= 0.338 Chirality : 0.042 0.177 1025 Planarity : 0.004 0.053 1088 Dihedral : 4.206 46.199 927 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.75 % Favored : 94.91 % Rotamer: Outliers : 1.61 % Allowed : 25.04 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.30), residues: 867 helix: 2.96 (0.25), residues: 386 sheet: 1.11 (0.40), residues: 185 loop : -1.03 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 69 HIS 0.002 0.001 HIS A 535 PHE 0.009 0.001 PHE A 295 TYR 0.009 0.001 TYR A 501 ARG 0.004 0.000 ARG D 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: D 29 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7586 (mm-30) REVERT: D 65 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8005 (mp0) outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 1.3837 time to fit residues: 75.5701 Evaluate side-chains 46 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 66 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 50.0000 chunk 10 optimal weight: 10.0000 chunk 18 optimal weight: 0.0000 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 50.0000 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** 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 = 0.3477 r_free = 0.3477 target = 0.068382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.049927 restraints weight = 71797.094| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 6.12 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6282 Z= 0.192 Angle : 0.695 13.180 8569 Z= 0.344 Chirality : 0.041 0.173 1025 Planarity : 0.004 0.054 1088 Dihedral : 4.070 46.277 927 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.21 % Favored : 94.44 % Rotamer: Outliers : 1.61 % Allowed : 25.22 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.01 (0.30), residues: 867 helix: 2.98 (0.25), residues: 387 sheet: 1.32 (0.41), residues: 177 loop : -0.95 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 37 HIS 0.002 0.000 HIS A 535 PHE 0.009 0.001 PHE A 360 TYR 0.008 0.001 TYR A 501 ARG 0.004 0.000 ARG D 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1876.52 seconds wall clock time: 35 minutes 22.02 seconds (2122.02 seconds total)