Starting phenix.real_space_refine on Thu Jul 2 10:54:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mhy_23836/07_2026/7mhy_23836.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mhy_23836/07_2026/7mhy_23836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mhy_23836/07_2026/7mhy_23836.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mhy_23836/07_2026/7mhy_23836.cif" model { file = "/net/cci-nas-00/data/ceres_data/7mhy_23836/07_2026/7mhy_23836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mhy_23836/07_2026/7mhy_23836.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mhy_23836/07_2026/7mhy_23836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mhy_23836/07_2026/7mhy_23836.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.402 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: 6 Type Number sf(0) Gaussians Fe 1 7.16 5 P 6 5.49 5 S 48 5.16 5 C 5264 2.51 5 N 1177 2.21 5 O 1408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7904 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 4003 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 474} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "M" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 887 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "N" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 812 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "O" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "P" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 683 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 88} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 714 Unusual residues: {'AJP': 14, 'HEM': 1, 'PKZ': 3} Classifications: {'undetermined': 18, 'water': 15} Link IDs: {None: 32} Unresolved non-hydrogen bonds: 796 Unresolved non-hydrogen angles: 1197 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 315 Planarities with less than four sites: {'PKZ:plan-1': 1, 'PKZ:plan-2': 1, 'PKZ:plan-3': 1, 'PKZ:plan-4': 1, 'PKZ:plan-5': 1} Unresolved non-hydrogen planarities: 26 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2668 SG CYS A 324 41.775 58.564 80.769 1.00 29.38 S Time building chain proxies: 1.89, per 1000 atoms: 0.24 Number of scatterers: 7904 At special positions: 0 Unit cell: (74.48, 90.972, 144.704, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 1 26.01 S 48 16.00 P 6 15.00 O 1408 8.00 N 1177 7.00 C 5264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 115 " distance=2.03 Simple disulfide: pdb=" SG CYS N 42 " - pdb=" SG CYS N 112 " distance=2.05 Simple disulfide: pdb=" SG CYS O 41 " - pdb=" SG CYS O 115 " distance=2.03 Simple disulfide: pdb=" SG CYS P 42 " - pdb=" SG CYS P 112 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 402.8 milliseconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1676 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 47.5% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 3 through 29 Processing helix chain 'A' and resid 32 through 38 removed outlier: 3.594A pdb=" N GLN A 38 " --> pdb=" O GLU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 70 Processing helix chain 'A' and resid 70 through 89 Processing helix chain 'A' and resid 92 through 129 removed outlier: 8.291A pdb=" N THR A 111 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Proline residue: A 112 - end of helix Processing helix chain 'A' and resid 132 through 148 removed outlier: 3.714A pdb=" N LEU A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 158 Processing helix chain 'A' and resid 163 through 190 removed outlier: 4.176A pdb=" N LEU A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.579A pdb=" N TYR A 199 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 236 through 265 removed outlier: 3.521A pdb=" N SER A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 246 " --> pdb=" O CYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 281 through 315 Proline residue: A 307 - end of helix Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.728A pdb=" N VAL A 354 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 379 removed outlier: 3.601A pdb=" N THR A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 407 Processing helix chain 'A' and resid 408 through 419 Processing helix chain 'A' and resid 420 through 449 removed outlier: 3.775A pdb=" N CYS A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 462 Processing helix chain 'A' and resid 467 through 488 Processing helix chain 'M' and resid 106 through 110 removed outlier: 3.567A pdb=" N SER M 110 " --> pdb=" O SER M 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 84 removed outlier: 3.624A pdb=" N LYS O 84 " --> pdb=" O ASP O 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 81 through 84' Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AA2, first strand: chain 'M' and resid 22 through 25 Processing sheet with id=AA3, first strand: chain 'M' and resid 29 through 31 removed outlier: 6.725A pdb=" N GLU M 29 " --> pdb=" O THR M 135 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU M 53 " --> pdb=" O TYR M 69 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR M 69 " --> pdb=" O LEU M 53 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP M 55 " --> pdb=" O ILE M 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 29 through 31 removed outlier: 6.725A pdb=" N GLU M 29 " --> pdb=" O THR M 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 23 through 26 Processing sheet with id=AA6, first strand: chain 'N' and resid 29 through 31 removed outlier: 6.701A pdb=" N LEU N 57 " --> pdb=" O TYR N 73 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR N 73 " --> pdb=" O LEU N 57 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP N 59 " --> pdb=" O LEU N 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 29 through 31 removed outlier: 3.859A pdb=" N THR N 121 " --> pdb=" O GLN N 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 22 through 25 Processing sheet with id=AA9, first strand: chain 'O' and resid 77 through 79 removed outlier: 6.815A pdb=" N TRP O 55 " --> pdb=" O MET O 67 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP O 69 " --> pdb=" O MET O 53 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET O 53 " --> pdb=" O TRP O 69 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR O 127 " --> pdb=" O ARG O 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 77 through 79 removed outlier: 6.815A pdb=" N TRP O 55 " --> pdb=" O MET O 67 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP O 69 " --> pdb=" O MET O 53 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET O 53 " --> pdb=" O TRP O 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 23 through 26 removed outlier: 3.547A pdb=" N SER P 41 " --> pdb=" O THR P 26 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 29 through 30 removed outlier: 6.919A pdb=" N TRP P 59 " --> pdb=" O LEU P 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 29 through 30 437 hydrogen bonds defined for protein. 1221 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: 1.37 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 2811 1.37 - 1.54: 5170 1.54 - 1.71: 144 1.71 - 1.88: 74 1.88 - 2.04: 4 Bond restraints: 8203 Sorted by residual: bond pdb=" O3B PKZ A 503 " pdb=" P3B PKZ A 503 " ideal model delta sigma weight residual 1.714 1.615 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" O3B PKZ A 502 " pdb=" P3B PKZ A 502 " ideal model delta sigma weight residual 1.714 1.616 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" N ILE N 72 " pdb=" CA ILE N 72 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.18e-02 7.18e+03 9.74e+00 bond pdb=" N VAL N 75 " pdb=" CA VAL N 75 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.73e+00 bond pdb=" N VAL N 49 " pdb=" CA VAL N 49 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.24e-02 6.50e+03 9.14e+00 ... (remaining 8198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 10761 1.98 - 3.96: 485 3.96 - 5.95: 102 5.95 - 7.93: 12 7.93 - 9.91: 3 Bond angle restraints: 11363 Sorted by residual: angle pdb=" CBP PKZ A 503 " pdb=" CAP PKZ A 503 " pdb=" OAP PKZ A 503 " ideal model delta sigma weight residual 112.71 102.80 9.91 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C06 AJP A 515 " pdb=" C07 AJP A 515 " pdb=" C12 AJP A 515 " ideal model delta sigma weight residual 120.30 130.01 -9.71 3.00e+00 1.11e-01 1.05e+01 angle pdb=" CA TYR A 180 " pdb=" CB TYR A 180 " pdb=" CG TYR A 180 " ideal model delta sigma weight residual 113.90 119.67 -5.77 1.80e+00 3.09e-01 1.03e+01 angle pdb=" C VAL N 75 " pdb=" CA VAL N 75 " pdb=" CB VAL N 75 " ideal model delta sigma weight residual 111.29 116.52 -5.23 1.64e+00 3.72e-01 1.02e+01 angle pdb=" CA VAL N 75 " pdb=" C VAL N 75 " pdb=" O VAL N 75 " ideal model delta sigma weight residual 120.78 116.80 3.98 1.25e+00 6.40e-01 1.01e+01 ... (remaining 11358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.72: 4000 24.72 - 49.44: 211 49.44 - 74.16: 24 74.16 - 98.88: 11 98.88 - 123.60: 45 Dihedral angle restraints: 4291 sinusoidal: 1658 harmonic: 2633 Sorted by residual: dihedral pdb=" C VAL N 75 " pdb=" N VAL N 75 " pdb=" CA VAL N 75 " pdb=" CB VAL N 75 " ideal model delta harmonic sigma weight residual -122.00 -137.82 15.82 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" N VAL N 75 " pdb=" C VAL N 75 " pdb=" CA VAL N 75 " pdb=" CB VAL N 75 " ideal model delta harmonic sigma weight residual 123.40 137.15 -13.75 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" CA VAL A 28 " pdb=" C VAL A 28 " pdb=" N SER A 29 " pdb=" CA SER A 29 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 4288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.206: 1175 1.206 - 2.411: 0 2.411 - 3.617: 0 3.617 - 4.823: 17 4.823 - 6.028: 139 Chirality restraints: 1331 Sorted by residual: chirality pdb=" C12 AJP A 511 " pdb=" C07 AJP A 511 " pdb=" C11 AJP A 511 " pdb=" C13 AJP A 511 " both_signs ideal model delta sigma weight residual False 3.01 -3.02 6.03 2.00e-01 2.50e+01 9.08e+02 chirality pdb=" C12 AJP A 516 " pdb=" C07 AJP A 516 " pdb=" C11 AJP A 516 " pdb=" C13 AJP A 516 " both_signs ideal model delta sigma weight residual False 3.01 -3.02 6.02 2.00e-01 2.50e+01 9.07e+02 chirality pdb=" C12 AJP A 506 " pdb=" C07 AJP A 506 " pdb=" C11 AJP A 506 " pdb=" C13 AJP A 506 " both_signs ideal model delta sigma weight residual False 3.01 -3.01 6.02 2.00e-01 2.50e+01 9.05e+02 ... (remaining 1328 not shown) Planarity restraints: 1243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P PKZ A 502 " -0.086 2.00e-02 2.50e+03 7.10e-02 6.30e+01 pdb=" C5P PKZ A 502 " 0.024 2.00e-02 2.50e+03 pdb=" C6P PKZ A 502 " -0.065 2.00e-02 2.50e+03 pdb=" N4P PKZ A 502 " 0.113 2.00e-02 2.50e+03 pdb=" O5P PKZ A 502 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 271 " -0.033 2.00e-02 2.50e+03 2.82e-02 1.59e+01 pdb=" CG TYR A 271 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR A 271 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 271 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 271 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 271 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 271 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 271 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P PKZ A 502 " 0.033 2.00e-02 2.50e+03 2.71e-02 9.15e+00 pdb=" C9P PKZ A 502 " -0.010 2.00e-02 2.50e+03 pdb=" CAP PKZ A 502 " 0.025 2.00e-02 2.50e+03 pdb=" N8P PKZ A 502 " -0.043 2.00e-02 2.50e+03 pdb=" O9P PKZ A 502 " -0.005 2.00e-02 2.50e+03 ... (remaining 1240 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 288 2.71 - 3.26: 7420 3.26 - 3.80: 12756 3.80 - 4.35: 16272 4.35 - 4.90: 27562 Nonbonded interactions: 64298 Sorted by model distance: nonbonded pdb=" OH TYR A 210 " pdb=" OD2 ASP A 314 " model vdw 2.160 3.040 nonbonded pdb=" O MET A 328 " pdb=" OH TYR A 479 " model vdw 2.265 3.040 nonbonded pdb=" O2B PKZ A 502 " pdb=" O7A PKZ A 502 " model vdw 2.278 3.040 nonbonded pdb=" O LEU A 143 " pdb=" OG1 THR A 146 " model vdw 2.327 3.040 nonbonded pdb=" O SER N 116 " pdb=" OG SER N 116 " model vdw 2.336 3.040 ... (remaining 64293 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.110 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: 0.410 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.010 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 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 : 0.010 0.543 8208 Z= 0.398 Angle : 0.959 9.911 11371 Z= 0.447 Chirality : 1.792 6.028 1331 Planarity : 0.005 0.071 1243 Dihedral : 20.904 123.595 2603 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.54 % Allowed : 0.67 % Favored : 98.79 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.28), residues: 888 helix: 1.92 (0.26), residues: 385 sheet: 0.61 (0.37), residues: 198 loop : -0.92 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 93 TYR 0.069 0.003 TYR A 271 PHE 0.030 0.003 PHE A 58 TRP 0.017 0.002 TRP A 465 HIS 0.012 0.002 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00836 / 0.38 ( 8203) covalent geometry : angle 0.95890 / 0.45 (11363) SS BOND : bond 0.00919 / 0.45 ( 4) SS BOND : angle 1.57148 / 0.84 ( 8) hydrogen bonds : bond 0.18603 / 12.34 ( 415) hydrogen bonds : angle 6.28051 / 4.60 ( 1221) Misc. bond : bond 0.54344 / 28.60 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 152 time to evaluate : 0.292 Fit side-chains TARDY: cannot create tardy model for: "SER A 29 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. outliers start: 4 outliers final: 3 residues processed: 155 average time/residue: 0.4955 time to fit residues: 81.9427 Evaluate side-chains 147 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain N residue 48 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 GLN ** 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 = 0.3567 r_free = 0.3567 target = 0.139266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.107139 restraints weight = 9753.022| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.77 r_work: 0.3019 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8208 Z= 0.170 Angle : 2.764 35.848 11371 Z= 0.947 Chirality : 0.271 2.049 1331 Planarity : 0.004 0.036 1243 Dihedral : 14.079 109.836 1115 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.62 % Allowed : 9.58 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.28), residues: 888 helix: 2.24 (0.26), residues: 399 sheet: 0.77 (0.37), residues: 201 loop : -0.82 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 176 TYR 0.026 0.002 TYR A 271 PHE 0.033 0.002 PHE A 17 TRP 0.012 0.001 TRP A 388 HIS 0.005 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 ( 8203) covalent geometry : angle 2.76459 / 0.95 (11363) SS BOND : bond 0.00591 / 0.29 ( 4) SS BOND : angle 1.87234 / 1.08 ( 8) hydrogen bonds : bond 0.05513 / 3.75 ( 415) hydrogen bonds : angle 4.61789 / 3.37 ( 1221) Misc. bond : bond 0.03155 / 1.66 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.326 Fit side-chains TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 230 GLN cc_start: 0.8588 (mt0) cc_final: 0.8326 (mt0) REVERT: N 77 ASN cc_start: 0.8541 (t0) cc_final: 0.8270 (t0) REVERT: P 58 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7293 (mp0) outliers start: 12 outliers final: 6 residues processed: 149 average time/residue: 0.4653 time to fit residues: 74.0849 Evaluate side-chains 140 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 89 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 81 optimal weight: 0.0170 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 ASN A 450 ASN N 54 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.139055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.107053 restraints weight = 9646.420| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.77 r_work: 0.3021 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8208 Z= 0.163 Angle : 2.708 34.840 11371 Z= 0.927 Chirality : 0.275 1.971 1331 Planarity : 0.004 0.034 1243 Dihedral : 13.738 107.902 1111 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.24 % Allowed : 12.55 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.28), residues: 888 helix: 2.29 (0.26), residues: 400 sheet: 0.81 (0.37), residues: 201 loop : -0.85 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 176 TYR 0.021 0.002 TYR A 180 PHE 0.026 0.002 PHE A 17 TRP 0.012 0.001 TRP A 388 HIS 0.005 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 8203) covalent geometry : angle 2.70893 / 0.93 (11363) SS BOND : bond 0.00657 / 0.32 ( 4) SS BOND : angle 1.55572 / 0.88 ( 8) hydrogen bonds : bond 0.05005 / 3.38 ( 415) hydrogen bonds : angle 4.34112 / 3.16 ( 1221) Misc. bond : bond 0.02905 / 1.53 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.304 Fit side-chains TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 148 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7931 (ptp-170) REVERT: A 232 GLN cc_start: 0.7366 (pp30) cc_final: 0.6550 (mp10) REVERT: A 407 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7266 (tm-30) REVERT: N 77 ASN cc_start: 0.8533 (t0) cc_final: 0.8221 (t0) REVERT: P 58 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7272 (mp0) outliers start: 24 outliers final: 14 residues processed: 150 average time/residue: 0.4867 time to fit residues: 78.1856 Evaluate side-chains 146 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 89 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 ASN N 54 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 GLN ** 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 = 0.3549 r_free = 0.3549 target = 0.137668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.105362 restraints weight = 9806.605| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.80 r_work: 0.2999 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8208 Z= 0.186 Angle : 2.708 34.974 11371 Z= 0.929 Chirality : 0.275 1.969 1331 Planarity : 0.004 0.035 1243 Dihedral : 13.693 110.410 1111 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.10 % Allowed : 14.71 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.28), residues: 888 helix: 2.25 (0.26), residues: 400 sheet: 0.78 (0.38), residues: 201 loop : -0.93 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 85 TYR 0.020 0.002 TYR A 180 PHE 0.027 0.002 PHE A 17 TRP 0.014 0.001 TRP A 388 HIS 0.005 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 8203) covalent geometry : angle 2.70844 / 0.93 (11363) SS BOND : bond 0.00709 / 0.35 ( 4) SS BOND : angle 1.56731 / 0.85 ( 8) hydrogen bonds : bond 0.05342 / 3.62 ( 415) hydrogen bonds : angle 4.38378 / 3.19 ( 1221) Misc. bond : bond 0.02877 / 1.51 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.255 Fit side-chains TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 148 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7930 (ptp-170) REVERT: A 407 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7249 (tm-30) REVERT: A 427 PHE cc_start: 0.8264 (m-80) cc_final: 0.7981 (m-80) REVERT: N 77 ASN cc_start: 0.8558 (t0) cc_final: 0.8223 (t0) REVERT: P 58 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7310 (mp0) outliers start: 23 outliers final: 16 residues processed: 142 average time/residue: 0.4840 time to fit residues: 73.4803 Evaluate side-chains 143 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 36 SER Chi-restraints excluded: chain M residue 82 LYS Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 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 = 0.3560 r_free = 0.3560 target = 0.138639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.106209 restraints weight = 9741.981| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.81 r_work: 0.3013 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8208 Z= 0.165 Angle : 2.690 34.674 11371 Z= 0.921 Chirality : 0.275 1.962 1331 Planarity : 0.004 0.035 1243 Dihedral : 13.338 105.589 1111 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.05 % Allowed : 14.44 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.29), residues: 888 helix: 2.33 (0.26), residues: 400 sheet: 0.81 (0.38), residues: 201 loop : -0.89 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 176 TYR 0.021 0.002 TYR A 180 PHE 0.025 0.002 PHE A 17 TRP 0.013 0.001 TRP A 388 HIS 0.004 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 8203) covalent geometry : angle 2.69109 / 0.92 (11363) SS BOND : bond 0.00609 / 0.30 ( 4) SS BOND : angle 1.40061 / 0.77 ( 8) hydrogen bonds : bond 0.04926 / 3.33 ( 415) hydrogen bonds : angle 4.30097 / 3.12 ( 1221) Misc. bond : bond 0.02635 / 1.39 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.296 Fit side-chains TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 79 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8473 (ttm) REVERT: A 148 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7890 (ptp-170) REVERT: A 407 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7254 (tm-30) REVERT: A 427 PHE cc_start: 0.8255 (m-80) cc_final: 0.7983 (m-80) REVERT: M 109 ASP cc_start: 0.8484 (m-30) cc_final: 0.8273 (m-30) REVERT: N 77 ASN cc_start: 0.8547 (t0) cc_final: 0.8243 (t0) REVERT: O 100 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7974 (tt) REVERT: P 58 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7305 (mp0) outliers start: 30 outliers final: 23 residues processed: 144 average time/residue: 0.4812 time to fit residues: 74.2300 Evaluate side-chains 150 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain M residue 36 SER Chi-restraints excluded: chain M residue 82 LYS Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 89 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 ASN ** N 114 GLN ** 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 = 0.3573 r_free = 0.3573 target = 0.139858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.107565 restraints weight = 9718.815| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.80 r_work: 0.3030 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8208 Z= 0.150 Angle : 2.676 34.485 11371 Z= 0.914 Chirality : 0.276 1.951 1331 Planarity : 0.004 0.035 1243 Dihedral : 13.272 106.365 1111 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.18 % Allowed : 15.52 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.29), residues: 888 helix: 2.41 (0.26), residues: 400 sheet: 0.81 (0.38), residues: 201 loop : -0.87 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 30 TYR 0.022 0.001 TYR A 180 PHE 0.023 0.002 PHE A 17 TRP 0.012 0.001 TRP A 467 HIS 0.004 0.001 HIS A 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 8203) covalent geometry : angle 2.67664 / 0.91 (11363) SS BOND : bond 0.00537 / 0.26 ( 4) SS BOND : angle 1.30342 / 0.71 ( 8) hydrogen bonds : bond 0.04646 / 3.14 ( 415) hydrogen bonds : angle 4.23141 / 3.07 ( 1221) Misc. bond : bond 0.02566 / 1.35 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.283 Fit side-chains TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 79 MET cc_start: 0.8703 (ttt) cc_final: 0.8452 (ttm) REVERT: A 403 ARG cc_start: 0.7325 (ttt90) cc_final: 0.7056 (ttm110) REVERT: A 407 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7229 (tm-30) REVERT: A 427 PHE cc_start: 0.8246 (m-80) cc_final: 0.7985 (m-80) REVERT: M 101 GLN cc_start: 0.8624 (tt0) cc_final: 0.8320 (tt0) REVERT: N 49 VAL cc_start: 0.8859 (p) cc_final: 0.8641 (p) REVERT: N 77 ASN cc_start: 0.8571 (t0) cc_final: 0.8223 (t0) REVERT: O 100 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7966 (tt) REVERT: P 58 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7285 (mp0) outliers start: 31 outliers final: 24 residues processed: 146 average time/residue: 0.4771 time to fit residues: 74.6176 Evaluate side-chains 149 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain M residue 36 SER Chi-restraints excluded: chain M residue 82 LYS Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 67 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 ASN ** N 114 GLN ** 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 = 0.3587 r_free = 0.3587 target = 0.141162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.108983 restraints weight = 9684.298| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.79 r_work: 0.3055 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8208 Z= 0.139 Angle : 2.665 34.171 11371 Z= 0.910 Chirality : 0.276 1.951 1331 Planarity : 0.004 0.035 1243 Dihedral : 13.084 105.496 1111 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.24 % Allowed : 17.00 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.29), residues: 888 helix: 2.51 (0.26), residues: 400 sheet: 0.84 (0.38), residues: 201 loop : -0.83 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 85 TYR 0.022 0.001 TYR A 180 PHE 0.021 0.001 PHE A 17 TRP 0.013 0.001 TRP A 467 HIS 0.003 0.001 HIS A 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 8203) covalent geometry : angle 2.66575 / 0.91 (11363) SS BOND : bond 0.00579 / 0.28 ( 4) SS BOND : angle 1.31363 / 0.71 ( 8) hydrogen bonds : bond 0.04386 / 2.96 ( 415) hydrogen bonds : angle 4.16520 / 3.02 ( 1221) Misc. bond : bond 0.02210 / 1.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.297 Fit side-chains TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 79 MET cc_start: 0.8712 (ttt) cc_final: 0.8467 (ttm) REVERT: A 403 ARG cc_start: 0.7341 (ttt90) cc_final: 0.6931 (ttm110) REVERT: A 427 PHE cc_start: 0.8229 (m-80) cc_final: 0.7964 (m-80) REVERT: M 101 GLN cc_start: 0.8645 (tt0) cc_final: 0.8270 (tt0) REVERT: N 49 VAL cc_start: 0.8827 (p) cc_final: 0.8619 (p) REVERT: N 77 ASN cc_start: 0.8506 (t0) cc_final: 0.8238 (t0) REVERT: O 100 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7953 (tt) REVERT: P 58 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7249 (mp0) outliers start: 24 outliers final: 16 residues processed: 145 average time/residue: 0.4621 time to fit residues: 71.9431 Evaluate side-chains 143 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 56 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 0.0020 chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 488 GLN ** N 114 GLN ** 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 = 0.3599 r_free = 0.3599 target = 0.142182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.110005 restraints weight = 9626.125| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.79 r_work: 0.3071 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8208 Z= 0.132 Angle : 2.659 33.914 11371 Z= 0.907 Chirality : 0.277 1.954 1331 Planarity : 0.004 0.034 1243 Dihedral : 12.932 105.228 1111 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.91 % Allowed : 17.27 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.29), residues: 888 helix: 2.55 (0.26), residues: 400 sheet: 0.73 (0.38), residues: 204 loop : -0.76 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 176 TYR 0.023 0.001 TYR A 180 PHE 0.020 0.001 PHE A 17 TRP 0.014 0.001 TRP A 467 HIS 0.003 0.001 HIS A 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 8203) covalent geometry : angle 2.66008 / 0.91 (11363) SS BOND : bond 0.00652 / 0.32 ( 4) SS BOND : angle 1.24383 / 0.68 ( 8) hydrogen bonds : bond 0.04190 / 2.83 ( 415) hydrogen bonds : angle 4.12551 / 3.00 ( 1221) Misc. bond : bond 0.02144 / 1.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.296 Fit side-chains TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 79 MET cc_start: 0.8693 (ttt) cc_final: 0.8441 (ttm) REVERT: A 403 ARG cc_start: 0.7302 (ttt90) cc_final: 0.6980 (ttm110) REVERT: A 427 PHE cc_start: 0.8225 (m-80) cc_final: 0.7961 (m-80) REVERT: N 77 ASN cc_start: 0.8487 (t0) cc_final: 0.8257 (t0) REVERT: N 94 ASP cc_start: 0.8644 (m-30) cc_final: 0.8388 (m-30) REVERT: O 100 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7927 (tt) REVERT: P 58 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7265 (mp0) outliers start: 29 outliers final: 20 residues processed: 146 average time/residue: 0.4460 time to fit residues: 70.1770 Evaluate side-chains 144 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain A residue 488 GLN Chi-restraints excluded: chain M residue 36 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 78 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 ASN A 488 GLN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.141817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.109652 restraints weight = 9623.758| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.79 r_work: 0.3066 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8208 Z= 0.136 Angle : 2.660 33.872 11371 Z= 0.908 Chirality : 0.277 1.954 1331 Planarity : 0.004 0.034 1243 Dihedral : 12.912 105.267 1111 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.97 % Allowed : 18.35 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.29), residues: 888 helix: 2.59 (0.26), residues: 400 sheet: 0.72 (0.38), residues: 204 loop : -0.77 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 148 TYR 0.022 0.001 TYR A 180 PHE 0.019 0.001 PHE N 113 TRP 0.014 0.001 TRP N 120 HIS 0.004 0.001 HIS A 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 8203) covalent geometry : angle 2.66104 / 0.91 (11363) SS BOND : bond 0.00490 / 0.24 ( 4) SS BOND : angle 1.32290 / 0.73 ( 8) hydrogen bonds : bond 0.04276 / 2.89 ( 415) hydrogen bonds : angle 4.13442 / 3.00 ( 1221) Misc. bond : bond 0.02135 / 1.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.308 Fit side-chains TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 79 MET cc_start: 0.8695 (ttt) cc_final: 0.8445 (ttm) REVERT: A 403 ARG cc_start: 0.7299 (ttt90) cc_final: 0.6980 (ttm110) REVERT: A 427 PHE cc_start: 0.8229 (m-80) cc_final: 0.7964 (m-80) REVERT: M 101 GLN cc_start: 0.8608 (tt0) cc_final: 0.8250 (tt0) REVERT: N 24 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.7945 (p) REVERT: N 94 ASP cc_start: 0.8659 (m-30) cc_final: 0.8400 (m-30) REVERT: O 100 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7943 (tt) REVERT: P 58 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7257 (mp0) outliers start: 22 outliers final: 19 residues processed: 142 average time/residue: 0.4600 time to fit residues: 70.0795 Evaluate side-chains 145 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain A residue 488 GLN Chi-restraints excluded: chain M residue 36 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 67 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 ASN A 488 GLN N 77 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.110873 restraints weight = 9647.617| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.80 r_work: 0.3084 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8208 Z= 0.127 Angle : 2.654 33.649 11371 Z= 0.905 Chirality : 0.278 1.956 1331 Planarity : 0.004 0.034 1243 Dihedral : 12.857 105.985 1111 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.10 % Allowed : 18.62 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.29), residues: 888 helix: 2.65 (0.26), residues: 398 sheet: 0.68 (0.38), residues: 204 loop : -0.80 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 148 TYR 0.023 0.001 TYR A 180 PHE 0.017 0.001 PHE N 113 TRP 0.015 0.001 TRP A 467 HIS 0.003 0.001 HIS A 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 8203) covalent geometry : angle 2.65488 / 0.91 (11363) SS BOND : bond 0.00446 / 0.22 ( 4) SS BOND : angle 1.22956 / 0.68 ( 8) hydrogen bonds : bond 0.04089 / 2.77 ( 415) hydrogen bonds : angle 4.12118 / 2.99 ( 1221) Misc. bond : bond 0.01938 / 1.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.292 Fit side-chains TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 79 MET cc_start: 0.8694 (ttt) cc_final: 0.8448 (ttm) REVERT: A 403 ARG cc_start: 0.7291 (ttt90) cc_final: 0.6980 (ttm110) REVERT: N 24 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.7900 (p) REVERT: N 94 ASP cc_start: 0.8645 (m-30) cc_final: 0.8392 (m-30) REVERT: P 58 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7276 (mp0) outliers start: 23 outliers final: 18 residues processed: 143 average time/residue: 0.4499 time to fit residues: 69.0768 Evaluate side-chains 144 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain A residue 488 GLN Chi-restraints excluded: chain M residue 36 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 118 VAL Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 50 optimal weight: 0.0030 chunk 12 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN A 392 ASN A 443 ASN N 77 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 54 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.110790 restraints weight = 9565.917| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.78 r_work: 0.3083 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8208 Z= 0.131 Angle : 2.658 33.606 11371 Z= 0.906 Chirality : 0.278 1.956 1331 Planarity : 0.004 0.034 1243 Dihedral : 12.842 106.103 1111 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.56 % Allowed : 19.43 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.29), residues: 888 helix: 2.65 (0.26), residues: 399 sheet: 0.68 (0.38), residues: 204 loop : -0.81 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 148 TYR 0.023 0.001 TYR A 180 PHE 0.019 0.001 PHE N 113 TRP 0.015 0.001 TRP A 467 HIS 0.003 0.001 HIS A 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 8203) covalent geometry : angle 2.65831 / 0.91 (11363) SS BOND : bond 0.00475 / 0.23 ( 4) SS BOND : angle 1.28021 / 0.70 ( 8) hydrogen bonds : bond 0.04137 / 2.79 ( 415) hydrogen bonds : angle 4.12355 / 2.99 ( 1221) Misc. bond : bond 0.02005 / 1.06 ( 1) =============================================================================== Job complete usr+sys time: 3156.98 seconds wall clock time: 54 minutes 45.41 seconds (3285.41 seconds total)