Starting phenix.real_space_refine on Sun Aug 24 02:15:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rl7_19333/08_2025/8rl7_19333_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rl7_19333/08_2025/8rl7_19333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rl7_19333/08_2025/8rl7_19333_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rl7_19333/08_2025/8rl7_19333_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rl7_19333/08_2025/8rl7_19333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rl7_19333/08_2025/8rl7_19333.map" } resolution = 3.76 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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 S 40 5.16 5 C 5340 2.51 5 N 1376 2.21 5 O 1464 1.98 5 H 8042 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16262 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1824 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1824 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 6283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6283 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 12, 'TRANS': 410} Chain breaks: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 6283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6283 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 12, 'TRANS': 410} Chain breaks: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.83, per 1000 atoms: 0.17 Number of scatterers: 16262 At special positions: 0 Unit cell: (189.841, 72.123, 85.387, 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) S 40 16.00 O 1464 8.00 N 1376 7.00 C 5340 6.00 H 8042 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS D 11 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " 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: 1.28 Conformation dependent library (CDL) restraints added in 491.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 73.8% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'A' and resid 101 through 125 removed outlier: 4.366A pdb=" N VAL A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ALA A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 136 through 165 removed outlier: 4.031A pdb=" N GLN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 166 through 186 removed outlier: 3.907A pdb=" N ILE A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 222 Proline residue: A 215 - end of helix removed outlier: 3.574A pdb=" N PHE A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 257 removed outlier: 4.166A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 259 through 281 removed outlier: 3.744A pdb=" N LEU A 263 " --> pdb=" O TRP A 259 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 298 through 312 Processing helix chain 'A' and resid 312 through 347 removed outlier: 3.822A pdb=" N VAL A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 360 through 390 removed outlier: 4.016A pdb=" N LEU A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.900A pdb=" N CYS A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 438 removed outlier: 3.844A pdb=" N ALA A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 451 removed outlier: 3.613A pdb=" N ALA A 444 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 471 Processing helix chain 'A' and resid 474 through 490 Processing helix chain 'A' and resid 493 through 539 removed outlier: 4.055A pdb=" N CYS A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Proline residue: A 509 - end of helix removed outlier: 4.632A pdb=" N VAL A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N SER A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 125 removed outlier: 4.365A pdb=" N VAL C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA C 123 " --> pdb=" O ARG C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 136 through 165 removed outlier: 4.026A pdb=" N GLN C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) Proline residue: C 156 - end of helix Processing helix chain 'C' and resid 166 through 186 removed outlier: 3.906A pdb=" N ILE C 170 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 222 Proline residue: C 215 - end of helix removed outlier: 3.588A pdb=" N PHE C 222 " --> pdb=" O ILE C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 257 removed outlier: 4.245A pdb=" N ILE C 238 " --> pdb=" O PHE C 234 " (cutoff:3.500A) Proline residue: C 239 - end of helix Processing helix chain 'C' and resid 259 through 281 removed outlier: 3.748A pdb=" N LEU C 263 " --> pdb=" O TRP C 259 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER C 266 " --> pdb=" O ALA C 262 " (cutoff:3.500A) Proline residue: C 267 - end of helix Processing helix chain 'C' and resid 298 through 312 Processing helix chain 'C' and resid 312 through 347 removed outlier: 3.826A pdb=" N VAL C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Proline residue: C 337 - end of helix Processing helix chain 'C' and resid 360 through 390 removed outlier: 3.929A pdb=" N LEU C 390 " --> pdb=" O ARG C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 394 through 421 removed outlier: 3.520A pdb=" N LEU C 398 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N CYS C 400 " --> pdb=" O ASP C 396 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE C 415 " --> pdb=" O ILE C 411 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 416 " --> pdb=" O CYS C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.836A pdb=" N ALA C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 451 removed outlier: 3.622A pdb=" N ALA C 444 " --> pdb=" O TRP C 440 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP C 445 " --> pdb=" O ALA C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 471 Processing helix chain 'C' and resid 474 through 490 Processing helix chain 'C' and resid 493 through 539 removed outlier: 4.031A pdb=" N CYS C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Proline residue: C 509 - end of helix removed outlier: 4.591A pdb=" N VAL C 527 " --> pdb=" O ALA C 523 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N SER C 528 " --> pdb=" O LEU C 524 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.938A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.597A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N CYS D 96 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU D 4 " --> pdb=" O TRP D 118 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS D 120 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU D 6 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.597A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) 681 hydrogen bonds defined for protein. 1992 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: 3.41 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8028 1.03 - 1.23: 32 1.23 - 1.43: 3592 1.43 - 1.62: 4736 1.62 - 1.82: 60 Bond restraints: 16448 Sorted by residual: bond pdb=" C SER C 528 " pdb=" N ASP C 529 " ideal model delta sigma weight residual 1.334 1.276 0.058 1.46e-02 4.69e+03 1.60e+01 bond pdb=" C LYS C 224 " pdb=" O LYS C 224 " ideal model delta sigma weight residual 1.235 1.271 -0.035 9.00e-03 1.23e+04 1.55e+01 bond pdb=" C TYR A 246 " pdb=" N ILE A 247 " ideal model delta sigma weight residual 1.334 1.376 -0.042 1.26e-02 6.30e+03 1.13e+01 bond pdb=" C TYR C 246 " pdb=" N ILE C 247 " ideal model delta sigma weight residual 1.334 1.376 -0.042 1.26e-02 6.30e+03 1.10e+01 bond pdb=" C GLY A 245 " pdb=" N TYR A 246 " ideal model delta sigma weight residual 1.335 1.293 0.042 1.31e-02 5.83e+03 1.02e+01 ... (remaining 16443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 29096 1.87 - 3.74: 364 3.74 - 5.62: 48 5.62 - 7.49: 4 7.49 - 9.36: 6 Bond angle restraints: 29518 Sorted by residual: angle pdb=" CA GLY B 121 " pdb=" C GLY B 121 " pdb=" O GLY B 121 " ideal model delta sigma weight residual 122.29 117.45 4.84 8.10e-01 1.52e+00 3.58e+01 angle pdb=" CA SER C 528 " pdb=" C SER C 528 " pdb=" N ASP C 529 " ideal model delta sigma weight residual 117.30 123.09 -5.79 1.16e+00 7.43e-01 2.49e+01 angle pdb=" CA SER C 232 " pdb=" C SER C 232 " pdb=" O SER C 232 " ideal model delta sigma weight residual 121.07 115.88 5.19 1.10e+00 8.26e-01 2.23e+01 angle pdb=" CA GLY D 121 " pdb=" C GLY D 121 " pdb=" O GLY D 121 " ideal model delta sigma weight residual 121.58 117.34 4.24 9.00e-01 1.23e+00 2.22e+01 angle pdb=" C SER C 232 " pdb=" N VAL C 233 " pdb=" CA VAL C 233 " ideal model delta sigma weight residual 120.46 126.88 -6.42 1.37e+00 5.33e-01 2.20e+01 ... (remaining 29513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 7046 16.59 - 33.19: 540 33.19 - 49.78: 133 49.78 - 66.37: 132 66.37 - 82.97: 2 Dihedral angle restraints: 7853 sinusoidal: 4063 harmonic: 3790 Sorted by residual: dihedral pdb=" CG ARG D 72 " pdb=" CD ARG D 72 " pdb=" NE ARG D 72 " pdb=" CZ ARG D 72 " ideal model delta sinusoidal sigma weight residual 90.00 131.59 -41.59 2 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CA LYS A 224 " pdb=" CB LYS A 224 " pdb=" CG LYS A 224 " pdb=" CD LYS A 224 " ideal model delta sinusoidal sigma weight residual -180.00 -125.60 -54.40 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CA CYS B 11 " pdb=" CB CYS B 11 " pdb=" SG CYS B 11 " pdb=" SG CYS D 11 " ideal model delta sinusoidal sigma weight residual -73.00 -123.97 50.97 1 2.00e+01 2.50e-03 8.89e+00 ... (remaining 7850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1024 0.041 - 0.082: 220 0.082 - 0.124: 83 0.124 - 0.165: 16 0.165 - 0.206: 9 Chirality restraints: 1352 Sorted by residual: chirality pdb=" C4' LMT A 601 " pdb=" C3' LMT A 601 " pdb=" C5' LMT A 601 " pdb=" O1B LMT A 601 " both_signs ideal model delta sigma weight residual False -2.55 -2.76 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C5' LMT C 601 " pdb=" C4' LMT C 601 " pdb=" C6' LMT C 601 " pdb=" O5' LMT C 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.30 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C4' LMT C 601 " pdb=" C3' LMT C 601 " pdb=" C5' LMT C 601 " pdb=" O1B LMT C 601 " both_signs ideal model delta sigma weight residual False -2.55 -2.76 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1349 not shown) Planarity restraints: 2480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 526 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.05e+00 pdb=" C PHE C 526 " 0.046 2.00e-02 2.50e+03 pdb=" O PHE C 526 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL C 527 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 223 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C THR C 223 " 0.043 2.00e-02 2.50e+03 pdb=" O THR C 223 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS C 224 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 72 " -0.199 9.50e-02 1.11e+02 6.65e-02 4.97e+00 pdb=" NE ARG D 72 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG D 72 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG D 72 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG D 72 " -0.006 2.00e-02 2.50e+03 pdb="HH11 ARG D 72 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG D 72 " -0.006 2.00e-02 2.50e+03 pdb="HH21 ARG D 72 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D 72 " -0.000 2.00e-02 2.50e+03 ... (remaining 2477 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 1714 2.24 - 2.83: 36600 2.83 - 3.42: 45245 3.42 - 4.01: 60321 4.01 - 4.60: 93143 Nonbonded interactions: 237023 Sorted by model distance: nonbonded pdb=" O GLY A 206 " pdb=" HG SER A 209 " model vdw 1.649 2.450 nonbonded pdb=" O GLY C 206 " pdb=" HG SER C 209 " model vdw 1.650 2.450 nonbonded pdb=" O ILE C 369 " pdb=" HG1 THR C 373 " model vdw 1.663 2.450 nonbonded pdb=" O ILE A 369 " pdb=" HG1 THR A 373 " model vdw 1.665 2.450 nonbonded pdb=" O LEU A 117 " pdb=" HG1 THR A 121 " model vdw 1.677 2.450 ... (remaining 237018 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.300 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: 0.110 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.180 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 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 : 0.005 0.058 8409 Z= 0.313 Angle : 0.705 9.362 11456 Z= 0.468 Chirality : 0.044 0.206 1352 Planarity : 0.006 0.087 1416 Dihedral : 12.701 82.966 2836 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.74 % Allowed : 0.49 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.89 (0.26), residues: 1084 helix: 1.54 (0.19), residues: 766 sheet: 1.12 (0.50), residues: 80 loop : 0.59 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 532 TYR 0.015 0.001 TYR C 246 PHE 0.011 0.001 PHE C 236 TRP 0.029 0.002 TRP A 496 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 8406) covalent geometry : angle 0.70552 (11450) SS BOND : bond 0.00186 ( 3) SS BOND : angle 0.55427 ( 6) hydrogen bonds : bond 0.12154 ( 663) hydrogen bonds : angle 6.22664 ( 1992) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 170 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 ASN cc_start: 0.7960 (t0) cc_final: 0.7741 (t0) REVERT: D 74 ASN cc_start: 0.7258 (m-40) cc_final: 0.6512 (m-40) REVERT: D 100 ASN cc_start: 0.8105 (t0) cc_final: 0.7807 (t0) outliers start: 6 outliers final: 3 residues processed: 173 average time/residue: 0.1873 time to fit residues: 44.1751 Evaluate side-chains 135 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 224 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 123 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 = 0.4088 r_free = 0.4088 target = 0.185933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.175710 restraints weight = 29120.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.177945 restraints weight = 21310.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.179188 restraints weight = 16608.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.180432 restraints weight = 13695.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.180848 restraints weight = 11747.820| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8409 Z= 0.212 Angle : 0.565 4.953 11456 Z= 0.319 Chirality : 0.038 0.129 1352 Planarity : 0.005 0.044 1416 Dihedral : 5.613 50.150 1258 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.21 % Allowed : 8.95 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.88 (0.25), residues: 1084 helix: 1.65 (0.19), residues: 778 sheet: 0.57 (0.45), residues: 96 loop : 0.27 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 394 TYR 0.013 0.002 TYR C 116 PHE 0.016 0.002 PHE A 415 TRP 0.024 0.001 TRP C 178 HIS 0.008 0.002 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 8406) covalent geometry : angle 0.56458 (11450) SS BOND : bond 0.00330 ( 3) SS BOND : angle 0.80146 ( 6) hydrogen bonds : bond 0.05464 ( 663) hydrogen bonds : angle 4.92915 ( 1992) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 ASN cc_start: 0.8256 (t0) cc_final: 0.7961 (t0) outliers start: 18 outliers final: 11 residues processed: 141 average time/residue: 0.1771 time to fit residues: 34.3703 Evaluate side-chains 132 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.183366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.173206 restraints weight = 29061.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.175147 restraints weight = 21569.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.176712 restraints weight = 16871.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.177733 restraints weight = 13845.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.177885 restraints weight = 11930.383| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8409 Z= 0.186 Angle : 0.516 4.928 11456 Z= 0.291 Chirality : 0.037 0.120 1352 Planarity : 0.005 0.056 1416 Dihedral : 5.455 43.761 1257 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.33 % Allowed : 10.42 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.29 (0.25), residues: 1084 helix: 1.96 (0.19), residues: 762 sheet: 0.44 (0.49), residues: 80 loop : 0.67 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 72 TYR 0.011 0.001 TYR A 116 PHE 0.015 0.002 PHE A 415 TRP 0.023 0.001 TRP C 178 HIS 0.005 0.002 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8406) covalent geometry : angle 0.51556 (11450) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.83616 ( 6) hydrogen bonds : bond 0.05306 ( 663) hydrogen bonds : angle 4.75563 ( 1992) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 126 LEU cc_start: 0.7701 (tt) cc_final: 0.7415 (tt) outliers start: 19 outliers final: 14 residues processed: 130 average time/residue: 0.1932 time to fit residues: 34.2246 Evaluate side-chains 125 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain C residue 178 TRP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 407 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 8 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.181924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.171744 restraints weight = 28859.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.173935 restraints weight = 21348.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.174963 restraints weight = 16642.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.176238 restraints weight = 13982.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.176609 restraints weight = 11988.710| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8409 Z= 0.169 Angle : 0.506 5.109 11456 Z= 0.282 Chirality : 0.037 0.119 1352 Planarity : 0.005 0.058 1416 Dihedral : 5.183 39.075 1257 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.57 % Allowed : 10.78 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.31 (0.25), residues: 1084 helix: 1.99 (0.19), residues: 764 sheet: 0.23 (0.47), residues: 80 loop : 0.68 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 109 TYR 0.011 0.001 TYR A 116 PHE 0.013 0.002 PHE A 415 TRP 0.025 0.001 TRP A 178 HIS 0.004 0.001 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8406) covalent geometry : angle 0.50569 (11450) SS BOND : bond 0.00085 ( 3) SS BOND : angle 0.50553 ( 6) hydrogen bonds : bond 0.05124 ( 663) hydrogen bonds : angle 4.63332 ( 1992) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 LEU cc_start: 0.7565 (tt) cc_final: 0.7296 (tp) REVERT: A 178 TRP cc_start: 0.7582 (OUTLIER) cc_final: 0.6665 (p-90) REVERT: C 126 LEU cc_start: 0.7598 (tt) cc_final: 0.7372 (tt) REVERT: C 160 TYR cc_start: 0.6035 (t80) cc_final: 0.5793 (t80) REVERT: C 178 TRP cc_start: 0.7593 (OUTLIER) cc_final: 0.6687 (p-90) outliers start: 21 outliers final: 18 residues processed: 129 average time/residue: 0.2024 time to fit residues: 35.9010 Evaluate side-chains 133 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 178 TRP Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 407 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.181412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.171302 restraints weight = 28723.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.173286 restraints weight = 21448.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.174783 restraints weight = 16737.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.175367 restraints weight = 13924.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.175989 restraints weight = 12316.697| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8409 Z= 0.162 Angle : 0.493 4.968 11456 Z= 0.276 Chirality : 0.036 0.125 1352 Planarity : 0.004 0.058 1416 Dihedral : 5.117 36.358 1257 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.21 % Allowed : 12.50 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.43 (0.25), residues: 1084 helix: 2.11 (0.19), residues: 752 sheet: 0.11 (0.46), residues: 80 loop : 0.75 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 394 TYR 0.011 0.001 TYR A 116 PHE 0.029 0.002 PHE C 366 TRP 0.026 0.001 TRP C 178 HIS 0.004 0.001 HIS C 468 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8406) covalent geometry : angle 0.49315 (11450) SS BOND : bond 0.00067 ( 3) SS BOND : angle 0.35229 ( 6) hydrogen bonds : bond 0.05028 ( 663) hydrogen bonds : angle 4.57687 ( 1992) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 178 TRP cc_start: 0.7640 (OUTLIER) cc_final: 0.6609 (p-90) REVERT: C 126 LEU cc_start: 0.7436 (tt) cc_final: 0.7226 (tt) REVERT: C 178 TRP cc_start: 0.7640 (OUTLIER) cc_final: 0.6614 (p-90) outliers start: 18 outliers final: 15 residues processed: 130 average time/residue: 0.1893 time to fit residues: 34.2668 Evaluate side-chains 130 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 178 TRP Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 407 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 0.0770 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.182446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.172318 restraints weight = 28702.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.174385 restraints weight = 21414.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.175398 restraints weight = 16675.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.176504 restraints weight = 13993.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.177437 restraints weight = 11884.928| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8409 Z= 0.137 Angle : 0.473 4.823 11456 Z= 0.263 Chirality : 0.036 0.127 1352 Planarity : 0.004 0.057 1416 Dihedral : 4.808 34.808 1257 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.57 % Allowed : 13.24 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.56 (0.25), residues: 1084 helix: 2.29 (0.19), residues: 740 sheet: 0.14 (0.46), residues: 80 loop : 0.61 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 304 TYR 0.010 0.001 TYR A 116 PHE 0.012 0.001 PHE C 415 TRP 0.024 0.001 TRP C 178 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8406) covalent geometry : angle 0.47273 (11450) SS BOND : bond 0.00049 ( 3) SS BOND : angle 0.39586 ( 6) hydrogen bonds : bond 0.04805 ( 663) hydrogen bonds : angle 4.46634 ( 1992) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: C 126 LEU cc_start: 0.7349 (tt) cc_final: 0.7058 (tt) outliers start: 21 outliers final: 21 residues processed: 127 average time/residue: 0.1927 time to fit residues: 33.8298 Evaluate side-chains 132 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 178 TRP Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 475 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.178346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.168255 restraints weight = 29070.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.169724 restraints weight = 21931.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.171377 restraints weight = 17565.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.172425 restraints weight = 14528.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.172850 restraints weight = 12716.948| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8409 Z= 0.148 Angle : 0.483 4.829 11456 Z= 0.268 Chirality : 0.036 0.125 1352 Planarity : 0.004 0.057 1416 Dihedral : 4.851 33.442 1257 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.82 % Allowed : 13.36 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.57 (0.25), residues: 1084 helix: 2.32 (0.19), residues: 740 sheet: 0.01 (0.45), residues: 80 loop : 0.58 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 102 TYR 0.011 0.001 TYR A 116 PHE 0.012 0.001 PHE C 415 TRP 0.028 0.001 TRP C 178 HIS 0.003 0.001 HIS C 468 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8406) covalent geometry : angle 0.48285 (11450) SS BOND : bond 0.00065 ( 3) SS BOND : angle 0.41827 ( 6) hydrogen bonds : bond 0.04812 ( 663) hydrogen bonds : angle 4.45605 ( 1992) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: C 126 LEU cc_start: 0.7522 (tt) cc_final: 0.7277 (tt) outliers start: 23 outliers final: 22 residues processed: 128 average time/residue: 0.1970 time to fit residues: 34.6420 Evaluate side-chains 137 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 178 TRP Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 475 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 40 optimal weight: 0.1980 chunk 73 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.178945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.155076 restraints weight = 29977.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.161255 restraints weight = 15472.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.165334 restraints weight = 9721.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.167997 restraints weight = 6803.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.169747 restraints weight = 5146.272| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8409 Z= 0.140 Angle : 0.475 4.780 11456 Z= 0.263 Chirality : 0.036 0.124 1352 Planarity : 0.004 0.056 1416 Dihedral : 4.707 33.827 1257 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.57 % Allowed : 13.60 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.62 (0.25), residues: 1084 helix: 2.38 (0.19), residues: 740 sheet: -0.00 (0.45), residues: 80 loop : 0.53 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 102 TYR 0.010 0.001 TYR A 116 PHE 0.012 0.001 PHE C 415 TRP 0.027 0.001 TRP C 178 HIS 0.002 0.001 HIS C 341 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8406) covalent geometry : angle 0.47458 (11450) SS BOND : bond 0.00082 ( 3) SS BOND : angle 0.30335 ( 6) hydrogen bonds : bond 0.04722 ( 663) hydrogen bonds : angle 4.41457 ( 1992) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7487 (mtm-85) REVERT: D 102 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7609 (mtm-85) REVERT: C 126 LEU cc_start: 0.7162 (tt) cc_final: 0.6941 (tt) outliers start: 21 outliers final: 21 residues processed: 127 average time/residue: 0.1927 time to fit residues: 33.8466 Evaluate side-chains 131 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 178 TRP Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 475 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.176799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.152572 restraints weight = 30137.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.158758 restraints weight = 15640.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.162841 restraints weight = 9838.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.165485 restraints weight = 6929.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.167315 restraints weight = 5276.271| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8409 Z= 0.166 Angle : 0.502 4.816 11456 Z= 0.279 Chirality : 0.036 0.122 1352 Planarity : 0.004 0.058 1416 Dihedral : 5.034 35.758 1257 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.57 % Allowed : 13.97 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.46 (0.25), residues: 1084 helix: 2.27 (0.19), residues: 742 sheet: -0.19 (0.46), residues: 80 loop : 0.47 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 102 TYR 0.011 0.001 TYR A 116 PHE 0.013 0.002 PHE C 526 TRP 0.029 0.001 TRP C 178 HIS 0.004 0.002 HIS C 468 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8406) covalent geometry : angle 0.50181 (11450) SS BOND : bond 0.00091 ( 3) SS BOND : angle 0.43491 ( 6) hydrogen bonds : bond 0.04917 ( 663) hydrogen bonds : angle 4.51580 ( 1992) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.448 Fit side-chains REVERT: C 126 LEU cc_start: 0.7208 (tt) cc_final: 0.6896 (tt) outliers start: 21 outliers final: 20 residues processed: 127 average time/residue: 0.2016 time to fit residues: 35.6273 Evaluate side-chains 126 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 178 TRP Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 475 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.176012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.152128 restraints weight = 29976.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.158195 restraints weight = 15611.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.162168 restraints weight = 9855.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.164732 restraints weight = 6970.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.166617 restraints weight = 5328.648| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8409 Z= 0.174 Angle : 0.511 4.853 11456 Z= 0.285 Chirality : 0.037 0.121 1352 Planarity : 0.004 0.058 1416 Dihedral : 5.033 42.176 1253 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.45 % Allowed : 14.34 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.38 (0.25), residues: 1084 helix: 2.22 (0.19), residues: 742 sheet: -0.33 (0.46), residues: 80 loop : 0.44 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 394 TYR 0.010 0.001 TYR A 116 PHE 0.013 0.002 PHE C 526 TRP 0.029 0.001 TRP C 178 HIS 0.004 0.001 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8406) covalent geometry : angle 0.51137 (11450) SS BOND : bond 0.00081 ( 3) SS BOND : angle 0.39150 ( 6) hydrogen bonds : bond 0.04986 ( 663) hydrogen bonds : angle 4.56489 ( 1992) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue MET 271 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue MET 306 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.415 Fit side-chains REVERT: C 126 LEU cc_start: 0.7470 (tt) cc_final: 0.7247 (tt) outliers start: 20 outliers final: 20 residues processed: 126 average time/residue: 0.2115 time to fit residues: 36.7605 Evaluate side-chains 126 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 178 TRP Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 475 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 81 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.174181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.149984 restraints weight = 30361.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.156033 restraints weight = 15882.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.159978 restraints weight = 10061.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.162580 restraints weight = 7157.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.164325 restraints weight = 5495.182| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8409 Z= 0.201 Angle : 0.540 5.086 11456 Z= 0.302 Chirality : 0.037 0.120 1352 Planarity : 0.005 0.060 1416 Dihedral : 5.731 58.158 1253 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.45 % Allowed : 14.09 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.18 (0.25), residues: 1084 helix: 2.10 (0.19), residues: 740 sheet: -0.52 (0.46), residues: 80 loop : 0.32 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 394 TYR 0.011 0.001 TYR A 116 PHE 0.016 0.002 PHE C 526 TRP 0.031 0.001 TRP C 178 HIS 0.004 0.002 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 8406) covalent geometry : angle 0.54001 (11450) SS BOND : bond 0.00107 ( 3) SS BOND : angle 0.44203 ( 6) hydrogen bonds : bond 0.05230 ( 663) hydrogen bonds : angle 4.68920 ( 1992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2746.26 seconds wall clock time: 47 minutes 34.17 seconds (2854.17 seconds total)