Starting phenix.real_space_refine on Thu Jul 2 03:42:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e1m_27825/07_2026/8e1m_27825.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e1m_27825/07_2026/8e1m_27825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e1m_27825/07_2026/8e1m_27825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e1m_27825/07_2026/8e1m_27825.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e1m_27825/07_2026/8e1m_27825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e1m_27825/07_2026/8e1m_27825.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8e1m_27825/07_2026/8e1m_27825.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e1m_27825/07_2026/8e1m_27825.cif" } resolution = 2.9 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= 0.003 sd= 0.027 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 P 3 5.49 5 S 29 5.16 5 C 3627 2.51 5 N 980 2.21 5 O 1052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5691 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 955 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 958 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1921 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 14, 'HIS:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 104 Chain: "L" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 837 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 103} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 901 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.01, per 1000 atoms: 0.18 Number of scatterers: 5691 At special positions: 0 Unit cell: (93.45, 122.85, 79.8, 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 29 16.00 P 3 15.00 O 1052 8.00 N 980 7.00 C 3627 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 114 " 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: 0.32 Conformation dependent library (CDL) restraints added in 216.7 milliseconds 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 9 sheets defined 53.3% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 9 through 41 removed outlier: 3.970A pdb=" N ILE A 14 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN A 16 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 4.199A pdb=" N ARG A 46 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 84 Proline residue: A 59 - end of helix removed outlier: 3.681A pdb=" N SER A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 102 removed outlier: 3.694A pdb=" N ILE A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 138 removed outlier: 3.608A pdb=" N ARG A 112 " --> pdb=" O TRP A 108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 123 removed outlier: 3.717A pdb=" N ASP B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 169 Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 174 through 190 Processing helix chain 'B' and resid 195 through 220 removed outlier: 3.525A pdb=" N GLY B 199 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 126 Processing helix chain 'C' and resid 126 through 152 Proline residue: C 149 - end of helix Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 166 through 172 removed outlier: 3.767A pdb=" N SER C 169 " --> pdb=" O GLY C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 190 removed outlier: 3.525A pdb=" N LYS C 183 " --> pdb=" O GLN C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 265 removed outlier: 3.662A pdb=" N PHE C 265 " --> pdb=" O VAL C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 285 through 296 Processing helix chain 'C' and resid 296 through 308 Processing helix chain 'C' and resid 309 through 317 removed outlier: 3.870A pdb=" N LYS C 315 " --> pdb=" O LYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 335 removed outlier: 3.502A pdb=" N VAL C 324 " --> pdb=" O ALA C 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 109 removed outlier: 3.830A pdb=" N THR H 109 " --> pdb=" O ALA H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 122 Processing sheet with id=AA1, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.045A pdb=" N ILE C 362 " --> pdb=" O LYS C 355 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LYS C 355 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL C 364 " --> pdb=" O SER C 353 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 366 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE C 351 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY C 368 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL C 349 " --> pdb=" O GLY C 368 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP C 345 " --> pdb=" O GLN C 372 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE C 374 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE C 343 " --> pdb=" O ILE C 374 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 337 through 339 removed outlier: 5.005A pdb=" N ARG C 404 " --> pdb=" O PRO C 363 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN C 375 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASN C 392 " --> pdb=" O ASN C 375 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N TYR C 377 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N GLU C 390 " --> pdb=" O TYR C 377 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N LYS C 379 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 12.788A pdb=" N GLY C 388 " --> pdb=" O LYS C 379 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU C 421 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR C 403 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE C 419 " --> pdb=" O THR C 403 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 25 through 27 removed outlier: 3.531A pdb=" N ASP L 94 " --> pdb=" O SER L 91 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER L 96 " --> pdb=" O SER L 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 30 through 33 removed outlier: 7.084A pdb=" N LEU L 31 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N MET L 57 " --> pdb=" O TYR L 73 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR L 73 " --> pdb=" O MET L 57 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 30 through 33 removed outlier: 7.084A pdb=" N LEU L 31 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR L 121 " --> pdb=" O GLN L 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 50 through 51 Processing sheet with id=AA7, first strand: chain 'H' and resid 22 through 26 Processing sheet with id=AA8, first strand: chain 'H' and resid 76 through 78 removed outlier: 6.843A pdb=" N TRP H 55 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL H 69 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL H 53 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY H 52 " --> pdb=" O TYR H 117 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR H 125 " --> pdb=" O ARG H 116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 76 through 78 removed outlier: 6.843A pdb=" N TRP H 55 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL H 69 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL H 53 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY H 52 " --> pdb=" O TYR H 117 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1128 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: 0.92 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1826 1.34 - 1.46: 1421 1.46 - 1.59: 2506 1.59 - 1.71: 6 1.71 - 1.84: 46 Bond restraints: 5805 Sorted by residual: bond pdb=" CA7 CDL A 301 " pdb=" OA8 CDL A 301 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.15e+02 bond pdb=" CB7 CDL A 301 " pdb=" OB8 CDL A 301 " ideal model delta sigma weight residual 1.334 1.446 -0.112 1.10e-02 8.26e+03 1.04e+02 bond pdb=" CB5 CDL A 301 " pdb=" OB6 CDL A 301 " ideal model delta sigma weight residual 1.342 1.450 -0.108 1.50e-02 4.44e+03 5.23e+01 bond pdb=" CA5 CDL A 301 " pdb=" OA6 CDL A 301 " ideal model delta sigma weight residual 1.342 1.449 -0.107 1.50e-02 4.44e+03 5.12e+01 bond pdb=" C8 PTY B 301 " pdb=" O7 PTY B 301 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.77e+01 ... (remaining 5800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 7661 2.19 - 4.38: 139 4.38 - 6.57: 31 6.57 - 8.76: 3 8.76 - 10.94: 6 Bond angle restraints: 7840 Sorted by residual: angle pdb=" C51 CDL A 301 " pdb=" CB5 CDL A 301 " pdb=" OB6 CDL A 301 " ideal model delta sigma weight residual 111.33 121.20 -9.87 1.32e+00 5.72e-01 5.58e+01 angle pdb=" C11 CDL A 301 " pdb=" CA5 CDL A 301 " pdb=" OA6 CDL A 301 " ideal model delta sigma weight residual 111.33 120.23 -8.90 1.32e+00 5.72e-01 4.53e+01 angle pdb=" C31 CDL A 301 " pdb=" CA7 CDL A 301 " pdb=" OA8 CDL A 301 " ideal model delta sigma weight residual 111.64 121.14 -9.50 1.65e+00 3.69e-01 3.33e+01 angle pdb=" OB6 CDL A 301 " pdb=" CB5 CDL A 301 " pdb=" OB7 CDL A 301 " ideal model delta sigma weight residual 123.92 118.41 5.51 1.00e+00 9.92e-01 3.01e+01 angle pdb=" C71 CDL A 301 " pdb=" CB7 CDL A 301 " pdb=" OB8 CDL A 301 " ideal model delta sigma weight residual 111.64 120.27 -8.63 1.65e+00 3.69e-01 2.75e+01 ... (remaining 7835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.84: 3211 23.84 - 47.68: 177 47.68 - 71.52: 19 71.52 - 95.36: 3 95.36 - 119.20: 1 Dihedral angle restraints: 3411 sinusoidal: 1283 harmonic: 2128 Sorted by residual: dihedral pdb=" CB CYS A 10 " pdb=" SG CYS A 10 " pdb=" SG CYS A 77 " pdb=" CB CYS A 77 " ideal model delta sinusoidal sigma weight residual -86.00 -124.76 38.76 1 1.00e+01 1.00e-02 2.11e+01 dihedral pdb=" N1 PTY B 301 " pdb=" C2 PTY B 301 " pdb=" C3 PTY B 301 " pdb=" O11 PTY B 301 " ideal model delta sinusoidal sigma weight residual 65.33 -53.87 119.20 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" CA ILE B 166 " pdb=" C ILE B 166 " pdb=" N ASP B 167 " pdb=" CA ASP B 167 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 3408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 508 0.031 - 0.063: 235 0.063 - 0.094: 68 0.094 - 0.125: 38 0.125 - 0.156: 7 Chirality restraints: 856 Sorted by residual: chirality pdb=" CA ILE L 72 " pdb=" N ILE L 72 " pdb=" C ILE L 72 " pdb=" CB ILE L 72 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CA ILE C 362 " pdb=" N ILE C 362 " pdb=" C ILE C 362 " pdb=" CB ILE C 362 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ILE L 130 " pdb=" N ILE L 130 " pdb=" C ILE L 130 " pdb=" CB ILE L 130 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 853 not shown) Planarity restraints: 1003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 145 " -0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO B 146 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 8 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A 9 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 9 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 9 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 67 " 0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO L 68 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO L 68 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 68 " 0.021 5.00e-02 4.00e+02 ... (remaining 1000 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 263 2.72 - 3.27: 5714 3.27 - 3.81: 9339 3.81 - 4.36: 12101 4.36 - 4.90: 20858 Nonbonded interactions: 48275 Sorted by model distance: nonbonded pdb=" O LEU B 97 " pdb=" OG1 THR B 101 " model vdw 2.179 3.040 nonbonded pdb=" OD1 ASP L 50 " pdb=" OG SER L 55 " model vdw 2.181 3.040 nonbonded pdb=" OG SER L 48 " pdb=" OD2 ASP L 50 " model vdw 2.185 3.040 nonbonded pdb=" NZ LYS L 63 " pdb=" O ASP L 105 " model vdw 2.231 3.120 nonbonded pdb=" NZ LYS C 278 " pdb=" O PRO C 282 " model vdw 2.249 3.120 ... (remaining 48270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.270 Find NCS groups from input model: 0.030 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:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 5808 Z= 0.364 Angle : 0.770 10.945 7846 Z= 0.412 Chirality : 0.043 0.156 856 Planarity : 0.004 0.049 1003 Dihedral : 14.278 119.204 2050 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.31), residues: 748 helix: -0.30 (0.26), residues: 370 sheet: -0.54 (0.45), residues: 142 loop : -0.63 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 38 TYR 0.016 0.002 TYR H 117 PHE 0.012 0.002 PHE A 96 TRP 0.019 0.002 TRP H 66 HIS 0.003 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.36 ( 5805) covalent geometry : angle 0.76531 / 0.41 ( 7840) SS BOND : bond 0.00267 / 0.13 ( 3) SS BOND : angle 3.10585 / 1.66 ( 6) hydrogen bonds : bond 0.22590 / 15.01 ( 380) hydrogen bonds : angle 9.56264 / 7.11 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 200 TYR cc_start: 0.7366 (m-80) cc_final: 0.6891 (m-80) outliers start: 0 outliers final: 2 residues processed: 111 average time/residue: 0.4983 time to fit residues: 57.9784 Evaluate side-chains 85 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain B residue 161 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 30.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN L 66 GLN H 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.061049 restraints weight = 12771.179| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.57 r_work: 0.2771 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5808 Z= 0.159 Angle : 0.594 8.607 7846 Z= 0.309 Chirality : 0.043 0.146 856 Planarity : 0.005 0.043 1003 Dihedral : 8.845 62.143 894 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.29 % Allowed : 10.70 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.31), residues: 748 helix: 1.37 (0.26), residues: 372 sheet: -0.23 (0.45), residues: 142 loop : -0.27 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 170 TYR 0.010 0.001 TYR H 117 PHE 0.017 0.001 PHE A 96 TRP 0.011 0.001 TRP A 108 HIS 0.004 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 ( 5805) covalent geometry : angle 0.59307 / 0.31 ( 7840) SS BOND : bond 0.00190 / 0.09 ( 3) SS BOND : angle 1.59879 / 0.84 ( 6) hydrogen bonds : bond 0.04215 / 2.90 ( 380) hydrogen bonds : angle 5.17729 / 3.88 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8270 (m) cc_final: 0.7999 (p) REVERT: A 76 ASP cc_start: 0.9041 (t0) cc_final: 0.8768 (t0) REVERT: B 127 ASN cc_start: 0.7890 (t0) cc_final: 0.7620 (t0) REVERT: B 204 MET cc_start: 0.9150 (mtm) cc_final: 0.8942 (mtm) REVERT: L 103 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7975 (mt-10) REVERT: L 127 LYS cc_start: 0.9033 (tttp) cc_final: 0.8736 (tttp) REVERT: L 129 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8058 (mt-10) REVERT: H 24 LYS cc_start: 0.8966 (tppp) cc_final: 0.8525 (mtmp) outliers start: 7 outliers final: 4 residues processed: 96 average time/residue: 0.4423 time to fit residues: 44.6578 Evaluate side-chains 90 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain L residue 105 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 123 ASN L 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.060848 restraints weight = 12772.854| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.56 r_work: 0.2770 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5808 Z= 0.154 Angle : 0.550 9.232 7846 Z= 0.285 Chirality : 0.042 0.144 856 Planarity : 0.004 0.045 1003 Dihedral : 8.257 65.089 890 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.21 % Allowed : 12.73 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.32), residues: 748 helix: 2.13 (0.26), residues: 372 sheet: -0.13 (0.45), residues: 142 loop : -0.23 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 170 TYR 0.010 0.001 TYR H 117 PHE 0.015 0.001 PHE A 96 TRP 0.009 0.001 TRP A 32 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 5805) covalent geometry : angle 0.54973 / 0.28 ( 7840) SS BOND : bond 0.00218 / 0.10 ( 3) SS BOND : angle 1.00728 / 0.53 ( 6) hydrogen bonds : bond 0.03679 / 2.51 ( 380) hydrogen bonds : angle 4.55844 / 3.40 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8202 (m) cc_final: 0.7885 (p) REVERT: A 131 MET cc_start: 0.7942 (mmt) cc_final: 0.7698 (mmm) REVERT: B 127 ASN cc_start: 0.7818 (t0) cc_final: 0.7509 (t0) REVERT: B 162 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8232 (mp) REVERT: B 195 LEU cc_start: 0.8155 (mm) cc_final: 0.7828 (tm) REVERT: B 198 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7631 (mmt) REVERT: B 200 TYR cc_start: 0.8679 (m-80) cc_final: 0.8398 (m-10) REVERT: B 204 MET cc_start: 0.9179 (mtm) cc_final: 0.8905 (mtm) REVERT: C 179 GLN cc_start: 0.8885 (mp10) cc_final: 0.8681 (mm-40) REVERT: C 431 THR cc_start: 0.8471 (m) cc_final: 0.7975 (p) REVERT: L 103 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8280 (mt-10) REVERT: L 127 LYS cc_start: 0.8973 (tttp) cc_final: 0.8652 (tttp) REVERT: L 129 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7938 (mt-10) REVERT: H 24 LYS cc_start: 0.9005 (tppp) cc_final: 0.8638 (mtmp) outliers start: 12 outliers final: 3 residues processed: 97 average time/residue: 0.4687 time to fit residues: 47.9120 Evaluate side-chains 91 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 175 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 60 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 50 optimal weight: 0.0050 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 335 GLN L 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.085149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.062911 restraints weight = 13027.135| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.54 r_work: 0.2835 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5808 Z= 0.113 Angle : 0.520 10.011 7846 Z= 0.265 Chirality : 0.041 0.142 856 Planarity : 0.004 0.055 1003 Dihedral : 7.549 61.911 890 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.03 % Allowed : 14.21 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.32), residues: 748 helix: 2.38 (0.26), residues: 374 sheet: 0.03 (0.45), residues: 142 loop : -0.11 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 181 TYR 0.008 0.001 TYR C 325 PHE 0.012 0.001 PHE A 96 TRP 0.009 0.001 TRP A 32 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 5805) covalent geometry : angle 0.51982 / 0.26 ( 7840) SS BOND : bond 0.00286 / 0.15 ( 3) SS BOND : angle 1.05553 / 0.55 ( 6) hydrogen bonds : bond 0.03291 / 2.24 ( 380) hydrogen bonds : angle 4.23952 / 3.16 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8074 (mp0) REVERT: B 127 ASN cc_start: 0.7712 (t0) cc_final: 0.7410 (t0) REVERT: B 131 LYS cc_start: 0.8741 (ttmt) cc_final: 0.8256 (tttt) REVERT: B 162 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8309 (mp) REVERT: B 195 LEU cc_start: 0.8135 (mm) cc_final: 0.7837 (tm) REVERT: B 198 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7647 (mmt) REVERT: B 200 TYR cc_start: 0.8638 (m-80) cc_final: 0.8300 (m-10) REVERT: B 204 MET cc_start: 0.9183 (mtm) cc_final: 0.8899 (mtm) REVERT: C 431 THR cc_start: 0.8462 (m) cc_final: 0.8030 (p) REVERT: H 24 LYS cc_start: 0.8999 (tppp) cc_final: 0.8759 (mtmp) outliers start: 11 outliers final: 4 residues processed: 106 average time/residue: 0.4178 time to fit residues: 46.6552 Evaluate side-chains 96 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain H residue 86 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 47 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 21 optimal weight: 0.0170 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.082219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.060831 restraints weight = 12906.563| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.59 r_work: 0.2775 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5808 Z= 0.174 Angle : 0.553 8.965 7846 Z= 0.283 Chirality : 0.043 0.190 856 Planarity : 0.004 0.048 1003 Dihedral : 7.584 63.937 890 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.95 % Allowed : 14.94 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.32), residues: 748 helix: 2.51 (0.26), residues: 372 sheet: 0.17 (0.46), residues: 142 loop : -0.02 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 181 TYR 0.016 0.001 TYR B 159 PHE 0.012 0.001 PHE A 96 TRP 0.007 0.001 TRP A 32 HIS 0.004 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 5805) covalent geometry : angle 0.55214 / 0.28 ( 7840) SS BOND : bond 0.00280 / 0.14 ( 3) SS BOND : angle 1.30499 / 0.68 ( 6) hydrogen bonds : bond 0.03485 / 2.42 ( 380) hydrogen bonds : angle 4.11775 / 3.06 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8082 (mp0) REVERT: A 131 MET cc_start: 0.7872 (mmt) cc_final: 0.7536 (mmm) REVERT: B 127 ASN cc_start: 0.7829 (t0) cc_final: 0.7512 (t0) REVERT: B 131 LYS cc_start: 0.8735 (ttmt) cc_final: 0.8245 (tttt) REVERT: B 162 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8220 (mp) REVERT: B 195 LEU cc_start: 0.8134 (mm) cc_final: 0.7815 (tm) REVERT: B 198 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7678 (mmt) REVERT: B 200 TYR cc_start: 0.8635 (m-80) cc_final: 0.8310 (m-10) REVERT: B 204 MET cc_start: 0.9233 (mtm) cc_final: 0.8938 (mtm) REVERT: C 431 THR cc_start: 0.8535 (m) cc_final: 0.8055 (p) REVERT: L 127 LYS cc_start: 0.8954 (tttm) cc_final: 0.8700 (tttp) REVERT: L 129 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8025 (mt-10) REVERT: H 24 LYS cc_start: 0.8999 (tppp) cc_final: 0.8667 (mtmt) outliers start: 16 outliers final: 8 residues processed: 100 average time/residue: 0.4344 time to fit residues: 45.7295 Evaluate side-chains 102 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 94 LYS Chi-restraints excluded: chain H residue 109 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 26 optimal weight: 50.0000 chunk 32 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 408 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.081353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.059848 restraints weight = 12819.549| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.58 r_work: 0.2753 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5808 Z= 0.222 Angle : 0.590 9.697 7846 Z= 0.296 Chirality : 0.044 0.198 856 Planarity : 0.004 0.047 1003 Dihedral : 7.745 64.530 890 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.40 % Allowed : 15.68 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.32), residues: 748 helix: 2.50 (0.27), residues: 372 sheet: 0.24 (0.47), residues: 135 loop : -0.07 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 181 TYR 0.020 0.002 TYR B 159 PHE 0.012 0.001 PHE C 322 TRP 0.010 0.001 TRP H 66 HIS 0.004 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 ( 5805) covalent geometry : angle 0.58920 / 0.30 ( 7840) SS BOND : bond 0.00258 / 0.13 ( 3) SS BOND : angle 1.07580 / 0.55 ( 6) hydrogen bonds : bond 0.03587 / 2.49 ( 380) hydrogen bonds : angle 4.12281 / 3.05 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8088 (mp0) REVERT: A 131 MET cc_start: 0.7903 (mmt) cc_final: 0.7576 (mmm) REVERT: B 127 ASN cc_start: 0.7812 (t0) cc_final: 0.7538 (t0) REVERT: B 162 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8250 (mp) REVERT: B 195 LEU cc_start: 0.8148 (mm) cc_final: 0.7856 (tm) REVERT: B 198 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7709 (mmt) REVERT: B 200 TYR cc_start: 0.8621 (m-80) cc_final: 0.8317 (m-10) REVERT: B 204 MET cc_start: 0.9241 (mtm) cc_final: 0.8968 (mtm) REVERT: C 431 THR cc_start: 0.8420 (m) cc_final: 0.7943 (p) REVERT: L 57 MET cc_start: 0.9361 (OUTLIER) cc_final: 0.8785 (tpp) REVERT: L 104 GLU cc_start: 0.7649 (tp30) cc_final: 0.7420 (tm-30) REVERT: L 127 LYS cc_start: 0.8967 (tttm) cc_final: 0.8690 (tttp) REVERT: L 129 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8032 (mt-10) outliers start: 13 outliers final: 7 residues processed: 98 average time/residue: 0.3972 time to fit residues: 40.8985 Evaluate side-chains 99 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain L residue 57 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 109 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.081227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.059784 restraints weight = 12934.073| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.58 r_work: 0.2748 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5808 Z= 0.206 Angle : 0.583 10.433 7846 Z= 0.293 Chirality : 0.044 0.173 856 Planarity : 0.004 0.046 1003 Dihedral : 7.787 63.616 890 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.58 % Allowed : 16.61 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.32), residues: 748 helix: 2.53 (0.27), residues: 372 sheet: 0.26 (0.47), residues: 135 loop : -0.01 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 181 TYR 0.016 0.001 TYR B 159 PHE 0.012 0.001 PHE C 322 TRP 0.011 0.001 TRP H 66 HIS 0.004 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 ( 5805) covalent geometry : angle 0.58268 / 0.29 ( 7840) SS BOND : bond 0.00250 / 0.12 ( 3) SS BOND : angle 0.91256 / 0.47 ( 6) hydrogen bonds : bond 0.03518 / 2.44 ( 380) hydrogen bonds : angle 4.09144 / 3.02 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8101 (mp0) REVERT: A 131 MET cc_start: 0.7802 (mmt) cc_final: 0.7558 (mmm) REVERT: B 127 ASN cc_start: 0.7902 (t0) cc_final: 0.7697 (t0) REVERT: B 162 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8273 (mp) REVERT: B 195 LEU cc_start: 0.8210 (mm) cc_final: 0.7910 (tm) REVERT: B 198 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7734 (mmt) REVERT: B 200 TYR cc_start: 0.8627 (m-80) cc_final: 0.8342 (m-10) REVERT: B 204 MET cc_start: 0.9243 (mtm) cc_final: 0.8975 (mtm) REVERT: C 431 THR cc_start: 0.8465 (m) cc_final: 0.8005 (p) REVERT: L 57 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.8763 (tpp) REVERT: L 104 GLU cc_start: 0.7620 (tp30) cc_final: 0.7256 (tm-30) REVERT: L 127 LYS cc_start: 0.8962 (tttm) cc_final: 0.8700 (tttp) REVERT: L 129 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8030 (mt-10) REVERT: H 24 LYS cc_start: 0.9079 (mtpm) cc_final: 0.8486 (mtmp) outliers start: 14 outliers final: 10 residues processed: 101 average time/residue: 0.4233 time to fit residues: 44.8437 Evaluate side-chains 101 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain L residue 57 MET Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 109 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 27 optimal weight: 0.2980 chunk 67 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.082597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.061101 restraints weight = 12631.309| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.58 r_work: 0.2785 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5808 Z= 0.142 Angle : 0.579 10.861 7846 Z= 0.289 Chirality : 0.044 0.202 856 Planarity : 0.004 0.048 1003 Dihedral : 7.523 60.989 890 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.03 % Allowed : 16.42 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.32), residues: 748 helix: 2.55 (0.27), residues: 372 sheet: 0.34 (0.47), residues: 135 loop : 0.04 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 181 TYR 0.014 0.001 TYR B 159 PHE 0.012 0.001 PHE A 96 TRP 0.010 0.001 TRP H 66 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 5805) covalent geometry : angle 0.57284 / 0.29 ( 7840) SS BOND : bond 0.00305 / 0.16 ( 3) SS BOND : angle 3.09187 / 1.65 ( 6) hydrogen bonds : bond 0.03352 / 2.31 ( 380) hydrogen bonds : angle 3.99762 / 2.95 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8121 (mp0) REVERT: A 131 MET cc_start: 0.7759 (mmt) cc_final: 0.7524 (mmm) REVERT: B 131 LYS cc_start: 0.8739 (ttmt) cc_final: 0.8251 (tttt) REVERT: B 162 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8254 (mp) REVERT: B 195 LEU cc_start: 0.8292 (mm) cc_final: 0.7978 (tm) REVERT: B 200 TYR cc_start: 0.8613 (m-80) cc_final: 0.8335 (m-10) REVERT: B 204 MET cc_start: 0.9226 (mtm) cc_final: 0.8976 (mtm) REVERT: C 431 THR cc_start: 0.8384 (m) cc_final: 0.7999 (p) REVERT: L 104 GLU cc_start: 0.7585 (tp30) cc_final: 0.7155 (tm-30) REVERT: L 127 LYS cc_start: 0.8930 (tttm) cc_final: 0.8674 (tttp) REVERT: L 129 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8050 (mt-10) REVERT: H 24 LYS cc_start: 0.9083 (mtpm) cc_final: 0.8502 (mtmp) outliers start: 11 outliers final: 7 residues processed: 99 average time/residue: 0.3811 time to fit residues: 39.6217 Evaluate side-chains 97 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 109 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 35 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.080786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.059225 restraints weight = 12849.971| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.57 r_work: 0.2737 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 5808 Z= 0.254 Angle : 0.632 9.904 7846 Z= 0.324 Chirality : 0.045 0.218 856 Planarity : 0.004 0.050 1003 Dihedral : 7.872 63.800 890 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.58 % Allowed : 16.05 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.32), residues: 748 helix: 2.48 (0.27), residues: 373 sheet: 0.30 (0.47), residues: 135 loop : -0.16 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 85 TYR 0.017 0.002 TYR H 117 PHE 0.013 0.001 PHE A 96 TRP 0.011 0.001 TRP H 66 HIS 0.004 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.25 ( 5805) covalent geometry : angle 0.62678 / 0.32 ( 7840) SS BOND : bond 0.00206 / 0.10 ( 3) SS BOND : angle 2.97427 / 1.57 ( 6) hydrogen bonds : bond 0.03678 / 2.56 ( 380) hydrogen bonds : angle 4.13470 / 3.05 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8121 (mp0) REVERT: A 131 MET cc_start: 0.7891 (mmt) cc_final: 0.7629 (mmm) REVERT: B 195 LEU cc_start: 0.8332 (mm) cc_final: 0.8036 (tm) REVERT: B 200 TYR cc_start: 0.8624 (m-80) cc_final: 0.8373 (m-10) REVERT: B 204 MET cc_start: 0.9256 (mtm) cc_final: 0.9017 (mtm) REVERT: C 431 THR cc_start: 0.8441 (m) cc_final: 0.7993 (p) REVERT: L 57 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.8781 (tpp) REVERT: L 104 GLU cc_start: 0.7639 (tp30) cc_final: 0.7180 (tt0) REVERT: H 24 LYS cc_start: 0.9078 (mtpm) cc_final: 0.8490 (mtmp) outliers start: 14 outliers final: 9 residues processed: 95 average time/residue: 0.4237 time to fit residues: 42.1918 Evaluate side-chains 97 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain L residue 57 MET Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 56 optimal weight: 0.0980 chunk 66 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.083166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.061823 restraints weight = 12806.700| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.59 r_work: 0.2809 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5808 Z= 0.126 Angle : 0.589 12.417 7846 Z= 0.296 Chirality : 0.043 0.172 856 Planarity : 0.004 0.047 1003 Dihedral : 7.363 58.042 890 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.48 % Allowed : 17.16 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.32), residues: 748 helix: 2.57 (0.27), residues: 375 sheet: 0.37 (0.46), residues: 135 loop : -0.12 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 181 TYR 0.011 0.001 TYR B 159 PHE 0.012 0.001 PHE A 96 TRP 0.010 0.001 TRP H 66 HIS 0.002 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 5805) covalent geometry : angle 0.58535 / 0.29 ( 7840) SS BOND : bond 0.00231 / 0.11 ( 3) SS BOND : angle 2.30154 / 1.23 ( 6) hydrogen bonds : bond 0.03177 / 2.18 ( 380) hydrogen bonds : angle 3.94130 / 2.89 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8101 (mp0) REVERT: A 131 MET cc_start: 0.7830 (mmt) cc_final: 0.7582 (mmm) REVERT: B 195 LEU cc_start: 0.8234 (mm) cc_final: 0.7920 (tm) REVERT: B 200 TYR cc_start: 0.8574 (m-80) cc_final: 0.8313 (m-10) REVERT: B 204 MET cc_start: 0.9235 (mtm) cc_final: 0.8987 (mtm) REVERT: C 431 THR cc_start: 0.8367 (m) cc_final: 0.7947 (p) REVERT: L 103 GLU cc_start: 0.8585 (mp0) cc_final: 0.8278 (pm20) REVERT: L 104 GLU cc_start: 0.7423 (tp30) cc_final: 0.6946 (tt0) REVERT: H 24 LYS cc_start: 0.9073 (mtpm) cc_final: 0.8506 (mtmp) outliers start: 8 outliers final: 4 residues processed: 96 average time/residue: 0.4085 time to fit residues: 41.2140 Evaluate side-chains 93 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 50.0000 chunk 3 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 40.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 408 GLN L 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.082638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.061381 restraints weight = 12696.010| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.58 r_work: 0.2788 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5808 Z= 0.152 Angle : 0.604 11.953 7846 Z= 0.304 Chirality : 0.043 0.212 856 Planarity : 0.004 0.046 1003 Dihedral : 7.267 58.405 890 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.92 % Allowed : 18.45 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.32), residues: 748 helix: 2.67 (0.27), residues: 373 sheet: 0.47 (0.47), residues: 135 loop : -0.07 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 85 TYR 0.011 0.001 TYR H 117 PHE 0.012 0.001 PHE A 96 TRP 0.010 0.001 TRP H 66 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 5805) covalent geometry : angle 0.59728 / 0.30 ( 7840) SS BOND : bond 0.00258 / 0.13 ( 3) SS BOND : angle 3.26223 / 1.75 ( 6) hydrogen bonds : bond 0.03297 / 2.28 ( 380) hydrogen bonds : angle 3.93172 / 2.88 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1708.95 seconds wall clock time: 29 minutes 53.97 seconds (1793.97 seconds total)