Starting phenix.real_space_refine on Tue Feb 3 18:33:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kvd_62589/02_2026/9kvd_62589.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kvd_62589/02_2026/9kvd_62589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kvd_62589/02_2026/9kvd_62589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kvd_62589/02_2026/9kvd_62589.map" model { file = "/net/cci-nas-00/data/ceres_data/9kvd_62589/02_2026/9kvd_62589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kvd_62589/02_2026/9kvd_62589.cif" } resolution = 3.44 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= 0.001 sd= 0.021 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 3857 2.51 5 N 1031 2.21 5 O 1156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6067 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 854 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 714 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'ARG:plan': 4, 'GLU:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 839 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "F" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 743 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1400 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 11, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 4, 'ASP:plan': 6, 'TYR:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 783 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 720 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 8, 'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.37, per 1000 atoms: 0.23 Number of scatterers: 6067 At special positions: 0 Unit cell: (71.576, 98.806, 107.364, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1156 8.00 N 1031 7.00 C 3857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.02 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS B 211 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 143 " - pdb=" SG CYS F 210 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 143 " - pdb=" SG CYS G 214 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 376.3 milliseconds 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 21 sheets defined 3.6% alpha, 32.0% 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 28 through 32 removed outlier: 4.038A pdb=" N ARG A 31 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 32' Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.782A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.610A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 443' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.597A pdb=" N LEU A 18 " --> pdb=" O MET A 83 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A 78 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER A 71 " --> pdb=" O PHE A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.684A pdb=" N PHE A 109 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.522A pdb=" N SER B 130 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 194 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 193 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR B 195 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 133 through 136 removed outlier: 4.021A pdb=" N ALA B 136 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TRP B 158 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 133 through 136 removed outlier: 4.021A pdb=" N ALA B 136 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 213 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR B 220 " --> pdb=" O GLN B 213 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.733A pdb=" N PHE D 80 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.073A pdb=" N GLY D 34 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP D 37 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.860A pdb=" N ARG D 99 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY D 109 " --> pdb=" O ARG D 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 131 through 132 removed outlier: 6.498A pdb=" N TRP F 157 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AB3, first strand: chain 'F' and resid 140 through 144 removed outlier: 3.606A pdb=" N SER F 185 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.518A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.568A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB8, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.647A pdb=" N PHE E 79 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 58 through 60 removed outlier: 7.064A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU E 50 " --> pdb=" O TRP E 34 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TRP E 34 " --> pdb=" O GLU E 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 124 through 125 removed outlier: 3.727A pdb=" N THR G 198 " --> pdb=" O SER G 191 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AC3, first strand: chain 'G' and resid 161 through 163 removed outlier: 6.687A pdb=" N TRP G 161 " --> pdb=" O LEU G 173 " (cutoff:3.500A) 186 hydrogen bonds defined for protein. 429 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: 0.66 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1855 1.33 - 1.46: 1667 1.46 - 1.58: 2670 1.58 - 1.71: 0 1.71 - 1.83: 29 Bond restraints: 6221 Sorted by residual: bond pdb=" CA ASP A 111 " pdb=" C ASP A 111 " ideal model delta sigma weight residual 1.526 1.477 0.049 1.07e-02 8.73e+03 2.14e+01 bond pdb=" CA ASP A 102 " pdb=" C ASP A 102 " ideal model delta sigma weight residual 1.528 1.479 0.050 1.18e-02 7.18e+03 1.78e+01 bond pdb=" CA ARG A 98 " pdb=" C ARG A 98 " ideal model delta sigma weight residual 1.526 1.476 0.050 1.20e-02 6.94e+03 1.72e+01 bond pdb=" CA GLY A 100 " pdb=" C GLY A 100 " ideal model delta sigma weight residual 1.520 1.491 0.029 7.30e-03 1.88e+04 1.61e+01 bond pdb=" CA GLY A 105 " pdb=" C GLY A 105 " ideal model delta sigma weight residual 1.511 1.476 0.035 1.08e-02 8.57e+03 1.06e+01 ... (remaining 6216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 8090 2.08 - 4.16: 374 4.16 - 6.24: 46 6.24 - 8.31: 14 8.31 - 10.39: 4 Bond angle restraints: 8528 Sorted by residual: angle pdb=" C TYR D 61 " pdb=" N ASN D 62 " pdb=" CA ASN D 62 " ideal model delta sigma weight residual 121.61 132.00 -10.39 1.39e+00 5.18e-01 5.59e+01 angle pdb=" C VAL A 107 " pdb=" CA VAL A 107 " pdb=" CB VAL A 107 " ideal model delta sigma weight residual 110.98 103.88 7.10 1.37e+00 5.33e-01 2.69e+01 angle pdb=" N LEU B 156 " pdb=" CA LEU B 156 " pdb=" C LEU B 156 " ideal model delta sigma weight residual 110.42 117.88 -7.46 1.46e+00 4.69e-01 2.61e+01 angle pdb=" C ASP A 102 " pdb=" N PRO A 103 " pdb=" CA PRO A 103 " ideal model delta sigma weight residual 119.05 113.47 5.58 1.11e+00 8.12e-01 2.53e+01 angle pdb=" N GLY A 100 " pdb=" CA GLY A 100 " pdb=" C GLY A 100 " ideal model delta sigma weight residual 110.71 103.05 7.66 1.53e+00 4.27e-01 2.50e+01 ... (remaining 8523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 3396 15.07 - 30.13: 135 30.13 - 45.20: 33 45.20 - 60.26: 10 60.26 - 75.33: 3 Dihedral angle restraints: 3577 sinusoidal: 1111 harmonic: 2466 Sorted by residual: dihedral pdb=" CB CYS G 143 " pdb=" SG CYS G 143 " pdb=" SG CYS G 214 " pdb=" CB CYS G 214 " ideal model delta sinusoidal sigma weight residual 93.00 160.49 -67.49 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 151.78 -58.78 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CA CYS C 361 " pdb=" C CYS C 361 " pdb=" N VAL C 362 " pdb=" CA VAL C 362 " ideal model delta harmonic sigma weight residual 180.00 153.04 26.96 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 3574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 576 0.042 - 0.085: 239 0.085 - 0.127: 102 0.127 - 0.170: 30 0.170 - 0.212: 14 Chirality restraints: 961 Sorted by residual: chirality pdb=" CA CYS C 432 " pdb=" N CYS C 432 " pdb=" C CYS C 432 " pdb=" CB CYS C 432 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE G 174 " pdb=" N ILE G 174 " pdb=" C ILE G 174 " pdb=" CB ILE G 174 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA TYR G 175 " pdb=" N TYR G 175 " pdb=" C TYR G 175 " pdb=" CB TYR G 175 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 958 not shown) Planarity restraints: 1110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 102 " -0.048 5.00e-02 4.00e+02 7.28e-02 8.49e+00 pdb=" N PRO A 103 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 110 " 0.019 2.00e-02 2.50e+03 1.67e-02 6.95e+00 pdb=" CG TRP E 110 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP E 110 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP E 110 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 110 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 110 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 110 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 110 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 110 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 110 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 13 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.41e+00 pdb=" N PRO E 14 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " -0.032 5.00e-02 4.00e+02 ... (remaining 1107 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1584 2.79 - 3.32: 4918 3.32 - 3.85: 9781 3.85 - 4.37: 10777 4.37 - 4.90: 19664 Nonbonded interactions: 46724 Sorted by model distance: nonbonded pdb=" OH TYR F 213 " pdb=" OD1 ASN F 218 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR E 91 " pdb=" O VAL E 118 " model vdw 2.276 3.040 nonbonded pdb=" OG SER C 477 " pdb=" O VAL G 218 " model vdw 2.290 3.040 nonbonded pdb=" OG SER C 359 " pdb=" OG1 THR C 523 " model vdw 2.300 3.040 nonbonded pdb=" O ARG B 184 " pdb=" OG SER B 199 " model vdw 2.302 3.040 ... (remaining 46719 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: 5.010 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.420 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 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 0.054 6230 Z= 0.363 Angle : 1.022 10.393 8547 Z= 0.603 Chirality : 0.060 0.212 961 Planarity : 0.008 0.073 1109 Dihedral : 9.339 75.330 1989 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.73 % Allowed : 3.45 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -4.41 (0.23), residues: 842 helix: -5.23 (0.17), residues: 33 sheet: -2.68 (0.25), residues: 320 loop : -3.00 (0.22), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 403 TYR 0.025 0.003 TYR C 508 PHE 0.029 0.003 PHE C 347 TRP 0.044 0.004 TRP E 110 HIS 0.011 0.003 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00704 ( 6221) covalent geometry : angle 1.01865 ( 8528) SS BOND : bond 0.00555 ( 8) SS BOND : angle 1.66189 ( 16) hydrogen bonds : bond 0.28296 ( 168) hydrogen bonds : angle 11.28373 ( 429) link_NAG-ASN : bond 0.00695 ( 1) link_NAG-ASN : angle 3.28159 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: D 6 GLU cc_start: 0.7087 (mp0) cc_final: 0.6758 (mp0) REVERT: D 28 SER cc_start: 0.8395 (t) cc_final: 0.8127 (m) REVERT: D 33 TYR cc_start: 0.6842 (m-10) cc_final: 0.6491 (m-80) REVERT: C 468 ILE cc_start: 0.7292 (pt) cc_final: 0.7039 (pt) REVERT: C 470 THR cc_start: 0.8731 (p) cc_final: 0.8511 (p) REVERT: E 99 ARG cc_start: 0.7736 (ttm170) cc_final: 0.7491 (ttm170) REVERT: G 161 TRP cc_start: 0.7609 (m100) cc_final: 0.7263 (m100) REVERT: G 189 SER cc_start: 0.7785 (t) cc_final: 0.7556 (t) outliers start: 4 outliers final: 1 residues processed: 141 average time/residue: 0.0658 time to fit residues: 12.2645 Evaluate side-chains 123 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0270 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN D 60 ASN F 149 ASN ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 GLN F 173 ASN C 439 ASN C 450 ASN C 493 GLN E 54 ASN G 164 GLN G 168 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.120434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.108474 restraints weight = 10173.019| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.04 r_work: 0.3315 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6230 Z= 0.173 Angle : 0.640 7.234 8547 Z= 0.342 Chirality : 0.045 0.163 961 Planarity : 0.006 0.043 1109 Dihedral : 6.269 56.498 949 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.09 % Allowed : 11.27 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -3.57 (0.25), residues: 842 helix: -5.08 (0.30), residues: 27 sheet: -2.15 (0.24), residues: 358 loop : -2.36 (0.25), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 454 TYR 0.019 0.002 TYR G 175 PHE 0.018 0.002 PHE E 79 TRP 0.020 0.002 TRP A 113 HIS 0.010 0.003 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 6221) covalent geometry : angle 0.63812 ( 8528) SS BOND : bond 0.00331 ( 8) SS BOND : angle 1.17777 ( 16) hydrogen bonds : bond 0.04081 ( 168) hydrogen bonds : angle 7.16109 ( 429) link_NAG-ASN : bond 0.00038 ( 1) link_NAG-ASN : angle 1.44880 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 60 TYR cc_start: 0.7826 (m-80) cc_final: 0.7391 (m-80) REVERT: A 93 VAL cc_start: 0.8289 (m) cc_final: 0.8026 (p) REVERT: A 97 VAL cc_start: 0.7631 (OUTLIER) cc_final: 0.7408 (t) REVERT: F 174 ASN cc_start: 0.8267 (p0) cc_final: 0.8042 (p0) REVERT: F 213 TYR cc_start: 0.7999 (t80) cc_final: 0.7657 (t80) REVERT: C 457 ARG cc_start: 0.7705 (ttt-90) cc_final: 0.7092 (mtp-110) REVERT: C 470 THR cc_start: 0.8798 (p) cc_final: 0.8553 (p) outliers start: 17 outliers final: 12 residues processed: 140 average time/residue: 0.0564 time to fit residues: 10.5810 Evaluate side-chains 139 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 173 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 33 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 115 GLN ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 439 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.118408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.106556 restraints weight = 10089.068| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.00 r_work: 0.3293 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6230 Z= 0.216 Angle : 0.671 8.046 8547 Z= 0.356 Chirality : 0.046 0.154 961 Planarity : 0.005 0.040 1109 Dihedral : 6.282 56.428 949 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 5.09 % Allowed : 13.09 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -3.08 (0.26), residues: 842 helix: -4.85 (0.45), residues: 27 sheet: -1.67 (0.26), residues: 361 loop : -2.16 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 509 TYR 0.021 0.002 TYR G 175 PHE 0.021 0.003 PHE B 221 TRP 0.016 0.002 TRP A 113 HIS 0.014 0.004 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 6221) covalent geometry : angle 0.66976 ( 8528) SS BOND : bond 0.00335 ( 8) SS BOND : angle 1.11344 ( 16) hydrogen bonds : bond 0.04040 ( 168) hydrogen bonds : angle 6.72835 ( 429) link_NAG-ASN : bond 0.00076 ( 1) link_NAG-ASN : angle 1.54213 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 30 SER cc_start: 0.8232 (p) cc_final: 0.7826 (t) REVERT: A 60 TYR cc_start: 0.7843 (m-80) cc_final: 0.7423 (m-80) REVERT: A 93 VAL cc_start: 0.8264 (m) cc_final: 0.7994 (p) REVERT: B 227 VAL cc_start: 0.7815 (p) cc_final: 0.7407 (t) REVERT: F 213 TYR cc_start: 0.8102 (t80) cc_final: 0.7835 (t80) REVERT: F 226 THR cc_start: 0.7714 (t) cc_final: 0.7388 (m) REVERT: C 342 PHE cc_start: 0.7372 (m-80) cc_final: 0.7094 (m-80) REVERT: C 457 ARG cc_start: 0.7796 (ttt-90) cc_final: 0.7073 (mtp-110) REVERT: E 19 SER cc_start: 0.7608 (m) cc_final: 0.7238 (t) REVERT: E 20 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7151 (pt) REVERT: E 77 SER cc_start: 0.7631 (OUTLIER) cc_final: 0.7351 (p) REVERT: E 80 SER cc_start: 0.7401 (t) cc_final: 0.7123 (m) outliers start: 28 outliers final: 19 residues processed: 154 average time/residue: 0.0535 time to fit residues: 11.4463 Evaluate side-chains 156 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 173 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 35 optimal weight: 0.9980 chunk 77 optimal weight: 0.0030 chunk 73 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.108918 restraints weight = 10168.587| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.09 r_work: 0.3310 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6230 Z= 0.149 Angle : 0.606 6.977 8547 Z= 0.322 Chirality : 0.045 0.160 961 Planarity : 0.004 0.040 1109 Dihedral : 5.908 55.479 948 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.55 % Allowed : 13.82 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.84 (0.27), residues: 842 helix: -4.71 (0.51), residues: 27 sheet: -1.48 (0.26), residues: 361 loop : -2.03 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 509 TYR 0.017 0.002 TYR C 351 PHE 0.023 0.002 PHE A 68 TRP 0.018 0.002 TRP A 113 HIS 0.011 0.003 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6221) covalent geometry : angle 0.60418 ( 8528) SS BOND : bond 0.00358 ( 8) SS BOND : angle 1.00369 ( 16) hydrogen bonds : bond 0.03363 ( 168) hydrogen bonds : angle 6.14812 ( 429) link_NAG-ASN : bond 0.00145 ( 1) link_NAG-ASN : angle 1.38582 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 SER cc_start: 0.8217 (p) cc_final: 0.7796 (t) REVERT: A 60 TYR cc_start: 0.7877 (m-80) cc_final: 0.7562 (m-80) REVERT: A 93 VAL cc_start: 0.8262 (m) cc_final: 0.7963 (p) REVERT: D 28 SER cc_start: 0.8290 (t) cc_final: 0.8001 (m) REVERT: F 213 TYR cc_start: 0.8115 (t80) cc_final: 0.7849 (t80) REVERT: F 226 THR cc_start: 0.7760 (t) cc_final: 0.7393 (m) REVERT: C 342 PHE cc_start: 0.7307 (m-80) cc_final: 0.7009 (m-80) REVERT: C 401 VAL cc_start: 0.7049 (OUTLIER) cc_final: 0.6565 (t) REVERT: C 457 ARG cc_start: 0.7799 (ttt-90) cc_final: 0.6946 (mtp-110) REVERT: G 161 TRP cc_start: 0.7680 (m100) cc_final: 0.7428 (m100) outliers start: 25 outliers final: 19 residues processed: 150 average time/residue: 0.0596 time to fit residues: 12.2131 Evaluate side-chains 154 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 173 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 46 optimal weight: 0.0980 chunk 51 optimal weight: 0.0970 chunk 73 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 115 GLN F 156 HIS C 388 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN G 226 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.121193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109380 restraints weight = 10296.282| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.04 r_work: 0.3320 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6230 Z= 0.148 Angle : 0.593 6.880 8547 Z= 0.315 Chirality : 0.045 0.194 961 Planarity : 0.004 0.039 1109 Dihedral : 5.780 55.573 948 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.18 % Allowed : 15.64 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.63 (0.27), residues: 842 helix: -4.62 (0.54), residues: 27 sheet: -1.28 (0.27), residues: 363 loop : -1.94 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 509 TYR 0.025 0.002 TYR C 351 PHE 0.016 0.002 PHE A 68 TRP 0.010 0.002 TRP C 436 HIS 0.012 0.004 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6221) covalent geometry : angle 0.59149 ( 8528) SS BOND : bond 0.00290 ( 8) SS BOND : angle 1.01780 ( 16) hydrogen bonds : bond 0.03183 ( 168) hydrogen bonds : angle 5.86450 ( 429) link_NAG-ASN : bond 0.00142 ( 1) link_NAG-ASN : angle 1.34471 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 SER cc_start: 0.8202 (p) cc_final: 0.7798 (t) REVERT: A 60 TYR cc_start: 0.7879 (m-80) cc_final: 0.7617 (m-80) REVERT: A 83 MET cc_start: 0.7714 (mmm) cc_final: 0.6834 (mmm) REVERT: A 93 VAL cc_start: 0.8278 (m) cc_final: 0.7993 (p) REVERT: F 213 TYR cc_start: 0.8142 (t80) cc_final: 0.7768 (t80) REVERT: F 226 THR cc_start: 0.7734 (t) cc_final: 0.7399 (m) REVERT: C 342 PHE cc_start: 0.7290 (m-80) cc_final: 0.7032 (m-80) REVERT: C 457 ARG cc_start: 0.7844 (ttt-90) cc_final: 0.7054 (mmm160) outliers start: 23 outliers final: 19 residues processed: 150 average time/residue: 0.0482 time to fit residues: 10.2621 Evaluate side-chains 154 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 173 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 52 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 37 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 115 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN G 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.121348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.109663 restraints weight = 10190.680| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.01 r_work: 0.3328 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6230 Z= 0.151 Angle : 0.593 6.864 8547 Z= 0.314 Chirality : 0.044 0.158 961 Planarity : 0.004 0.038 1109 Dihedral : 5.719 55.609 948 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.91 % Allowed : 16.18 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.43 (0.28), residues: 842 helix: -4.56 (0.55), residues: 26 sheet: -1.08 (0.27), residues: 360 loop : -1.86 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 509 TYR 0.023 0.002 TYR C 351 PHE 0.014 0.002 PHE E 79 TRP 0.012 0.002 TRP A 113 HIS 0.011 0.002 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6221) covalent geometry : angle 0.59070 ( 8528) SS BOND : bond 0.00291 ( 8) SS BOND : angle 1.13323 ( 16) hydrogen bonds : bond 0.03153 ( 168) hydrogen bonds : angle 5.74424 ( 429) link_NAG-ASN : bond 0.00149 ( 1) link_NAG-ASN : angle 1.35201 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 SER cc_start: 0.8172 (p) cc_final: 0.7769 (t) REVERT: A 60 TYR cc_start: 0.7891 (m-80) cc_final: 0.7585 (m-80) REVERT: A 93 VAL cc_start: 0.8278 (m) cc_final: 0.8019 (p) REVERT: B 127 MET cc_start: 0.7117 (mmm) cc_final: 0.6581 (mmm) REVERT: F 177 PRO cc_start: 0.8105 (Cg_endo) cc_final: 0.7887 (Cg_exo) REVERT: F 226 THR cc_start: 0.7708 (t) cc_final: 0.7403 (m) REVERT: C 342 PHE cc_start: 0.7291 (m-80) cc_final: 0.7012 (m-80) REVERT: C 401 VAL cc_start: 0.6956 (OUTLIER) cc_final: 0.6461 (t) REVERT: C 457 ARG cc_start: 0.7846 (ttt-90) cc_final: 0.6960 (mtp-110) outliers start: 27 outliers final: 22 residues processed: 146 average time/residue: 0.0519 time to fit residues: 10.6062 Evaluate side-chains 155 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 173 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 48 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.120694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109353 restraints weight = 10078.418| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.90 r_work: 0.3328 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6230 Z= 0.194 Angle : 0.628 7.040 8547 Z= 0.334 Chirality : 0.045 0.154 961 Planarity : 0.004 0.039 1109 Dihedral : 5.855 56.037 948 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.91 % Allowed : 17.27 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.38 (0.28), residues: 842 helix: -4.46 (0.53), residues: 27 sheet: -0.99 (0.27), residues: 360 loop : -1.90 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 509 TYR 0.022 0.002 TYR C 351 PHE 0.017 0.002 PHE A 95 TRP 0.010 0.002 TRP C 353 HIS 0.013 0.003 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 6221) covalent geometry : angle 0.62571 ( 8528) SS BOND : bond 0.00317 ( 8) SS BOND : angle 1.21832 ( 16) hydrogen bonds : bond 0.03361 ( 168) hydrogen bonds : angle 5.77795 ( 429) link_NAG-ASN : bond 0.00121 ( 1) link_NAG-ASN : angle 1.42718 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 SER cc_start: 0.8129 (p) cc_final: 0.7743 (t) REVERT: A 35 HIS cc_start: 0.6722 (OUTLIER) cc_final: 0.6434 (p-80) REVERT: A 60 TYR cc_start: 0.7849 (m-80) cc_final: 0.7538 (m-80) REVERT: A 83 MET cc_start: 0.7621 (mmm) cc_final: 0.7210 (mmp) REVERT: A 93 VAL cc_start: 0.8266 (m) cc_final: 0.7964 (p) REVERT: A 94 TYR cc_start: 0.8045 (m-10) cc_final: 0.7770 (m-10) REVERT: F 177 PRO cc_start: 0.8130 (Cg_endo) cc_final: 0.7906 (Cg_exo) REVERT: F 226 THR cc_start: 0.7661 (t) cc_final: 0.7386 (m) outliers start: 27 outliers final: 24 residues processed: 155 average time/residue: 0.0499 time to fit residues: 10.7688 Evaluate side-chains 164 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 173 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 66 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.0570 chunk 35 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.122303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.110663 restraints weight = 10071.901| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.00 r_work: 0.3342 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6230 Z= 0.134 Angle : 0.590 6.802 8547 Z= 0.311 Chirality : 0.044 0.158 961 Planarity : 0.004 0.036 1109 Dihedral : 5.575 55.192 948 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.36 % Allowed : 19.27 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.27 (0.28), residues: 842 helix: -4.34 (0.53), residues: 27 sheet: -0.91 (0.27), residues: 370 loop : -1.84 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 509 TYR 0.021 0.002 TYR C 351 PHE 0.013 0.002 PHE E 79 TRP 0.013 0.002 TRP C 436 HIS 0.011 0.003 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6221) covalent geometry : angle 0.58813 ( 8528) SS BOND : bond 0.00275 ( 8) SS BOND : angle 1.07665 ( 16) hydrogen bonds : bond 0.03077 ( 168) hydrogen bonds : angle 5.57663 ( 429) link_NAG-ASN : bond 0.00172 ( 1) link_NAG-ASN : angle 1.43286 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 TYR cc_start: 0.7877 (m-80) cc_final: 0.7639 (m-80) REVERT: A 93 VAL cc_start: 0.8277 (m) cc_final: 0.7963 (p) REVERT: B 127 MET cc_start: 0.7153 (mmm) cc_final: 0.6577 (mmm) outliers start: 24 outliers final: 21 residues processed: 146 average time/residue: 0.0427 time to fit residues: 8.7504 Evaluate side-chains 154 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain G residue 173 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 487 ASN G 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.117843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.106192 restraints weight = 10248.780| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.94 r_work: 0.3292 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 6230 Z= 0.349 Angle : 0.796 8.918 8547 Z= 0.426 Chirality : 0.050 0.185 961 Planarity : 0.006 0.052 1109 Dihedral : 6.610 56.562 948 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 4.73 % Allowed : 19.64 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.62 (0.27), residues: 842 helix: -4.30 (0.57), residues: 27 sheet: -1.13 (0.27), residues: 364 loop : -2.10 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 509 TYR 0.028 0.003 TYR D 51 PHE 0.024 0.003 PHE C 429 TRP 0.017 0.003 TRP G 161 HIS 0.016 0.004 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00794 ( 6221) covalent geometry : angle 0.79199 ( 8528) SS BOND : bond 0.00518 ( 8) SS BOND : angle 1.74597 ( 16) hydrogen bonds : bond 0.04258 ( 168) hydrogen bonds : angle 6.37014 ( 429) link_NAG-ASN : bond 0.00086 ( 1) link_NAG-ASN : angle 1.93849 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 23 residues processed: 156 average time/residue: 0.0490 time to fit residues: 10.5473 Evaluate side-chains 165 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain G residue 173 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 62 optimal weight: 0.0170 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 28 optimal weight: 0.0170 overall best weight: 0.1854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN G 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.123029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.111446 restraints weight = 10095.105| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.94 r_work: 0.3366 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6230 Z= 0.116 Angle : 0.627 8.906 8547 Z= 0.329 Chirality : 0.045 0.241 961 Planarity : 0.004 0.047 1109 Dihedral : 5.777 54.326 948 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.91 % Allowed : 22.18 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.38 (0.28), residues: 842 helix: -4.16 (0.59), residues: 27 sheet: -0.98 (0.28), residues: 362 loop : -1.93 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 509 TYR 0.020 0.002 TYR F 213 PHE 0.025 0.002 PHE G 224 TRP 0.018 0.002 TRP C 436 HIS 0.008 0.002 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6221) covalent geometry : angle 0.62543 ( 8528) SS BOND : bond 0.00402 ( 8) SS BOND : angle 1.11058 ( 16) hydrogen bonds : bond 0.03171 ( 168) hydrogen bonds : angle 5.74146 ( 429) link_NAG-ASN : bond 0.00220 ( 1) link_NAG-ASN : angle 1.66379 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 7 SER cc_start: 0.7758 (OUTLIER) cc_final: 0.7196 (t) REVERT: A 83 MET cc_start: 0.6978 (mmp) cc_final: 0.6361 (mmm) REVERT: A 93 VAL cc_start: 0.8254 (m) cc_final: 0.7966 (p) REVERT: F 226 THR cc_start: 0.7579 (t) cc_final: 0.7360 (m) REVERT: C 401 VAL cc_start: 0.6772 (OUTLIER) cc_final: 0.6228 (t) REVERT: E 109 TYR cc_start: 0.7036 (m-80) cc_final: 0.6786 (m-80) outliers start: 16 outliers final: 12 residues processed: 147 average time/residue: 0.0401 time to fit residues: 8.4244 Evaluate side-chains 148 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain G residue 173 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 0.0000 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 77 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.119858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.108249 restraints weight = 10151.508| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.93 r_work: 0.3317 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6230 Z= 0.236 Angle : 0.702 8.003 8547 Z= 0.371 Chirality : 0.048 0.256 961 Planarity : 0.005 0.046 1109 Dihedral : 6.136 55.759 948 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 3.09 % Allowed : 22.00 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.38 (0.28), residues: 842 helix: -4.17 (0.58), residues: 27 sheet: -0.98 (0.28), residues: 362 loop : -1.92 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 509 TYR 0.023 0.003 TYR C 351 PHE 0.019 0.003 PHE C 490 TRP 0.018 0.002 TRP G 161 HIS 0.014 0.003 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 6221) covalent geometry : angle 0.69862 ( 8528) SS BOND : bond 0.00420 ( 8) SS BOND : angle 1.47525 ( 16) hydrogen bonds : bond 0.03738 ( 168) hydrogen bonds : angle 5.99024 ( 429) link_NAG-ASN : bond 0.00073 ( 1) link_NAG-ASN : angle 1.74441 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1319.65 seconds wall clock time: 23 minutes 13.88 seconds (1393.88 seconds total)