Starting phenix.real_space_refine on Sat Aug 23 16:48:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thz_41275/08_2025/8thz_41275_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thz_41275/08_2025/8thz_41275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8thz_41275/08_2025/8thz_41275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thz_41275/08_2025/8thz_41275.map" model { file = "/net/cci-nas-00/data/ceres_data/8thz_41275/08_2025/8thz_41275_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thz_41275/08_2025/8thz_41275_trim.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 40 5.16 5 C 4344 2.51 5 N 1153 2.21 5 O 1384 1.98 5 H 6400 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13321 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3280 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3192 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain: "A" Number of atoms: 3491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 3491 Classifications: {'peptide': 235} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 214} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1632 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1531 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.45, per 1000 atoms: 0.18 Number of scatterers: 13321 At special positions: 0 Unit cell: (73.92, 89.6, 129.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 O 1384 8.00 N 1153 7.00 C 4344 6.00 H 6400 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 223 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 503 " distance=2.03 Simple disulfide: pdb=" SG CYS A 452 " - pdb=" SG CYS A 620 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 564 " distance=2.03 Simple disulfide: pdb=" SG CYS A 508 " - pdb=" SG CYS A 552 " distance=2.04 Simple disulfide: pdb=" SG CYS A 569 " - pdb=" SG CYS A 597 " distance=2.03 Simple disulfide: pdb=" SG CYS A 581 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 607 " - pdb=" SG CYS A 644 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " 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 BETA1-3 " NAG B 1 " - " NAG B 2 " " BMA D 3 " - " BMA D 4 " " BMA G 3 " - " BMA G 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG N 1 " - " NAG N 2 " BETA1-6 " BMA G 3 " - " BMA G 5 " NAG-ASN " NAG B 1 " - " ASN A 448 " " NAG C 1 " - " ASN A 532 " " NAG D 1 " - " ASN A 540 " " NAG N 1 " - " ASN A 430 " Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 351.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1612 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 21 sheets defined 8.9% alpha, 38.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 134 through 139 Processing helix chain 'H' and resid 194 through 198 removed outlier: 3.726A pdb=" N GLY H 197 " --> pdb=" O SER H 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.964A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.569A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 187 Processing helix chain 'A' and resid 438 through 442 removed outlier: 3.703A pdb=" N LEU A 441 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 442 " --> pdb=" O ALA A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 442' Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 461 through 465 removed outlier: 3.805A pdb=" N GLU A 464 " --> pdb=" O PRO A 461 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE A 465 " --> pdb=" O ILE A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 461 through 465' Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.765A pdb=" N ASN E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 26 through 30 removed outlier: 3.513A pdb=" N ASP F 29 " --> pdb=" O LYS F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 82 removed outlier: 4.036A pdb=" N GLU F 82 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.717A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N MET H 48 " --> pdb=" O ALA H 61 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 608 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A 609 " --> pdb=" O TRP A 602 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP A 602 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.717A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N MET H 48 " --> pdb=" O ALA H 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 127 through 130 removed outlier: 6.098A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.515A pdb=" N VAL H 188 " --> pdb=" O HIS H 171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 158 through 161 Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.027A pdb=" N ALA L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.027A pdb=" N ALA L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.559A pdb=" N SER L 114 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N SER L 131 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU L 181 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 145 through 150 Processing sheet with id=AB3, first strand: chain 'A' and resid 426 through 427 removed outlier: 4.397A pdb=" N ALA A 426 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 426 through 427 removed outlier: 4.397A pdb=" N ALA A 426 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET A 555 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR A 553 " --> pdb=" O PRO A 505 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR A 507 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY A 551 " --> pdb=" O TYR A 507 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 497 through 498 Processing sheet with id=AB6, first strand: chain 'A' and resid 519 through 520 removed outlier: 3.509A pdb=" N ALA A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 17 through 18 Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 51 removed outlier: 3.682A pdb=" N MET E 48 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 51 removed outlier: 3.682A pdb=" N MET E 48 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 9 through 11 removed outlier: 3.512A pdb=" N TYR F 85 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP F 34 " --> pdb=" O VAL F 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 9 through 11 removed outlier: 3.512A pdb=" N TYR F 85 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 18 through 23 231 hydrogen bonds defined for protein. 546 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6400 1.04 - 1.25: 979 1.25 - 1.45: 2311 1.45 - 1.66: 3759 1.66 - 1.86: 50 Bond restraints: 13499 Sorted by residual: bond pdb=" C5 BMA D 4 " pdb=" O5 BMA D 4 " ideal model delta sigma weight residual 1.417 1.464 -0.047 2.00e-02 2.50e+03 5.58e+00 bond pdb=" CB CYS A 552 " pdb=" HB3 CYS A 552 " ideal model delta sigma weight residual 0.970 0.928 0.042 2.00e-02 2.50e+03 4.39e+00 bond pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " ideal model delta sigma weight residual 1.528 1.568 -0.040 2.00e-02 2.50e+03 3.93e+00 bond pdb=" C3 BMA D 3 " pdb=" C4 BMA D 3 " ideal model delta sigma weight residual 1.541 1.578 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 ... (remaining 13494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 23797 1.83 - 3.66: 326 3.66 - 5.49: 43 5.49 - 7.33: 11 7.33 - 9.16: 5 Bond angle restraints: 24182 Sorted by residual: angle pdb=" N CYS A 552 " pdb=" CA CYS A 552 " pdb=" C CYS A 552 " ideal model delta sigma weight residual 108.14 113.10 -4.96 1.52e+00 4.33e-01 1.06e+01 angle pdb=" C3 NAG N 1 " pdb=" C4 NAG N 1 " pdb=" C5 NAG N 1 " ideal model delta sigma weight residual 109.38 118.54 -9.16 3.00e+00 1.11e-01 9.32e+00 angle pdb=" C1 BMA G 4 " pdb=" O5 BMA G 4 " pdb=" C5 BMA G 4 " ideal model delta sigma weight residual 118.82 110.40 8.42 3.00e+00 1.11e-01 7.89e+00 angle pdb=" C ASP A 431 " pdb=" CA ASP A 431 " pdb=" CB ASP A 431 " ideal model delta sigma weight residual 111.82 115.68 -3.86 1.38e+00 5.25e-01 7.84e+00 angle pdb=" C CYS A 508 " pdb=" CA CYS A 508 " pdb=" HA CYS A 508 " ideal model delta sigma weight residual 109.00 100.78 8.22 3.00e+00 1.11e-01 7.51e+00 ... (remaining 24177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.76: 6074 25.76 - 51.51: 490 51.51 - 77.27: 111 77.27 - 103.02: 68 103.02 - 128.78: 27 Dihedral angle restraints: 6770 sinusoidal: 3738 harmonic: 3032 Sorted by residual: dihedral pdb=" CB CYS H 223 " pdb=" SG CYS H 223 " pdb=" SG CYS L 214 " pdb=" CB CYS L 214 " ideal model delta sinusoidal sigma weight residual -86.00 -137.84 51.84 1 1.00e+01 1.00e-02 3.67e+01 dihedral pdb=" CB CYS A 452 " pdb=" SG CYS A 452 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -36.17 -49.83 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" CB CYS A 569 " pdb=" SG CYS A 569 " pdb=" SG CYS A 597 " pdb=" CB CYS A 597 " ideal model delta sinusoidal sigma weight residual -86.00 -43.40 -42.60 1 1.00e+01 1.00e-02 2.53e+01 ... (remaining 6767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 990 0.083 - 0.166: 110 0.166 - 0.248: 4 0.248 - 0.331: 2 0.331 - 0.414: 3 Chirality restraints: 1109 Sorted by residual: chirality pdb=" C1 BMA G 5 " pdb=" O6 BMA G 3 " pdb=" C2 BMA G 5 " pdb=" O5 BMA G 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.49e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.46e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.11e+01 ... (remaining 1106 not shown) Planarity restraints: 2058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 219 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO H 220 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO H 220 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 220 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.020 2.00e-02 2.50e+03 1.80e-02 4.04e+00 pdb=" C7 NAG G 1 " -0.019 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.019 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.022 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 524 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 525 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 525 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 525 " -0.023 5.00e-02 4.00e+02 ... (remaining 2055 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 389 2.13 - 2.75: 23140 2.75 - 3.36: 35323 3.36 - 3.98: 46593 3.98 - 4.60: 71799 Nonbonded interactions: 177244 Sorted by model distance: nonbonded pdb=" OE1 GLU A 464 " pdb=" H GLU A 464 " model vdw 1.510 2.450 nonbonded pdb="HE22 GLN H 6 " pdb=" O TYR H 94 " model vdw 1.523 2.450 nonbonded pdb=" OE1 GLU E 89 " pdb=" H GLU E 89 " model vdw 1.530 2.450 nonbonded pdb=" OE1 GLN E 62 " pdb=" H GLN E 62 " model vdw 1.532 2.450 nonbonded pdb="HD21 ASN H 162 " pdb=" O THR H 200 " model vdw 1.583 2.450 ... (remaining 177239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'N' } 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: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.880 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 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 : 0.004 0.055 7128 Z= 0.194 Angle : 0.763 9.438 9751 Z= 0.364 Chirality : 0.054 0.414 1109 Planarity : 0.005 0.056 1225 Dihedral : 25.912 128.781 2733 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 0.54 % Allowed : 20.35 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.29), residues: 879 helix: -1.34 (0.81), residues: 37 sheet: 0.41 (0.30), residues: 326 loop : -1.87 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 53 TYR 0.009 0.001 TYR H 201 PHE 0.016 0.001 PHE A 522 TRP 0.011 0.001 TRP E 36 HIS 0.005 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 7099) covalent geometry : angle 0.74014 ( 9679) SS BOND : bond 0.00583 ( 15) SS BOND : angle 1.71017 ( 30) hydrogen bonds : bond 0.17762 ( 197) hydrogen bonds : angle 8.61870 ( 546) link_BETA1-3 : bond 0.00745 ( 3) link_BETA1-3 : angle 1.80461 ( 9) link_BETA1-4 : bond 0.01667 ( 6) link_BETA1-4 : angle 3.08692 ( 18) link_BETA1-6 : bond 0.01849 ( 1) link_BETA1-6 : angle 0.72145 ( 3) link_NAG-ASN : bond 0.00602 ( 4) link_NAG-ASN : angle 2.62537 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 75 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 112 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.7201 (pt0) REVERT: E 87 ARG cc_start: 0.5385 (tpm170) cc_final: 0.5156 (tpt90) outliers start: 4 outliers final: 3 residues processed: 101 average time/residue: 0.1673 time to fit residues: 22.0301 Evaluate side-chains 95 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain A residue 540 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.155280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.129159 restraints weight = 30040.420| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.77 r_work: 0.3640 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7128 Z= 0.183 Angle : 0.774 8.236 9751 Z= 0.370 Chirality : 0.051 0.264 1109 Planarity : 0.005 0.049 1225 Dihedral : 23.315 118.760 1276 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.47 % Favored : 89.42 % Rotamer: Outliers : 2.31 % Allowed : 19.00 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.28), residues: 879 helix: -0.77 (0.84), residues: 43 sheet: 0.42 (0.30), residues: 318 loop : -1.85 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 521 TYR 0.011 0.001 TYR H 95 PHE 0.017 0.002 PHE A 509 TRP 0.008 0.002 TRP A 420 HIS 0.003 0.001 HIS A 638 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 7099) covalent geometry : angle 0.75429 ( 9679) SS BOND : bond 0.00550 ( 15) SS BOND : angle 1.64902 ( 30) hydrogen bonds : bond 0.04633 ( 197) hydrogen bonds : angle 6.82322 ( 546) link_BETA1-3 : bond 0.00640 ( 3) link_BETA1-3 : angle 2.81455 ( 9) link_BETA1-4 : bond 0.00734 ( 6) link_BETA1-4 : angle 2.29673 ( 18) link_BETA1-6 : bond 0.00315 ( 1) link_BETA1-6 : angle 2.88546 ( 3) link_NAG-ASN : bond 0.00489 ( 4) link_NAG-ASN : angle 2.39576 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 75 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8153 (mt0) cc_final: 0.7793 (mp10) REVERT: H 178 GLN cc_start: 0.8166 (tt0) cc_final: 0.7902 (tt0) REVERT: E 67 ARG cc_start: 0.6522 (mtm-85) cc_final: 0.6290 (mtm180) REVERT: E 87 ARG cc_start: 0.5572 (tpm170) cc_final: 0.5369 (tpt90) outliers start: 17 outliers final: 11 residues processed: 106 average time/residue: 0.1863 time to fit residues: 25.8193 Evaluate side-chains 100 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 639 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.154498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.127687 restraints weight = 30163.747| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.86 r_work: 0.3609 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7128 Z= 0.149 Angle : 0.735 9.102 9751 Z= 0.343 Chirality : 0.049 0.253 1109 Planarity : 0.005 0.052 1225 Dihedral : 19.190 114.370 1272 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.90 % Favored : 89.87 % Rotamer: Outliers : 2.58 % Allowed : 19.81 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.28), residues: 879 helix: -0.78 (0.85), residues: 44 sheet: 0.47 (0.29), residues: 324 loop : -1.91 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 521 TYR 0.011 0.001 TYR H 95 PHE 0.013 0.001 PHE A 509 TRP 0.007 0.001 TRP H 47 HIS 0.005 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 7099) covalent geometry : angle 0.70523 ( 9679) SS BOND : bond 0.00554 ( 15) SS BOND : angle 1.64105 ( 30) hydrogen bonds : bond 0.03936 ( 197) hydrogen bonds : angle 6.12668 ( 546) link_BETA1-3 : bond 0.00486 ( 3) link_BETA1-3 : angle 3.50673 ( 9) link_BETA1-4 : bond 0.00650 ( 6) link_BETA1-4 : angle 2.23779 ( 18) link_BETA1-6 : bond 0.00637 ( 1) link_BETA1-6 : angle 3.43322 ( 3) link_NAG-ASN : bond 0.00407 ( 4) link_NAG-ASN : angle 3.33482 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 75 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.7979 (mt0) cc_final: 0.7741 (mp10) REVERT: H 178 GLN cc_start: 0.8096 (tt0) cc_final: 0.7830 (tt0) REVERT: A 627 PHE cc_start: 0.6495 (OUTLIER) cc_final: 0.5513 (t80) REVERT: E 23 GLU cc_start: 0.5096 (OUTLIER) cc_final: 0.4473 (pm20) outliers start: 19 outliers final: 13 residues processed: 109 average time/residue: 0.1512 time to fit residues: 22.0636 Evaluate side-chains 104 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 23 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.150660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.124280 restraints weight = 29952.545| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.81 r_work: 0.3571 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7128 Z= 0.171 Angle : 0.740 8.419 9751 Z= 0.351 Chirality : 0.049 0.280 1109 Planarity : 0.005 0.051 1225 Dihedral : 17.203 110.751 1272 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.47 % Favored : 89.31 % Rotamer: Outliers : 3.26 % Allowed : 19.27 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.28), residues: 879 helix: -0.70 (0.86), residues: 44 sheet: 0.37 (0.29), residues: 324 loop : -1.98 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 67 TYR 0.011 0.001 TYR H 95 PHE 0.014 0.002 PHE E 55 TRP 0.009 0.002 TRP A 420 HIS 0.003 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 7099) covalent geometry : angle 0.71110 ( 9679) SS BOND : bond 0.00596 ( 15) SS BOND : angle 1.76985 ( 30) hydrogen bonds : bond 0.03563 ( 197) hydrogen bonds : angle 5.80797 ( 546) link_BETA1-3 : bond 0.00351 ( 3) link_BETA1-3 : angle 3.61749 ( 9) link_BETA1-4 : bond 0.00638 ( 6) link_BETA1-4 : angle 2.35976 ( 18) link_BETA1-6 : bond 0.00272 ( 1) link_BETA1-6 : angle 3.16859 ( 3) link_NAG-ASN : bond 0.00449 ( 4) link_NAG-ASN : angle 2.97808 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 75 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8079 (mt0) cc_final: 0.7639 (mp10) REVERT: H 178 GLN cc_start: 0.8247 (tt0) cc_final: 0.7961 (tt0) REVERT: A 627 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.5789 (t80) REVERT: E 23 GLU cc_start: 0.5095 (OUTLIER) cc_final: 0.4484 (pm20) REVERT: E 83 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7421 (tt) outliers start: 24 outliers final: 17 residues processed: 117 average time/residue: 0.1494 time to fit residues: 23.3674 Evaluate side-chains 113 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain F residue 88 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 HIS F 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.149929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.122940 restraints weight = 30469.395| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.87 r_work: 0.3555 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7128 Z= 0.214 Angle : 0.754 8.357 9751 Z= 0.361 Chirality : 0.050 0.305 1109 Planarity : 0.006 0.063 1225 Dihedral : 16.522 108.056 1272 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.47 % Favored : 89.31 % Rotamer: Outliers : 3.39 % Allowed : 19.54 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.28), residues: 879 helix: -0.76 (0.86), residues: 44 sheet: 0.32 (0.29), residues: 330 loop : -2.16 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 521 TYR 0.012 0.001 TYR H 95 PHE 0.016 0.002 PHE E 55 TRP 0.009 0.002 TRP A 420 HIS 0.004 0.001 HIS A 638 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 7099) covalent geometry : angle 0.72492 ( 9679) SS BOND : bond 0.00644 ( 15) SS BOND : angle 1.93779 ( 30) hydrogen bonds : bond 0.03763 ( 197) hydrogen bonds : angle 5.85652 ( 546) link_BETA1-3 : bond 0.00292 ( 3) link_BETA1-3 : angle 3.30254 ( 9) link_BETA1-4 : bond 0.00617 ( 6) link_BETA1-4 : angle 2.45406 ( 18) link_BETA1-6 : bond 0.00183 ( 1) link_BETA1-6 : angle 3.07124 ( 3) link_NAG-ASN : bond 0.00451 ( 4) link_NAG-ASN : angle 3.04460 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 75 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8080 (mt0) cc_final: 0.7628 (mp10) REVERT: H 178 GLN cc_start: 0.8257 (tt0) cc_final: 0.7985 (tt0) REVERT: A 455 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.7138 (mtt180) REVERT: A 627 PHE cc_start: 0.6853 (OUTLIER) cc_final: 0.5844 (t80) REVERT: E 23 GLU cc_start: 0.5166 (OUTLIER) cc_final: 0.4541 (pm20) outliers start: 25 outliers final: 19 residues processed: 112 average time/residue: 0.1572 time to fit residues: 23.6292 Evaluate side-chains 111 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 589 HIS Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain F residue 88 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 52 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.151526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.124196 restraints weight = 30154.796| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.90 r_work: 0.3563 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7128 Z= 0.149 Angle : 0.722 8.581 9751 Z= 0.344 Chirality : 0.050 0.322 1109 Planarity : 0.005 0.052 1225 Dihedral : 15.382 105.717 1268 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.90 % Favored : 89.87 % Rotamer: Outliers : 2.85 % Allowed : 20.49 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.28), residues: 879 helix: -0.72 (0.87), residues: 44 sheet: 0.33 (0.29), residues: 324 loop : -2.10 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 521 TYR 0.009 0.001 TYR H 95 PHE 0.012 0.001 PHE A 509 TRP 0.010 0.002 TRP A 420 HIS 0.010 0.002 HIS A 589 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7099) covalent geometry : angle 0.69428 ( 9679) SS BOND : bond 0.00650 ( 15) SS BOND : angle 1.74799 ( 30) hydrogen bonds : bond 0.03332 ( 197) hydrogen bonds : angle 5.66454 ( 546) link_BETA1-3 : bond 0.00348 ( 3) link_BETA1-3 : angle 3.07367 ( 9) link_BETA1-4 : bond 0.00499 ( 6) link_BETA1-4 : angle 2.41951 ( 18) link_BETA1-6 : bond 0.00313 ( 1) link_BETA1-6 : angle 2.97371 ( 3) link_NAG-ASN : bond 0.00396 ( 4) link_NAG-ASN : angle 3.00136 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 75 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8000 (mt0) cc_final: 0.7654 (mp10) REVERT: H 178 GLN cc_start: 0.8090 (tt0) cc_final: 0.7820 (tt0) REVERT: A 455 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.7022 (mtt180) REVERT: A 589 HIS cc_start: 0.6016 (OUTLIER) cc_final: 0.5083 (t70) REVERT: A 627 PHE cc_start: 0.6549 (OUTLIER) cc_final: 0.5513 (t80) REVERT: E 23 GLU cc_start: 0.5022 (OUTLIER) cc_final: 0.4306 (pm20) outliers start: 21 outliers final: 15 residues processed: 112 average time/residue: 0.1646 time to fit residues: 24.5978 Evaluate side-chains 109 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 589 HIS Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain F residue 91 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 33 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 75 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.151120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.123621 restraints weight = 30169.367| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.94 r_work: 0.3555 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7128 Z= 0.167 Angle : 0.727 8.641 9751 Z= 0.345 Chirality : 0.049 0.328 1109 Planarity : 0.005 0.051 1225 Dihedral : 14.487 102.085 1268 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.58 % Favored : 89.19 % Rotamer: Outliers : 3.39 % Allowed : 20.35 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.28), residues: 879 helix: -0.75 (0.87), residues: 44 sheet: 0.39 (0.30), residues: 318 loop : -2.08 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 521 TYR 0.010 0.001 TYR H 95 PHE 0.012 0.001 PHE E 55 TRP 0.009 0.002 TRP A 420 HIS 0.008 0.001 HIS A 589 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 7099) covalent geometry : angle 0.70060 ( 9679) SS BOND : bond 0.00581 ( 15) SS BOND : angle 1.73788 ( 30) hydrogen bonds : bond 0.03346 ( 197) hydrogen bonds : angle 5.63605 ( 546) link_BETA1-3 : bond 0.00293 ( 3) link_BETA1-3 : angle 2.74008 ( 9) link_BETA1-4 : bond 0.00620 ( 6) link_BETA1-4 : angle 2.49083 ( 18) link_BETA1-6 : bond 0.00285 ( 1) link_BETA1-6 : angle 2.75881 ( 3) link_NAG-ASN : bond 0.00397 ( 4) link_NAG-ASN : angle 3.03353 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 75 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8014 (mt0) cc_final: 0.7646 (mp10) REVERT: H 178 GLN cc_start: 0.8110 (tt0) cc_final: 0.7848 (tt0) REVERT: A 455 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.7033 (mtt180) REVERT: A 627 PHE cc_start: 0.6548 (OUTLIER) cc_final: 0.5492 (t80) REVERT: E 23 GLU cc_start: 0.4966 (OUTLIER) cc_final: 0.4251 (pm20) outliers start: 25 outliers final: 19 residues processed: 110 average time/residue: 0.1517 time to fit residues: 22.4190 Evaluate side-chains 113 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 91 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 58 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 77 optimal weight: 0.0370 chunk 7 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.151540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.124547 restraints weight = 30198.506| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.88 r_work: 0.3568 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7128 Z= 0.139 Angle : 0.701 8.755 9751 Z= 0.333 Chirality : 0.048 0.341 1109 Planarity : 0.005 0.052 1225 Dihedral : 13.191 93.931 1268 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.56 % Favored : 90.22 % Rotamer: Outliers : 3.26 % Allowed : 20.35 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.28), residues: 879 helix: -0.73 (0.87), residues: 44 sheet: 0.43 (0.30), residues: 318 loop : -2.02 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 521 TYR 0.009 0.001 TYR H 95 PHE 0.012 0.001 PHE A 509 TRP 0.011 0.001 TRP A 420 HIS 0.006 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7099) covalent geometry : angle 0.67714 ( 9679) SS BOND : bond 0.00555 ( 15) SS BOND : angle 1.57226 ( 30) hydrogen bonds : bond 0.03099 ( 197) hydrogen bonds : angle 5.44561 ( 546) link_BETA1-3 : bond 0.00322 ( 3) link_BETA1-3 : angle 2.35564 ( 9) link_BETA1-4 : bond 0.00777 ( 6) link_BETA1-4 : angle 2.39263 ( 18) link_BETA1-6 : bond 0.00542 ( 1) link_BETA1-6 : angle 2.22358 ( 3) link_NAG-ASN : bond 0.00369 ( 4) link_NAG-ASN : angle 3.06879 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 75 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.7990 (mt0) cc_final: 0.7675 (mp10) REVERT: H 178 GLN cc_start: 0.8076 (tt0) cc_final: 0.7794 (tt0) REVERT: A 455 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.7022 (mtt180) REVERT: A 469 TRP cc_start: 0.6498 (m-10) cc_final: 0.5916 (m100) REVERT: E 23 GLU cc_start: 0.5017 (OUTLIER) cc_final: 0.4286 (pm20) outliers start: 24 outliers final: 19 residues processed: 111 average time/residue: 0.1548 time to fit residues: 22.9227 Evaluate side-chains 113 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 91 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 27 optimal weight: 0.0270 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.151539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.125221 restraints weight = 29865.856| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.87 r_work: 0.3548 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7128 Z= 0.121 Angle : 0.686 8.907 9751 Z= 0.324 Chirality : 0.048 0.349 1109 Planarity : 0.005 0.053 1225 Dihedral : 12.110 88.500 1268 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.10 % Favored : 90.67 % Rotamer: Outliers : 3.12 % Allowed : 20.62 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.28), residues: 879 helix: -0.77 (0.87), residues: 44 sheet: 0.56 (0.30), residues: 318 loop : -1.91 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 521 TYR 0.008 0.001 TYR H 95 PHE 0.013 0.001 PHE A 509 TRP 0.010 0.001 TRP H 47 HIS 0.006 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7099) covalent geometry : angle 0.66233 ( 9679) SS BOND : bond 0.00480 ( 15) SS BOND : angle 1.41871 ( 30) hydrogen bonds : bond 0.02861 ( 197) hydrogen bonds : angle 5.23263 ( 546) link_BETA1-3 : bond 0.00317 ( 3) link_BETA1-3 : angle 2.09316 ( 9) link_BETA1-4 : bond 0.00643 ( 6) link_BETA1-4 : angle 2.56331 ( 18) link_BETA1-6 : bond 0.00779 ( 1) link_BETA1-6 : angle 1.23042 ( 3) link_NAG-ASN : bond 0.00373 ( 4) link_NAG-ASN : angle 3.15592 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 75 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8041 (mt0) cc_final: 0.7669 (mp10) REVERT: H 178 GLN cc_start: 0.8124 (tt0) cc_final: 0.7802 (tt0) REVERT: L 170 ASP cc_start: 0.7107 (t0) cc_final: 0.6770 (t0) REVERT: A 469 TRP cc_start: 0.6437 (m-10) cc_final: 0.5867 (m100) REVERT: E 23 GLU cc_start: 0.4983 (OUTLIER) cc_final: 0.4252 (pm20) outliers start: 23 outliers final: 19 residues processed: 116 average time/residue: 0.1616 time to fit residues: 25.2887 Evaluate side-chains 113 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 91 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 31 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.150110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.124029 restraints weight = 29907.134| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.83 r_work: 0.3536 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7128 Z= 0.149 Angle : 0.704 9.034 9751 Z= 0.333 Chirality : 0.048 0.353 1109 Planarity : 0.005 0.052 1225 Dihedral : 11.713 86.854 1268 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.78 % Favored : 89.99 % Rotamer: Outliers : 3.39 % Allowed : 20.08 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.28), residues: 879 helix: -0.71 (0.87), residues: 44 sheet: 0.60 (0.30), residues: 318 loop : -1.96 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 521 TYR 0.010 0.001 TYR H 95 PHE 0.012 0.001 PHE E 55 TRP 0.011 0.002 TRP A 420 HIS 0.005 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 7099) covalent geometry : angle 0.67837 ( 9679) SS BOND : bond 0.00590 ( 15) SS BOND : angle 1.60897 ( 30) hydrogen bonds : bond 0.02990 ( 197) hydrogen bonds : angle 5.26081 ( 546) link_BETA1-3 : bond 0.00271 ( 3) link_BETA1-3 : angle 2.05322 ( 9) link_BETA1-4 : bond 0.00709 ( 6) link_BETA1-4 : angle 2.67392 ( 18) link_BETA1-6 : bond 0.00671 ( 1) link_BETA1-6 : angle 1.41629 ( 3) link_NAG-ASN : bond 0.00392 ( 4) link_NAG-ASN : angle 3.19541 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 75 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue LEU 413 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8098 (mt0) cc_final: 0.7644 (mp10) REVERT: H 178 GLN cc_start: 0.8291 (tt0) cc_final: 0.7962 (tt0) REVERT: A 469 TRP cc_start: 0.6574 (m-10) cc_final: 0.5939 (m100) REVERT: E 23 GLU cc_start: 0.5086 (OUTLIER) cc_final: 0.4338 (pm20) outliers start: 25 outliers final: 21 residues processed: 111 average time/residue: 0.1418 time to fit residues: 21.3711 Evaluate side-chains 114 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 155 GLU Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 91 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 34 optimal weight: 0.0040 chunk 37 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.148737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.123705 restraints weight = 30257.186| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.69 r_work: 0.3528 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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 : 0.005 0.048 7128 Z= 0.214 Angle : 0.761 9.171 9751 Z= 0.366 Chirality : 0.050 0.358 1109 Planarity : 0.005 0.051 1225 Dihedral : 11.747 83.979 1268 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.15 % Favored : 88.62 % Rotamer: Outliers : 3.26 % Allowed : 20.08 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.28), residues: 879 helix: -1.35 (0.81), residues: 44 sheet: 0.48 (0.30), residues: 320 loop : -2.14 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 521 TYR 0.013 0.002 TYR A 594 PHE 0.018 0.002 PHE E 55 TRP 0.011 0.002 TRP A 420 HIS 0.004 0.001 HIS A 638 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 7099) covalent geometry : angle 0.73183 ( 9679) SS BOND : bond 0.00630 ( 15) SS BOND : angle 2.21309 ( 30) hydrogen bonds : bond 0.03520 ( 197) hydrogen bonds : angle 5.46923 ( 546) link_BETA1-3 : bond 0.00259 ( 3) link_BETA1-3 : angle 2.03224 ( 9) link_BETA1-4 : bond 0.00731 ( 6) link_BETA1-4 : angle 2.85380 ( 18) link_BETA1-6 : bond 0.00684 ( 1) link_BETA1-6 : angle 1.32614 ( 3) link_NAG-ASN : bond 0.00422 ( 4) link_NAG-ASN : angle 3.25168 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2868.33 seconds wall clock time: 49 minutes 20.52 seconds (2960.52 seconds total)