Starting phenix.real_space_refine on Thu May 15 17:47:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thz_41275/05_2025/8thz_41275_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thz_41275/05_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_41275/05_2025/8thz_41275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thz_41275/05_2025/8thz_41275.map" model { file = "/net/cci-nas-00/data/ceres_data/8thz_41275/05_2025/8thz_41275_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thz_41275/05_2025/8thz_41275_trim.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'ARG:plan': 1, 'ASP: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: 7.02, per 1000 atoms: 0.53 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: 3.86 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.33 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: 5.20 Time building geometry restraints manager: 4.51 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: 1.930 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: 0.220 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.990 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.280 ------------------------------------------------------------------------------- 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 : 7.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP E 36 HIS 0.005 0.001 HIS A 488 PHE 0.016 0.001 PHE A 522 TYR 0.009 0.001 TYR H 201 ARG 0.008 0.001 ARG F 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 4) link_NAG-ASN : angle 2.62537 ( 12) link_BETA1-4 : bond 0.01667 ( 6) link_BETA1-4 : angle 3.08692 ( 18) hydrogen bonds : bond 0.17762 ( 197) hydrogen bonds : angle 8.61870 ( 546) link_BETA1-6 : bond 0.01849 ( 1) link_BETA1-6 : angle 0.72145 ( 3) SS BOND : bond 0.00583 ( 15) SS BOND : angle 1.71017 ( 30) link_BETA1-3 : bond 0.00745 ( 3) link_BETA1-3 : angle 1.80461 ( 9) covalent geometry : bond 0.00412 ( 7099) covalent geometry : angle 0.74014 ( 9679) *********************** 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 : 0.999 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: 0.4170 time to fit residues: 55.2080 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 : 0.987 ------------------------------------------------------------------------------- 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 73 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 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 541 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.156182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.130086 restraints weight = 29606.644| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.77 r_work: 0.3655 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7128 Z= 0.159 Angle : 0.766 8.107 9751 Z= 0.362 Chirality : 0.051 0.296 1109 Planarity : 0.005 0.049 1225 Dihedral : 23.124 118.676 1276 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.47 % Favored : 89.42 % Rotamer: Outliers : 1.90 % Allowed : 19.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.28), residues: 879 helix: -0.93 (0.82), residues: 44 sheet: 0.41 (0.30), residues: 318 loop : -1.79 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 420 HIS 0.005 0.001 HIS A 458 PHE 0.017 0.002 PHE A 509 TYR 0.011 0.001 TYR H 95 ARG 0.007 0.001 ARG A 521 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 4) link_NAG-ASN : angle 2.34946 ( 12) link_BETA1-4 : bond 0.00585 ( 6) link_BETA1-4 : angle 2.43659 ( 18) hydrogen bonds : bond 0.04491 ( 197) hydrogen bonds : angle 6.76772 ( 546) link_BETA1-6 : bond 0.00629 ( 1) link_BETA1-6 : angle 2.71995 ( 3) SS BOND : bond 0.00598 ( 15) SS BOND : angle 1.49081 ( 30) link_BETA1-3 : bond 0.00530 ( 3) link_BETA1-3 : angle 2.85697 ( 9) covalent geometry : bond 0.00367 ( 7099) covalent geometry : angle 0.74557 ( 9679) *********************** 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 109 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.004 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: 0.8150 (mt0) cc_final: 0.7791 (mp10) REVERT: H 178 GLN cc_start: 0.8172 (tt0) cc_final: 0.7908 (tt0) REVERT: E 67 ARG cc_start: 0.6494 (mtm-85) cc_final: 0.6258 (mtm180) outliers start: 14 outliers final: 8 residues processed: 106 average time/residue: 0.4260 time to fit residues: 59.0505 Evaluate side-chains 97 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 85 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 22 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.154454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.127605 restraints weight = 30065.011| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.86 r_work: 0.3607 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1106 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= 0.151 Angle : 0.733 8.811 9751 Z= 0.343 Chirality : 0.049 0.254 1109 Planarity : 0.005 0.052 1225 Dihedral : 18.952 114.311 1272 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.24 % Favored : 89.53 % Rotamer: Outliers : 2.85 % Allowed : 19.27 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.28), residues: 879 helix: -0.74 (0.85), residues: 44 sheet: 0.48 (0.29), residues: 324 loop : -1.92 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS A 488 PHE 0.018 0.001 PHE A 509 TYR 0.011 0.001 TYR H 95 ARG 0.002 0.000 ARG H 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 4) link_NAG-ASN : angle 3.33055 ( 12) link_BETA1-4 : bond 0.00565 ( 6) link_BETA1-4 : angle 2.22853 ( 18) hydrogen bonds : bond 0.03885 ( 197) hydrogen bonds : angle 6.05021 ( 546) link_BETA1-6 : bond 0.00386 ( 1) link_BETA1-6 : angle 3.27040 ( 3) SS BOND : bond 0.00887 ( 15) SS BOND : angle 1.83876 ( 30) link_BETA1-3 : bond 0.00437 ( 3) link_BETA1-3 : angle 3.46097 ( 9) covalent geometry : bond 0.00353 ( 7099) covalent geometry : angle 0.70261 ( 9679) *********************** 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 116 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.052 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: 0.7985 (mt0) cc_final: 0.7730 (mp10) REVERT: H 178 GLN cc_start: 0.8095 (tt0) cc_final: 0.7819 (tt0) REVERT: A 627 PHE cc_start: 0.6492 (OUTLIER) cc_final: 0.5509 (t80) REVERT: E 23 GLU cc_start: 0.5078 (OUTLIER) cc_final: 0.4463 (pm20) outliers start: 21 outliers final: 13 residues processed: 112 average time/residue: 0.4201 time to fit residues: 61.8796 Evaluate side-chains 105 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 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 62 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 22 optimal weight: 0.0870 chunk 50 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.152357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.125406 restraints weight = 29939.120| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.87 r_work: 0.3587 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7128 Z= 0.154 Angle : 0.730 8.579 9751 Z= 0.344 Chirality : 0.049 0.281 1109 Planarity : 0.005 0.052 1225 Dihedral : 17.063 111.437 1272 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.13 % Favored : 89.65 % Rotamer: Outliers : 2.85 % Allowed : 19.40 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.28), residues: 879 helix: -0.77 (0.85), residues: 44 sheet: 0.40 (0.29), residues: 326 loop : -1.94 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 420 HIS 0.005 0.001 HIS A 488 PHE 0.013 0.001 PHE A 509 TYR 0.010 0.001 TYR H 95 ARG 0.008 0.001 ARG E 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 4) link_NAG-ASN : angle 2.97272 ( 12) link_BETA1-4 : bond 0.00670 ( 6) link_BETA1-4 : angle 2.32051 ( 18) hydrogen bonds : bond 0.03406 ( 197) hydrogen bonds : angle 5.73782 ( 546) link_BETA1-6 : bond 0.00264 ( 1) link_BETA1-6 : angle 3.23212 ( 3) SS BOND : bond 0.00607 ( 15) SS BOND : angle 1.67573 ( 30) link_BETA1-3 : bond 0.00312 ( 3) link_BETA1-3 : angle 3.69659 ( 9) covalent geometry : bond 0.00364 ( 7099) covalent geometry : angle 0.70064 ( 9679) *********************** 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 116 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.109 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: H 3 GLN cc_start: 0.8025 (mt0) cc_final: 0.7724 (mp10) REVERT: H 178 GLN cc_start: 0.8100 (tt0) cc_final: 0.7820 (tt0) REVERT: A 627 PHE cc_start: 0.6546 (OUTLIER) cc_final: 0.5546 (t80) REVERT: E 23 GLU cc_start: 0.5058 (OUTLIER) cc_final: 0.4396 (pm20) outliers start: 21 outliers final: 15 residues processed: 111 average time/residue: 0.4043 time to fit residues: 61.1370 Evaluate side-chains 108 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 H residue 208 LYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.151232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.124279 restraints weight = 30140.234| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.86 r_work: 0.3571 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1552 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= 0.180 Angle : 0.734 8.535 9751 Z= 0.348 Chirality : 0.049 0.314 1109 Planarity : 0.005 0.051 1225 Dihedral : 15.820 107.850 1272 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.35 % Favored : 89.42 % Rotamer: Outliers : 3.53 % Allowed : 19.13 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.28), residues: 879 helix: -0.73 (0.87), residues: 44 sheet: 0.39 (0.29), residues: 326 loop : -2.06 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 47 HIS 0.004 0.001 HIS A 488 PHE 0.015 0.002 PHE E 55 TYR 0.012 0.001 TYR H 95 ARG 0.002 0.000 ARG H 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 4) link_NAG-ASN : angle 3.04269 ( 12) link_BETA1-4 : bond 0.00620 ( 6) link_BETA1-4 : angle 2.40696 ( 18) hydrogen bonds : bond 0.03487 ( 197) hydrogen bonds : angle 5.68995 ( 546) link_BETA1-6 : bond 0.00331 ( 1) link_BETA1-6 : angle 3.06473 ( 3) SS BOND : bond 0.00588 ( 15) SS BOND : angle 1.81147 ( 30) link_BETA1-3 : bond 0.00355 ( 3) link_BETA1-3 : angle 3.20268 ( 9) covalent geometry : bond 0.00427 ( 7099) covalent geometry : angle 0.70536 ( 9679) *********************** 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 120 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.988 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: 0.8066 (mt0) cc_final: 0.7619 (mp10) REVERT: H 178 GLN cc_start: 0.8258 (tt0) cc_final: 0.7956 (tt0) REVERT: A 455 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.7105 (mtt180) REVERT: A 627 PHE cc_start: 0.6791 (OUTLIER) cc_final: 0.5783 (t80) REVERT: E 23 GLU cc_start: 0.5023 (OUTLIER) cc_final: 0.4302 (pm20) outliers start: 26 outliers final: 18 residues processed: 114 average time/residue: 0.4093 time to fit residues: 61.6591 Evaluate side-chains 112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 198 THR Chi-restraints excluded: chain H residue 206 ASN 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 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 5 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 50 optimal weight: 0.0770 overall best weight: 0.9340 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.151481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.124528 restraints weight = 30442.135| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.89 r_work: 0.3570 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1731 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= 0.170 Angle : 0.728 8.710 9751 Z= 0.345 Chirality : 0.049 0.330 1109 Planarity : 0.005 0.060 1225 Dihedral : 14.319 101.588 1268 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.13 % Favored : 89.65 % Rotamer: Outliers : 2.85 % Allowed : 20.35 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.28), residues: 879 helix: -0.69 (0.88), residues: 44 sheet: 0.38 (0.29), residues: 324 loop : -2.11 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 420 HIS 0.005 0.001 HIS A 488 PHE 0.013 0.001 PHE E 55 TYR 0.010 0.001 TYR A 613 ARG 0.009 0.000 ARG A 521 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 4) link_NAG-ASN : angle 3.01078 ( 12) link_BETA1-4 : bond 0.00685 ( 6) link_BETA1-4 : angle 2.45572 ( 18) hydrogen bonds : bond 0.03328 ( 197) hydrogen bonds : angle 5.57187 ( 546) link_BETA1-6 : bond 0.00292 ( 1) link_BETA1-6 : angle 2.77415 ( 3) SS BOND : bond 0.00604 ( 15) SS BOND : angle 1.80779 ( 30) link_BETA1-3 : bond 0.00345 ( 3) link_BETA1-3 : angle 2.73789 ( 9) covalent geometry : bond 0.00409 ( 7099) covalent geometry : angle 0.70097 ( 9679) *********************** 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 : 1.014 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: 0.7989 (mt0) cc_final: 0.7668 (mp10) REVERT: H 178 GLN cc_start: 0.8101 (tt0) cc_final: 0.7853 (tt0) REVERT: A 455 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.7062 (mtt180) REVERT: A 627 PHE cc_start: 0.6584 (OUTLIER) cc_final: 0.5552 (t80) REVERT: E 23 GLU cc_start: 0.4945 (OUTLIER) cc_final: 0.4229 (pm20) outliers start: 21 outliers final: 15 residues processed: 112 average time/residue: 0.4308 time to fit residues: 63.6660 Evaluate side-chains 113 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 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 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 E residue 35 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 33 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 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 = 0.4040 r_free = 0.4040 target = 0.151981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.124833 restraints weight = 30371.251| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.90 r_work: 0.3570 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7128 Z= 0.144 Angle : 0.702 8.726 9751 Z= 0.332 Chirality : 0.049 0.336 1109 Planarity : 0.005 0.052 1225 Dihedral : 13.338 95.148 1268 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.67 % Favored : 90.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.28), residues: 879 helix: -0.72 (0.87), residues: 44 sheet: 0.44 (0.30), residues: 318 loop : -2.03 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 420 HIS 0.005 0.001 HIS A 488 PHE 0.012 0.001 PHE A 509 TYR 0.010 0.001 TYR E 95 ARG 0.005 0.000 ARG A 521 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 4) link_NAG-ASN : angle 3.06961 ( 12) link_BETA1-4 : bond 0.00742 ( 6) link_BETA1-4 : angle 2.44245 ( 18) hydrogen bonds : bond 0.03115 ( 197) hydrogen bonds : angle 5.42777 ( 546) link_BETA1-6 : bond 0.00502 ( 1) link_BETA1-6 : angle 2.38870 ( 3) SS BOND : bond 0.00564 ( 15) SS BOND : angle 1.66666 ( 30) link_BETA1-3 : bond 0.00309 ( 3) link_BETA1-3 : angle 2.43702 ( 9) covalent geometry : bond 0.00346 ( 7099) covalent geometry : angle 0.67613 ( 9679) *********************** 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 121 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 1.070 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: H 3 GLN cc_start: 0.7998 (mt0) cc_final: 0.7652 (mp10) REVERT: H 178 GLN cc_start: 0.8085 (tt0) cc_final: 0.7831 (tt0) REVERT: L 170 ASP cc_start: 0.7102 (t0) cc_final: 0.6739 (t0) REVERT: A 455 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.7017 (mtt180) REVERT: A 591 GLU cc_start: 0.5256 (mp0) cc_final: 0.5046 (mp0) REVERT: A 627 PHE cc_start: 0.6519 (OUTLIER) cc_final: 0.5478 (t80) REVERT: E 23 GLU cc_start: 0.4918 (OUTLIER) cc_final: 0.4209 (pm20) outliers start: 25 outliers final: 18 residues processed: 114 average time/residue: 0.3997 time to fit residues: 60.8770 Evaluate side-chains 115 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 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 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 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 18 optimal weight: 0.0980 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.149891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.123352 restraints weight = 30050.020| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.90 r_work: 0.3519 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1972 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= 0.151 Angle : 0.705 8.927 9751 Z= 0.335 Chirality : 0.048 0.350 1109 Planarity : 0.005 0.052 1225 Dihedral : 12.431 89.690 1268 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.24 % Favored : 89.53 % Rotamer: Outliers : 3.66 % Allowed : 19.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.28), residues: 879 helix: -0.77 (0.87), residues: 44 sheet: 0.47 (0.30), residues: 324 loop : -2.05 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 420 HIS 0.004 0.001 HIS A 488 PHE 0.012 0.001 PHE A 509 TYR 0.010 0.001 TYR A 613 ARG 0.005 0.000 ARG A 521 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 4) link_NAG-ASN : angle 3.12184 ( 12) link_BETA1-4 : bond 0.00734 ( 6) link_BETA1-4 : angle 2.61632 ( 18) hydrogen bonds : bond 0.03056 ( 197) hydrogen bonds : angle 5.35924 ( 546) link_BETA1-6 : bond 0.00755 ( 1) link_BETA1-6 : angle 1.17807 ( 3) SS BOND : bond 0.00564 ( 15) SS BOND : angle 1.64930 ( 30) link_BETA1-3 : bond 0.00278 ( 3) link_BETA1-3 : angle 2.13662 ( 9) covalent geometry : bond 0.00362 ( 7099) covalent geometry : angle 0.67990 ( 9679) *********************** 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 123 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 1.081 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: 0.8056 (mt0) cc_final: 0.7640 (mp10) REVERT: H 178 GLN cc_start: 0.8145 (tt0) cc_final: 0.7842 (tt0) REVERT: L 170 ASP cc_start: 0.7112 (t0) cc_final: 0.6687 (t0) REVERT: A 469 TRP cc_start: 0.6403 (m-10) cc_final: 0.5855 (m100) REVERT: A 591 GLU cc_start: 0.5166 (mp0) cc_final: 0.4906 (mp0) REVERT: A 627 PHE cc_start: 0.6588 (OUTLIER) cc_final: 0.5465 (t80) REVERT: E 23 GLU cc_start: 0.4875 (OUTLIER) cc_final: 0.4147 (pm20) REVERT: E 74 GLU cc_start: 0.3844 (pt0) cc_final: 0.3139 (pm20) outliers start: 27 outliers final: 22 residues processed: 116 average time/residue: 0.4496 time to fit residues: 69.8567 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 : 1.572 ------------------------------------------------------------------------------- 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 519 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 539 LEU 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 16 SER 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 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 70 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.149729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.123350 restraints weight = 29641.165| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.87 r_work: 0.3523 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7128 Z= 0.155 Angle : 0.708 8.980 9751 Z= 0.336 Chirality : 0.048 0.353 1109 Planarity : 0.005 0.051 1225 Dihedral : 11.940 87.941 1268 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.01 % Favored : 89.76 % Rotamer: Outliers : 3.12 % Allowed : 20.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.28), residues: 879 helix: -0.79 (0.87), residues: 44 sheet: 0.49 (0.30), residues: 324 loop : -2.06 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 420 HIS 0.004 0.001 HIS A 488 PHE 0.012 0.001 PHE A 509 TYR 0.010 0.001 TYR H 95 ARG 0.004 0.000 ARG A 521 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 4) link_NAG-ASN : angle 3.17695 ( 12) link_BETA1-4 : bond 0.00705 ( 6) link_BETA1-4 : angle 2.70683 ( 18) hydrogen bonds : bond 0.03047 ( 197) hydrogen bonds : angle 5.30444 ( 546) link_BETA1-6 : bond 0.00522 ( 1) link_BETA1-6 : angle 1.39740 ( 3) SS BOND : bond 0.00551 ( 15) SS BOND : angle 1.70144 ( 30) link_BETA1-3 : bond 0.00295 ( 3) link_BETA1-3 : angle 2.07555 ( 9) covalent geometry : bond 0.00372 ( 7099) covalent geometry : angle 0.68242 ( 9679) *********************** 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 118 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 1.000 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: H 3 GLN cc_start: 0.8085 (mt0) cc_final: 0.7591 (mp10) REVERT: H 178 GLN cc_start: 0.8286 (tt0) cc_final: 0.7949 (tt0) REVERT: L 170 ASP cc_start: 0.7176 (t0) cc_final: 0.6724 (t0) REVERT: A 469 TRP cc_start: 0.6456 (m-10) cc_final: 0.5906 (m100) REVERT: A 591 GLU cc_start: 0.5360 (mp0) cc_final: 0.5112 (mp0) REVERT: E 23 GLU cc_start: 0.5028 (OUTLIER) cc_final: 0.4307 (pm20) outliers start: 23 outliers final: 20 residues processed: 111 average time/residue: 0.4104 time to fit residues: 61.6993 Evaluate side-chains 115 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 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 519 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 539 LEU 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 44 VAL 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 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 58 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.151799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.126565 restraints weight = 29812.033| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.72 r_work: 0.3568 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7128 Z= 0.133 Angle : 0.691 9.062 9751 Z= 0.326 Chirality : 0.048 0.358 1109 Planarity : 0.005 0.052 1225 Dihedral : 11.349 84.667 1268 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.22 % Favored : 90.56 % Rotamer: Outliers : 2.99 % Allowed : 20.08 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.28), residues: 879 helix: -0.81 (0.87), residues: 44 sheet: 0.52 (0.30), residues: 330 loop : -2.01 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 420 HIS 0.005 0.001 HIS A 488 PHE 0.012 0.001 PHE A 509 TYR 0.008 0.001 TYR H 95 ARG 0.004 0.000 ARG A 521 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 4) link_NAG-ASN : angle 3.23877 ( 12) link_BETA1-4 : bond 0.00687 ( 6) link_BETA1-4 : angle 2.62378 ( 18) hydrogen bonds : bond 0.02847 ( 197) hydrogen bonds : angle 5.17344 ( 546) link_BETA1-6 : bond 0.00809 ( 1) link_BETA1-6 : angle 1.35610 ( 3) SS BOND : bond 0.00505 ( 15) SS BOND : angle 1.50123 ( 30) link_BETA1-3 : bond 0.00344 ( 3) link_BETA1-3 : angle 2.02950 ( 9) covalent geometry : bond 0.00319 ( 7099) covalent geometry : angle 0.66627 ( 9679) ********************** 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 121 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 1.155 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: 0.8105 (mt0) cc_final: 0.7703 (mp10) REVERT: H 178 GLN cc_start: 0.8260 (tt0) cc_final: 0.7947 (tt0) REVERT: L 170 ASP cc_start: 0.7137 (t0) cc_final: 0.6769 (t0) REVERT: A 469 TRP cc_start: 0.6410 (m-10) cc_final: 0.5903 (m100) REVERT: A 591 GLU cc_start: 0.5394 (mp0) cc_final: 0.5138 (mp0) REVERT: E 23 GLU cc_start: 0.5004 (OUTLIER) cc_final: 0.4274 (pm20) REVERT: E 74 GLU cc_start: 0.4193 (pt0) cc_final: 0.3447 (pm20) outliers start: 22 outliers final: 21 residues processed: 114 average time/residue: 0.3772 time to fit residues: 58.9460 Evaluate side-chains 118 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 519 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 539 LEU 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 44 VAL 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 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 34 optimal weight: 0.0470 chunk 56 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.152116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.126922 restraints weight = 29907.446| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.72 r_work: 0.3570 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2245 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= 0.124 Angle : 0.683 9.125 9751 Z= 0.322 Chirality : 0.047 0.359 1109 Planarity : 0.005 0.052 1225 Dihedral : 10.874 80.646 1268 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.22 % Favored : 90.56 % Rotamer: Outliers : 2.71 % Allowed : 20.49 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.28), residues: 879 helix: -0.79 (0.86), residues: 44 sheet: 0.66 (0.30), residues: 325 loop : -1.99 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 420 HIS 0.005 0.001 HIS A 488 PHE 0.012 0.001 PHE A 509 TYR 0.009 0.001 TYR F 48 ARG 0.004 0.000 ARG A 521 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 4) link_NAG-ASN : angle 3.32423 ( 12) link_BETA1-4 : bond 0.00641 ( 6) link_BETA1-4 : angle 2.57999 ( 18) hydrogen bonds : bond 0.02737 ( 197) hydrogen bonds : angle 5.07903 ( 546) link_BETA1-6 : bond 0.00794 ( 1) link_BETA1-6 : angle 1.38146 ( 3) SS BOND : bond 0.00479 ( 15) SS BOND : angle 1.43282 ( 30) link_BETA1-3 : bond 0.00294 ( 3) link_BETA1-3 : angle 1.97423 ( 9) covalent geometry : bond 0.00298 ( 7099) covalent geometry : angle 0.65877 ( 9679) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6552.82 seconds wall clock time: 113 minutes 10.17 seconds (6790.17 seconds total)