Starting phenix.real_space_refine on Sun Nov 17 09:46:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thz_41275/11_2024/8thz_41275_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thz_41275/11_2024/8thz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thz_41275/11_2024/8thz_41275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thz_41275/11_2024/8thz_41275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thz_41275/11_2024/8thz_41275_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thz_41275/11_2024/8thz_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-5513/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: 7.32, per 1000 atoms: 0.55 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: 3.77 Conformation dependent library (CDL) restraints added in 1.2 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: 1.28 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: 5.65 Time building geometry restraints manager: 4.42 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: 1.880 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: 0.260 Extract box with map and model: 0.530 Check model and map are aligned: 0.170 Set scattering table: 0.140 Process input model: 33.150 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.170 ------------------------------------------------------------------------------- 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 7099 Z= 0.272 Angle : 0.740 9.157 9679 Z= 0.358 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 *********************** 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 : 1.239 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: 0.4441 time to fit residues: 58.9929 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 : 1.114 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7099 Z= 0.256 Angle : 0.747 8.058 9679 Z= 0.360 Chirality : 0.051 0.276 1109 Planarity : 0.005 0.049 1225 Dihedral : 23.218 118.839 1276 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.47 % Favored : 89.42 % Rotamer: Outliers : 2.17 % Allowed : 19.00 % Favored : 78.83 % 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: -0.92 (0.82), residues: 44 sheet: 0.42 (0.30), residues: 318 loop : -1.81 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 420 HIS 0.003 0.001 HIS A 638 PHE 0.017 0.002 PHE A 509 TYR 0.011 0.001 TYR H 95 ARG 0.006 0.000 ARG A 521 *********************** 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: 16 poor density : 94 time to evaluate : 1.056 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: E 67 ARG cc_start: 0.6320 (mtm-85) cc_final: 0.6116 (mtm180) outliers start: 16 outliers final: 9 residues processed: 106 average time/residue: 0.4457 time to fit residues: 61.9387 Evaluate side-chains 97 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 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 43 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7099 Z= 0.297 Angle : 0.736 8.895 9679 Z= 0.354 Chirality : 0.050 0.259 1109 Planarity : 0.005 0.049 1225 Dihedral : 19.090 113.202 1272 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.04 % Favored : 88.74 % Rotamer: Outliers : 3.12 % Allowed : 20.08 % 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: -1.49 (0.28), residues: 879 helix: -0.73 (0.86), residues: 44 sheet: 0.39 (0.29), residues: 324 loop : -2.06 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 36 HIS 0.004 0.001 HIS A 488 PHE 0.016 0.002 PHE E 55 TYR 0.013 0.001 TYR H 95 ARG 0.002 0.000 ARG H 99 *********************** 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 115 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 1.098 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: A 627 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.5847 (t80) REVERT: E 23 GLU cc_start: 0.5183 (OUTLIER) cc_final: 0.4514 (pm20) outliers start: 23 outliers final: 16 residues processed: 112 average time/residue: 0.4303 time to fit residues: 63.6053 Evaluate side-chains 103 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 208 LYS 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 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 78 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 22 optimal weight: 0.0970 chunk 70 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7099 Z= 0.224 Angle : 0.701 8.361 9679 Z= 0.336 Chirality : 0.049 0.279 1109 Planarity : 0.005 0.052 1225 Dihedral : 17.509 111.405 1272 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.99 % Favored : 90.78 % Rotamer: Outliers : 2.58 % Allowed : 20.08 % 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: -0.77 (0.85), residues: 44 sheet: 0.32 (0.29), residues: 326 loop : -2.00 (0.26), residues: 509 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 H 95 ARG 0.004 0.000 ARG H 217 *********************** 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 111 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 1.287 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: A 627 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.5790 (t80) REVERT: E 23 GLU cc_start: 0.5053 (OUTLIER) cc_final: 0.4368 (pm20) outliers start: 19 outliers final: 13 residues processed: 106 average time/residue: 0.4099 time to fit residues: 58.7750 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 : 1.147 ------------------------------------------------------------------------------- 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 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 47 optimal weight: 0.8980 chunk 1 optimal weight: 0.0570 chunk 62 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7099 Z= 0.193 Angle : 0.668 8.491 9679 Z= 0.319 Chirality : 0.049 0.315 1109 Planarity : 0.005 0.054 1225 Dihedral : 15.488 108.443 1272 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.10 % Favored : 90.67 % Rotamer: Outliers : 2.99 % Allowed : 19.95 % 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 (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 (0.28), residues: 879 helix: -0.71 (0.87), residues: 44 sheet: 0.45 (0.29), residues: 324 loop : -1.95 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.005 0.001 HIS A 488 PHE 0.014 0.001 PHE A 509 TYR 0.008 0.001 TYR A 613 ARG 0.002 0.000 ARG H 217 *********************** 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 125 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 170 ASP cc_start: 0.7051 (t0) cc_final: 0.6767 (t0) REVERT: A 455 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.7098 (mtt180) REVERT: E 23 GLU cc_start: 0.4946 (OUTLIER) cc_final: 0.4200 (pm20) outliers start: 22 outliers final: 16 residues processed: 119 average time/residue: 0.4237 time to fit residues: 66.7727 Evaluate side-chains 110 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 589 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.0050 chunk 6 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 0.0050 overall best weight: 0.4608 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7099 Z= 0.206 Angle : 0.671 8.764 9679 Z= 0.323 Chirality : 0.048 0.329 1109 Planarity : 0.005 0.054 1225 Dihedral : 14.230 103.894 1268 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.87 % Favored : 90.90 % Rotamer: Outliers : 2.71 % Allowed : 20.35 % 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: -1.28 (0.28), residues: 879 helix: -0.72 (0.87), residues: 44 sheet: 0.56 (0.30), residues: 318 loop : -1.90 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.011 0.001 HIS A 589 PHE 0.012 0.001 PHE A 509 TYR 0.008 0.001 TYR H 95 ARG 0.008 0.000 ARG A 521 *********************** 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 115 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 1.127 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: A 455 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.7091 (mtt180) REVERT: A 555 MET cc_start: 0.8169 (mmm) cc_final: 0.7654 (mmm) REVERT: A 589 HIS cc_start: 0.5333 (OUTLIER) cc_final: 0.4678 (t70) REVERT: A 591 GLU cc_start: 0.5265 (mp0) cc_final: 0.5033 (mp0) REVERT: E 23 GLU cc_start: 0.4953 (OUTLIER) cc_final: 0.4200 (pm20) outliers start: 20 outliers final: 14 residues processed: 110 average time/residue: 0.4252 time to fit residues: 62.5754 Evaluate side-chains 107 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 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 E residue 23 GLU Chi-restraints excluded: chain F residue 88 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.0670 chunk 33 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 HIS E 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7099 Z= 0.210 Angle : 0.668 8.818 9679 Z= 0.320 Chirality : 0.048 0.335 1109 Planarity : 0.005 0.053 1225 Dihedral : 13.433 97.981 1268 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.22 % Favored : 90.56 % Rotamer: Outliers : 3.53 % Allowed : 19.67 % 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: -1.25 (0.28), residues: 879 helix: -0.71 (0.87), residues: 44 sheet: 0.58 (0.30), residues: 324 loop : -1.90 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 90 HIS 0.014 0.001 HIS A 589 PHE 0.012 0.001 PHE A 509 TYR 0.009 0.001 TYR H 95 ARG 0.006 0.000 ARG A 521 *********************** 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 117 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 1.466 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: A 455 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.7088 (mtt180) REVERT: A 469 TRP cc_start: 0.6204 (m-10) cc_final: 0.5880 (m100) REVERT: A 555 MET cc_start: 0.8172 (mmm) cc_final: 0.7653 (mmm) REVERT: E 23 GLU cc_start: 0.4964 (OUTLIER) cc_final: 0.4213 (pm20) outliers start: 26 outliers final: 18 residues processed: 112 average time/residue: 0.4439 time to fit residues: 66.8798 Evaluate side-chains 111 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 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 514 VAL 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 E residue 23 GLU Chi-restraints excluded: chain E residue 35 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 76 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7099 Z= 0.204 Angle : 0.660 8.944 9679 Z= 0.316 Chirality : 0.048 0.345 1109 Planarity : 0.005 0.053 1225 Dihedral : 12.631 93.889 1268 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.99 % Favored : 90.78 % Rotamer: Outliers : 2.99 % Allowed : 20.22 % 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: -1.24 (0.28), residues: 879 helix: -0.70 (0.87), residues: 44 sheet: 0.58 (0.30), residues: 318 loop : -1.86 (0.26), 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 0.009 0.001 TYR H 95 ARG 0.005 0.000 ARG A 521 *********************** 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 116 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.7057 (mtt180) REVERT: A 469 TRP cc_start: 0.6173 (m-10) cc_final: 0.5826 (m100) REVERT: A 555 MET cc_start: 0.8170 (mmm) cc_final: 0.7653 (mmm) REVERT: E 23 GLU cc_start: 0.4953 (OUTLIER) cc_final: 0.4203 (pm20) outliers start: 22 outliers final: 19 residues processed: 111 average time/residue: 0.4172 time to fit residues: 61.6529 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 : 1.387 ------------------------------------------------------------------------------- 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 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 514 VAL 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 E residue 23 GLU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain F residue 60 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 HIS F 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7099 Z= 0.244 Angle : 0.678 9.111 9679 Z= 0.326 Chirality : 0.048 0.356 1109 Planarity : 0.005 0.052 1225 Dihedral : 11.863 87.956 1268 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.67 % Favored : 90.10 % Rotamer: Outliers : 3.12 % Allowed : 20.08 % 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: -0.67 (0.88), residues: 44 sheet: 0.58 (0.30), residues: 318 loop : -1.91 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 420 HIS 0.003 0.001 HIS A 638 PHE 0.013 0.001 PHE E 55 TYR 0.011 0.001 TYR H 95 ARG 0.005 0.000 ARG A 521 *********************** 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 115 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 1.180 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: A 455 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.7130 (mtt180) REVERT: A 469 TRP cc_start: 0.6144 (m-10) cc_final: 0.5817 (m100) REVERT: E 23 GLU cc_start: 0.4811 (OUTLIER) cc_final: 0.4059 (pm20) REVERT: E 74 GLU cc_start: 0.4055 (pt0) cc_final: 0.3327 (pm20) outliers start: 23 outliers final: 18 residues processed: 111 average time/residue: 0.4146 time to fit residues: 61.3592 Evaluate side-chains 111 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 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 514 VAL 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 608 LEU 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 86 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 54 optimal weight: 0.0570 chunk 73 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7099 Z= 0.234 Angle : 0.675 9.196 9679 Z= 0.325 Chirality : 0.048 0.366 1109 Planarity : 0.005 0.052 1225 Dihedral : 11.389 85.635 1268 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.33 % Favored : 90.44 % Rotamer: Outliers : 2.99 % Allowed : 20.35 % 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: -1.24 (0.28), residues: 879 helix: -0.69 (0.87), residues: 44 sheet: 0.57 (0.30), residues: 330 loop : -1.92 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 420 HIS 0.004 0.001 HIS A 488 PHE 0.012 0.001 PHE A 509 TYR 0.009 0.001 TYR H 95 ARG 0.004 0.000 ARG A 521 ********************** 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 114 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 170 ASP cc_start: 0.7060 (t0) cc_final: 0.6848 (t0) REVERT: A 455 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.7136 (mtt180) REVERT: A 469 TRP cc_start: 0.6111 (m-10) cc_final: 0.5778 (m100) REVERT: E 23 GLU cc_start: 0.4901 (OUTLIER) cc_final: 0.4169 (pm20) REVERT: E 74 GLU cc_start: 0.4131 (pt0) cc_final: 0.3451 (pm20) outliers start: 22 outliers final: 17 residues processed: 109 average time/residue: 0.4182 time to fit residues: 60.4847 Evaluate side-chains 111 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 514 VAL 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 608 LEU 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 19 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 79 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.150315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.124399 restraints weight = 29703.313| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.82 r_work: 0.3546 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7099 Z= 0.221 Angle : 0.668 9.207 9679 Z= 0.321 Chirality : 0.047 0.363 1109 Planarity : 0.005 0.052 1225 Dihedral : 11.049 82.571 1268 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.33 % Favored : 90.44 % Rotamer: Outliers : 2.71 % Allowed : 20.62 % 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: -1.23 (0.28), residues: 879 helix: -0.73 (0.86), residues: 44 sheet: 0.58 (0.30), residues: 330 loop : -1.90 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 420 HIS 0.004 0.001 HIS A 488 PHE 0.012 0.001 PHE A 509 TYR 0.009 0.001 TYR H 95 ARG 0.005 0.000 ARG A 521 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3907.79 seconds wall clock time: 70 minutes 21.09 seconds (4221.09 seconds total)