Starting phenix.real_space_refine on Thu Jul 2 23:03:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fqf_29386/07_2026/8fqf_29386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fqf_29386/07_2026/8fqf_29386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fqf_29386/07_2026/8fqf_29386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fqf_29386/07_2026/8fqf_29386.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fqf_29386/07_2026/8fqf_29386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fqf_29386/07_2026/8fqf_29386.map" } resolution = 2.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 77 5.16 5 Cl 2 4.86 5 C 7005 2.51 5 N 1709 2.21 5 O 2102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10895 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1177 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Chain: "B" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 bond proxies already assigned to first conformer: 1253 Chain: "C" Number of atoms: 1183 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Conformer: "C" Number of residues, atoms: 148, 1159 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Chain: "D" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 bond proxies already assigned to first conformer: 1253 Chain: "E" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1451 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1451 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1467 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1467 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ACYS A 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 589 " occ=0.50 residue: pdb=" N ASER A 615 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 615 " occ=0.50 residue: pdb=" N ACYS B 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 589 " occ=0.50 residue: pdb=" N ACYS C 589 " occ=0.25 ... (16 atoms not shown) pdb=" SG CCYS C 589 " occ=0.50 residue: pdb=" N ASER C 615 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 615 " occ=0.50 residue: pdb=" N ACYS D 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 589 " occ=0.50 Time building chain proxies: 3.35, per 1000 atoms: 0.31 Number of scatterers: 10895 At special positions: 0 Unit cell: (113.98, 113.16, 91.02, 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) Cl 2 17.00 S 77 16.00 O 2102 8.00 N 1709 7.00 C 7005 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 703.4 milliseconds 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2522 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 72.8% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 625 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 826 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 618 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 789 through 791 No H-bonds generated for 'chain 'B' and resid 789 through 791' Processing helix chain 'B' and resid 792 through 826 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 549 No H-bonds generated for 'chain 'C' and resid 547 through 549' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 625 Processing helix chain 'C' and resid 788 through 824 removed outlier: 3.777A pdb=" N VAL C 792 " --> pdb=" O SER C 788 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLY C 794 " --> pdb=" O SER C 790 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 795 " --> pdb=" O ASN C 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 618 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 792 through 826 Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 127 Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.620A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 125 Processing helix chain 'G' and resid 126 through 128 No H-bonds generated for 'chain 'G' and resid 126 through 128' Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.560A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 105 through 129 Processing helix chain 'F' and resid 132 through 162 Processing helix chain 'F' and resid 177 through 216 Processing helix chain 'H' and resid 6 through 30 Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 105 through 129 Processing helix chain 'H' and resid 132 through 162 Processing helix chain 'H' and resid 177 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 551 through 552 Processing sheet with id=AA2, first strand: chain 'B' and resid 509 through 510 Processing sheet with id=AA3, first strand: chain 'C' and resid 551 through 552 Processing sheet with id=AA4, first strand: chain 'D' and resid 509 through 510 Processing sheet with id=AA5, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AA6, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AA7, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AA8, first strand: chain 'H' and resid 77 through 79 862 hydrogen bonds defined for protein. 2501 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: 1.74 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3235 1.35 - 1.46: 3076 1.46 - 1.58: 4503 1.58 - 1.70: 0 1.70 - 1.82: 117 Bond restraints: 10931 Sorted by residual: bond pdb=" CB GLU H 191 " pdb=" CG GLU H 191 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.32e-01 bond pdb=" CA ASP F 5 " pdb=" CB ASP F 5 " ideal model delta sigma weight residual 1.530 1.544 -0.014 2.00e-02 2.50e+03 4.79e-01 bond pdb=" CB ASP F 5 " pdb=" CG ASP F 5 " ideal model delta sigma weight residual 1.516 1.532 -0.016 2.50e-02 1.60e+03 4.22e-01 bond pdb=" CG MET B 825 " pdb=" SD MET B 825 " ideal model delta sigma weight residual 1.803 1.819 -0.016 2.50e-02 1.60e+03 4.05e-01 bond pdb=" CG GLU H 191 " pdb=" CD GLU H 191 " ideal model delta sigma weight residual 1.516 1.532 -0.016 2.50e-02 1.60e+03 4.01e-01 ... (remaining 10926 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 14670 1.64 - 3.28: 115 3.28 - 4.93: 19 4.93 - 6.57: 1 6.57 - 8.21: 4 Bond angle restraints: 14809 Sorted by residual: angle pdb=" CB MET B 825 " pdb=" CG MET B 825 " pdb=" SD MET B 825 " ideal model delta sigma weight residual 112.70 120.91 -8.21 3.00e+00 1.11e-01 7.49e+00 angle pdb=" N ASP F 5 " pdb=" CA ASP F 5 " pdb=" C ASP F 5 " ideal model delta sigma weight residual 111.00 104.14 6.86 2.80e+00 1.28e-01 6.01e+00 angle pdb=" C ASP F 86 " pdb=" N ALA F 87 " pdb=" CA ALA F 87 " ideal model delta sigma weight residual 121.54 125.59 -4.05 1.91e+00 2.74e-01 4.50e+00 angle pdb=" C ASP H 86 " pdb=" N ALA H 87 " pdb=" CA ALA H 87 " ideal model delta sigma weight residual 121.54 125.55 -4.01 1.91e+00 2.74e-01 4.40e+00 angle pdb=" CA LEU E 11 " pdb=" CB LEU E 11 " pdb=" CG LEU E 11 " ideal model delta sigma weight residual 116.30 122.98 -6.68 3.50e+00 8.16e-02 3.64e+00 ... (remaining 14804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 5423 17.73 - 35.46: 610 35.46 - 53.18: 164 53.18 - 70.91: 29 70.91 - 88.64: 11 Dihedral angle restraints: 6237 sinusoidal: 2299 harmonic: 3938 Sorted by residual: dihedral pdb=" CB CYS E 67 " pdb=" SG CYS E 67 " pdb=" SG CYS E 77 " pdb=" CB CYS E 77 " ideal model delta sinusoidal sigma weight residual -86.00 -126.95 40.95 1 1.00e+01 1.00e-02 2.35e+01 dihedral pdb=" SG CYS G 67 " pdb=" CB CYS G 77 " pdb=" SG CYS G 77 " pdb=" CA CYS G 77 " ideal model delta sinusoidal sigma weight residual -73.00 -9.75 -63.25 1 2.00e+01 2.50e-03 1.32e+01 dihedral pdb=" CA PHE A 571 " pdb=" C PHE A 571 " pdb=" N GLY A 572 " pdb=" CA GLY A 572 " ideal model delta harmonic sigma weight residual 180.00 163.00 17.00 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 6234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1080 0.028 - 0.055: 384 0.055 - 0.083: 156 0.083 - 0.111: 49 0.111 - 0.138: 6 Chirality restraints: 1675 Sorted by residual: chirality pdb=" CA ASP F 5 " pdb=" N ASP F 5 " pdb=" C ASP F 5 " pdb=" CB ASP F 5 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA PHE E 127 " pdb=" N PHE E 127 " pdb=" C PHE E 127 " pdb=" CB PHE E 127 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA VAL G 57 " pdb=" N VAL G 57 " pdb=" C VAL G 57 " pdb=" CB VAL G 57 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 1672 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 801 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.15e+00 pdb=" C GLY C 801 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY C 801 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY C 802 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 808 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C LEU D 808 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU D 808 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL D 809 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 808 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.01e+00 pdb=" C LEU B 808 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU B 808 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL B 809 " 0.010 2.00e-02 2.50e+03 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2097 2.76 - 3.30: 10797 3.30 - 3.83: 21152 3.83 - 4.37: 22364 4.37 - 4.90: 38366 Nonbonded interactions: 94776 Sorted by model distance: nonbonded pdb=" O HOH D 902 " pdb=" O HOH D 913 " model vdw 2.227 3.040 nonbonded pdb=" O HOH B 902 " pdb=" O HOH B 914 " model vdw 2.228 3.040 nonbonded pdb=" O ILE G 26 " pdb=" OG1 THR G 30 " model vdw 2.229 3.040 nonbonded pdb=" O ILE E 26 " pdb=" OG1 THR E 30 " model vdw 2.231 3.040 nonbonded pdb=" O HOH B 910 " pdb=" O HOH B 931 " model vdw 2.244 3.040 ... (remaining 94771 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 'A' and (resid 511 through 552 or resid 564 through 588 or resid 590 thro \ ugh 614 or resid 616 through 826)) selection = (chain 'B' and (resid 511 through 588 or resid 590 through 614 or resid 616 thro \ ugh 626 or resid 784 through 824 or (resid 825 and (name N or name CA or name C \ or name O or name CB )) or resid 826)) selection = (chain 'C' and (resid 511 through 552 or resid 564 through 588 or resid 590 thro \ ugh 614 or resid 616 through 826)) selection = (chain 'D' and (resid 511 through 588 or resid 590 through 614 or resid 616 thro \ ugh 626 or resid 784 through 824 or (resid 825 and (name N or name CA or name C \ or name O or name CB )) or resid 826)) } ncs_group { reference = (chain 'E' and (resid 5 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 214)) selection = (chain 'F' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 214)) selection = (chain 'G' and (resid 5 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 214)) selection = (chain 'H' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 214)) } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.070 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 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 : 0.002 0.023 10939 Z= 0.115 Angle : 0.428 8.210 14825 Z= 0.241 Chirality : 0.035 0.138 1675 Planarity : 0.004 0.028 1810 Dihedral : 16.293 88.638 3691 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.54 % Allowed : 19.39 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.17 (0.23), residues: 1339 helix: 3.07 (0.16), residues: 948 sheet: -2.38 (1.39), residues: 10 loop : -0.39 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 65 TYR 0.020 0.001 TYR C 549 PHE 0.020 0.001 PHE E 127 TRP 0.006 0.001 TRP F 178 HIS 0.004 0.001 HIS F 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.12 (10931) covalent geometry : angle 0.42814 / 0.24 (14809) SS BOND : bond 0.00120 / 0.06 ( 8) SS BOND : angle 0.62096 / 0.37 ( 16) hydrogen bonds : bond 0.11078 / 7.52 ( 862) hydrogen bonds : angle 4.73655 / 3.38 ( 2501) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.374 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 165 average time/residue: 0.5070 time to fit residues: 91.0485 Evaluate side-chains 164 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 158 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 11 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 586 GLN D 586 GLN F 205 HIS H 72 ASN H 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.194397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.144649 restraints weight = 30458.159| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 4.30 r_work: 0.3074 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.0658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10939 Z= 0.129 Angle : 0.446 5.942 14825 Z= 0.251 Chirality : 0.036 0.132 1675 Planarity : 0.003 0.030 1810 Dihedral : 4.772 55.931 1479 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.59 % Allowed : 16.98 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.85 (0.23), residues: 1339 helix: 3.64 (0.16), residues: 954 sheet: -1.98 (1.44), residues: 10 loop : -0.40 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 99 TYR 0.019 0.002 TYR C 549 PHE 0.019 0.002 PHE E 127 TRP 0.006 0.001 TRP D 578 HIS 0.004 0.001 HIS F 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (10931) covalent geometry : angle 0.44512 / 0.25 (14809) SS BOND : bond 0.00158 / 0.08 ( 8) SS BOND : angle 0.98575 / 0.55 ( 16) hydrogen bonds : bond 0.04950 / 3.23 ( 862) hydrogen bonds : angle 3.46068 / 2.46 ( 2501) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: D 825 MET cc_start: 0.4551 (tpp) cc_final: 0.4289 (ptm) REVERT: G 131 ARG cc_start: 0.5707 (OUTLIER) cc_final: 0.5203 (mtp-110) REVERT: H 65 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7176 (mtp-110) REVERT: H 130 THR cc_start: 0.7129 (t) cc_final: 0.6818 (m) outliers start: 29 outliers final: 14 residues processed: 180 average time/residue: 0.4618 time to fit residues: 90.7613 Evaluate side-chains 178 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 126 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 586 GLN D 586 GLN F 205 HIS H 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.194274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.143939 restraints weight = 33138.251| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 4.63 r_work: 0.3085 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10939 Z= 0.119 Angle : 0.428 5.991 14825 Z= 0.241 Chirality : 0.035 0.134 1675 Planarity : 0.003 0.030 1810 Dihedral : 4.349 56.453 1474 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.77 % Allowed : 16.98 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.94 (0.23), residues: 1339 helix: 3.70 (0.16), residues: 954 sheet: None (None), residues: 0 loop : -0.42 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 65 TYR 0.017 0.001 TYR C 549 PHE 0.020 0.001 PHE E 127 TRP 0.007 0.001 TRP H 178 HIS 0.004 0.001 HIS F 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (10931) covalent geometry : angle 0.42713 / 0.24 (14809) SS BOND : bond 0.00155 / 0.08 ( 8) SS BOND : angle 0.96400 / 0.54 ( 16) hydrogen bonds : bond 0.04674 / 3.05 ( 862) hydrogen bonds : angle 3.34253 / 2.37 ( 2501) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.264 Fit side-chains REVERT: B 813 GLU cc_start: 0.8310 (tt0) cc_final: 0.7854 (tt0) REVERT: D 813 GLU cc_start: 0.8348 (tt0) cc_final: 0.7900 (tt0) REVERT: D 825 MET cc_start: 0.4679 (tpp) cc_final: 0.4424 (ptm) REVERT: E 99 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6790 (mpp80) REVERT: E 131 ARG cc_start: 0.5970 (OUTLIER) cc_final: 0.5358 (mmp-170) REVERT: G 131 ARG cc_start: 0.5708 (OUTLIER) cc_final: 0.5171 (mtp-110) REVERT: F 78 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7303 (ttpt) REVERT: H 65 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7230 (mtp-110) REVERT: H 130 THR cc_start: 0.7207 (t) cc_final: 0.6809 (m) outliers start: 31 outliers final: 12 residues processed: 183 average time/residue: 0.4239 time to fit residues: 84.7927 Evaluate side-chains 179 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 78 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 123 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.191567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.140505 restraints weight = 33400.517| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 4.74 r_work: 0.3046 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10939 Z= 0.176 Angle : 0.504 6.322 14825 Z= 0.284 Chirality : 0.039 0.136 1675 Planarity : 0.004 0.044 1810 Dihedral : 4.659 57.287 1474 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.68 % Allowed : 16.62 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.61 (0.23), residues: 1339 helix: 3.41 (0.16), residues: 950 sheet: 0.34 (0.95), residues: 40 loop : -0.42 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 594 TYR 0.023 0.002 TYR F 181 PHE 0.019 0.002 PHE E 127 TRP 0.009 0.002 TRP C 606 HIS 0.006 0.001 HIS F 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (10931) covalent geometry : angle 0.50285 / 0.28 (14809) SS BOND : bond 0.00292 / 0.15 ( 8) SS BOND : angle 1.05058 / 0.60 ( 16) hydrogen bonds : bond 0.05518 / 3.60 ( 862) hydrogen bonds : angle 3.56113 / 2.53 ( 2501) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.421 Fit side-chains REVERT: B 813 GLU cc_start: 0.8336 (tt0) cc_final: 0.7915 (tt0) REVERT: D 813 GLU cc_start: 0.8362 (tt0) cc_final: 0.7883 (tt0) REVERT: D 825 MET cc_start: 0.4619 (tpp) cc_final: 0.4417 (ptm) REVERT: E 99 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6975 (mpp80) REVERT: E 131 ARG cc_start: 0.6086 (OUTLIER) cc_final: 0.5560 (mmp-170) REVERT: F 78 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7296 (ttpt) REVERT: H 65 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6985 (mtp-110) REVERT: H 130 THR cc_start: 0.7211 (t) cc_final: 0.6827 (m) outliers start: 30 outliers final: 13 residues processed: 170 average time/residue: 0.4783 time to fit residues: 88.6529 Evaluate side-chains 168 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 69 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 105 optimal weight: 0.0470 chunk 107 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 119 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 205 HIS G 205 HIS F 205 HIS H 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.194723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.144200 restraints weight = 33734.862| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 4.77 r_work: 0.3101 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10939 Z= 0.110 Angle : 0.415 6.336 14825 Z= 0.233 Chirality : 0.035 0.137 1675 Planarity : 0.003 0.029 1810 Dihedral : 4.288 56.953 1474 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.23 % Allowed : 17.34 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.97 (0.23), residues: 1339 helix: 3.74 (0.16), residues: 954 sheet: None (None), residues: 0 loop : -0.43 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 99 TYR 0.017 0.001 TYR C 549 PHE 0.019 0.001 PHE E 127 TRP 0.009 0.001 TRP H 178 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.11 (10931) covalent geometry : angle 0.41446 / 0.23 (14809) SS BOND : bond 0.00295 / 0.11 ( 8) SS BOND : angle 0.94574 / 0.54 ( 16) hydrogen bonds : bond 0.04423 / 2.88 ( 862) hydrogen bonds : angle 3.28199 / 2.33 ( 2501) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.318 Fit side-chains REVERT: B 570 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7386 (mm-30) REVERT: B 813 GLU cc_start: 0.8350 (tt0) cc_final: 0.7845 (tt0) REVERT: D 570 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7388 (mm-30) REVERT: D 813 GLU cc_start: 0.8363 (tt0) cc_final: 0.7887 (tt0) REVERT: E 31 ASP cc_start: 0.7177 (m-30) cc_final: 0.6958 (m-30) REVERT: E 99 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6815 (mpp80) REVERT: E 131 ARG cc_start: 0.5932 (OUTLIER) cc_final: 0.5385 (mmp-170) REVERT: G 131 ARG cc_start: 0.5762 (OUTLIER) cc_final: 0.5342 (mmm160) REVERT: F 78 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7301 (ttpt) REVERT: H 65 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7211 (mtp-110) outliers start: 25 outliers final: 9 residues processed: 179 average time/residue: 0.4320 time to fit residues: 84.4921 Evaluate side-chains 179 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 112 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 205 HIS G 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.193845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.144975 restraints weight = 29518.194| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 4.23 r_work: 0.3068 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10939 Z= 0.121 Angle : 0.431 6.379 14825 Z= 0.243 Chirality : 0.036 0.140 1675 Planarity : 0.003 0.030 1810 Dihedral : 4.305 57.557 1474 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.14 % Allowed : 17.43 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.93 (0.23), residues: 1339 helix: 3.67 (0.16), residues: 954 sheet: -0.07 (1.26), residues: 20 loop : -0.36 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 65 TYR 0.018 0.001 TYR C 549 PHE 0.019 0.001 PHE E 127 TRP 0.008 0.001 TRP H 178 HIS 0.005 0.001 HIS E 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (10931) covalent geometry : angle 0.43036 / 0.24 (14809) SS BOND : bond 0.00164 / 0.08 ( 8) SS BOND : angle 0.93770 / 0.54 ( 16) hydrogen bonds : bond 0.04665 / 3.04 ( 862) hydrogen bonds : angle 3.32602 / 2.36 ( 2501) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.260 Fit side-chains REVERT: B 570 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7437 (mm-30) REVERT: B 813 GLU cc_start: 0.8383 (tt0) cc_final: 0.7924 (tt0) REVERT: D 570 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7415 (mm-30) REVERT: D 813 GLU cc_start: 0.8415 (tt0) cc_final: 0.7952 (tt0) REVERT: E 99 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.7031 (mpp80) REVERT: E 131 ARG cc_start: 0.5990 (OUTLIER) cc_final: 0.5464 (mmp-170) REVERT: G 131 ARG cc_start: 0.5767 (OUTLIER) cc_final: 0.5031 (mtp180) REVERT: F 78 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7258 (ttpt) REVERT: H 65 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7206 (mtp-110) outliers start: 24 outliers final: 11 residues processed: 175 average time/residue: 0.4319 time to fit residues: 82.4950 Evaluate side-chains 173 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.193197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.145102 restraints weight = 27730.882| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 4.02 r_work: 0.3054 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10939 Z= 0.132 Angle : 0.448 6.543 14825 Z= 0.253 Chirality : 0.036 0.138 1675 Planarity : 0.003 0.030 1810 Dihedral : 4.373 57.966 1474 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.59 % Allowed : 16.89 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.85 (0.23), residues: 1339 helix: 3.59 (0.16), residues: 954 sheet: -0.03 (1.26), residues: 20 loop : -0.35 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 65 TYR 0.018 0.002 TYR H 181 PHE 0.019 0.002 PHE E 127 TRP 0.008 0.001 TRP H 178 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (10931) covalent geometry : angle 0.44748 / 0.25 (14809) SS BOND : bond 0.00178 / 0.09 ( 8) SS BOND : angle 0.94818 / 0.54 ( 16) hydrogen bonds : bond 0.04867 / 3.17 ( 862) hydrogen bonds : angle 3.37866 / 2.40 ( 2501) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: B 570 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7477 (mm-30) REVERT: B 813 GLU cc_start: 0.8376 (tt0) cc_final: 0.7913 (tt0) REVERT: D 570 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7467 (mm-30) REVERT: D 813 GLU cc_start: 0.8424 (tt0) cc_final: 0.7962 (tt0) REVERT: E 95 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6088 (tm-30) REVERT: E 99 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6871 (mpp80) REVERT: E 131 ARG cc_start: 0.5989 (OUTLIER) cc_final: 0.5444 (mmp-170) REVERT: G 131 ARG cc_start: 0.5826 (OUTLIER) cc_final: 0.5136 (mtp180) REVERT: F 78 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7240 (ttpt) REVERT: H 65 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7069 (mtp-110) outliers start: 29 outliers final: 16 residues processed: 171 average time/residue: 0.5378 time to fit residues: 100.1205 Evaluate side-chains 178 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 123 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.193190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.143590 restraints weight = 29184.893| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 4.28 r_work: 0.3067 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10939 Z= 0.133 Angle : 0.451 6.671 14825 Z= 0.254 Chirality : 0.037 0.140 1675 Planarity : 0.003 0.031 1810 Dihedral : 4.383 57.884 1474 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.59 % Allowed : 17.07 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.83 (0.23), residues: 1339 helix: 3.58 (0.16), residues: 954 sheet: 0.01 (1.26), residues: 20 loop : -0.34 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 65 TYR 0.019 0.002 TYR H 181 PHE 0.019 0.002 PHE E 127 TRP 0.008 0.001 TRP F 178 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (10931) covalent geometry : angle 0.44997 / 0.25 (14809) SS BOND : bond 0.00185 / 0.09 ( 8) SS BOND : angle 0.95404 / 0.55 ( 16) hydrogen bonds : bond 0.04867 / 3.17 ( 862) hydrogen bonds : angle 3.38147 / 2.40 ( 2501) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: B 570 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7468 (mm-30) REVERT: B 813 GLU cc_start: 0.8384 (tt0) cc_final: 0.7931 (tt0) REVERT: D 570 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7456 (mm-30) REVERT: D 813 GLU cc_start: 0.8436 (tt0) cc_final: 0.7970 (tt0) REVERT: E 95 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6149 (tm-30) REVERT: E 99 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6885 (mpp80) REVERT: E 131 ARG cc_start: 0.6005 (OUTLIER) cc_final: 0.5474 (mmp-170) REVERT: G 131 ARG cc_start: 0.5883 (OUTLIER) cc_final: 0.5187 (mtp180) REVERT: F 65 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7135 (mtp-110) REVERT: F 78 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7290 (ttpt) REVERT: H 65 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7076 (mtp-110) outliers start: 29 outliers final: 15 residues processed: 170 average time/residue: 0.5421 time to fit residues: 100.2288 Evaluate side-chains 177 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 127 optimal weight: 0.0570 chunk 128 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 205 HIS G 205 HIS F 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.194900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.146379 restraints weight = 28972.780| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 4.18 r_work: 0.3091 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10939 Z= 0.110 Angle : 0.419 6.611 14825 Z= 0.235 Chirality : 0.035 0.140 1675 Planarity : 0.003 0.030 1810 Dihedral : 4.239 57.640 1474 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.97 % Allowed : 17.87 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.03 (0.23), residues: 1339 helix: 3.74 (0.16), residues: 956 sheet: 0.02 (1.28), residues: 20 loop : -0.34 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 65 TYR 0.016 0.001 TYR C 549 PHE 0.019 0.001 PHE E 127 TRP 0.009 0.001 TRP F 178 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.11 (10931) covalent geometry : angle 0.41806 / 0.23 (14809) SS BOND : bond 0.00105 / 0.05 ( 8) SS BOND : angle 0.90859 / 0.52 ( 16) hydrogen bonds : bond 0.04412 / 2.87 ( 862) hydrogen bonds : angle 3.26314 / 2.32 ( 2501) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: B 570 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: B 813 GLU cc_start: 0.8398 (tt0) cc_final: 0.7934 (tt0) REVERT: D 570 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7409 (mm-30) REVERT: D 813 GLU cc_start: 0.8395 (tt0) cc_final: 0.7927 (tt0) REVERT: E 95 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6192 (tm-30) REVERT: E 99 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6882 (mpp80) REVERT: E 131 ARG cc_start: 0.5923 (OUTLIER) cc_final: 0.5406 (mmp-170) REVERT: G 131 ARG cc_start: 0.5737 (OUTLIER) cc_final: 0.5070 (mmp-170) REVERT: F 65 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7217 (mtp-110) REVERT: F 78 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7258 (ttpt) REVERT: H 65 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7203 (mtp-110) outliers start: 22 outliers final: 13 residues processed: 168 average time/residue: 0.5333 time to fit residues: 97.3952 Evaluate side-chains 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.193022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.142584 restraints weight = 28851.363| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 4.20 r_work: 0.3055 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10939 Z= 0.152 Angle : 0.481 6.734 14825 Z= 0.271 Chirality : 0.038 0.139 1675 Planarity : 0.003 0.039 1810 Dihedral : 4.475 58.320 1474 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.06 % Allowed : 17.43 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.79 (0.23), residues: 1339 helix: 3.53 (0.16), residues: 954 sheet: 0.23 (0.94), residues: 40 loop : -0.35 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 594 TYR 0.024 0.002 TYR G 32 PHE 0.020 0.002 PHE E 127 TRP 0.007 0.002 TRP A 606 HIS 0.005 0.001 HIS E 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (10931) covalent geometry : angle 0.48070 / 0.27 (14809) SS BOND : bond 0.00214 / 0.10 ( 8) SS BOND : angle 0.96862 / 0.57 ( 16) hydrogen bonds : bond 0.05078 / 3.31 ( 862) hydrogen bonds : angle 3.42796 / 2.44 ( 2501) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: B 570 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7480 (mm-30) REVERT: B 813 GLU cc_start: 0.8373 (tt0) cc_final: 0.7918 (tt0) REVERT: D 570 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7456 (mm-30) REVERT: D 813 GLU cc_start: 0.8411 (tt0) cc_final: 0.7906 (tt0) REVERT: E 95 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6153 (tm-30) REVERT: E 99 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6914 (mpp80) REVERT: E 131 ARG cc_start: 0.6064 (OUTLIER) cc_final: 0.5561 (mmp-170) REVERT: G 131 ARG cc_start: 0.5868 (OUTLIER) cc_final: 0.5205 (mmp-170) REVERT: F 65 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7147 (mtp-110) REVERT: F 78 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7268 (ttpt) REVERT: H 65 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7154 (mtp-110) outliers start: 23 outliers final: 13 residues processed: 156 average time/residue: 0.5893 time to fit residues: 99.5617 Evaluate side-chains 168 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 0.0060 chunk 131 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 82 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 205 HIS G 205 HIS H 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.194461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.142641 restraints weight = 37363.933| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 5.08 r_work: 0.3101 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10939 Z= 0.115 Angle : 0.433 6.755 14825 Z= 0.242 Chirality : 0.036 0.141 1675 Planarity : 0.003 0.029 1810 Dihedral : 4.341 57.933 1474 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.97 % Allowed : 17.96 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.95 (0.23), residues: 1339 helix: 3.70 (0.16), residues: 954 sheet: None (None), residues: 0 loop : -0.39 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 99 TYR 0.019 0.001 TYR C 549 PHE 0.019 0.001 PHE E 127 TRP 0.009 0.001 TRP F 178 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (10931) covalent geometry : angle 0.43228 / 0.24 (14809) SS BOND : bond 0.00133 / 0.06 ( 8) SS BOND : angle 0.91201 / 0.53 ( 16) hydrogen bonds : bond 0.04531 / 2.95 ( 862) hydrogen bonds : angle 3.29901 / 2.35 ( 2501) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4272.54 seconds wall clock time: 73 minutes 35.82 seconds (4415.82 seconds total)