Starting phenix.real_space_refine on Tue May 13 17:19:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fqf_29386/05_2025/8fqf_29386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fqf_29386/05_2025/8fqf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fqf_29386/05_2025/8fqf_29386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fqf_29386/05_2025/8fqf_29386.map" model { file = "/net/cci-nas-00/data/ceres_data/8fqf_29386/05_2025/8fqf_29386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fqf_29386/05_2025/8fqf_29386.cif" } resolution = 2.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 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: 9.78, per 1000 atoms: 0.90 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: 2.83 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 0.97 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: 3.44 Time building geometry restraints manager: 3.30 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: 2.230 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.780 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.006 0.001 TRP F 178 HIS 0.004 0.001 HIS F 205 PHE 0.020 0.001 PHE E 127 TYR 0.020 0.001 TYR C 549 ARG 0.002 0.000 ARG H 65 Details of bonding type rmsd hydrogen bonds : bond 0.11078 ( 862) hydrogen bonds : angle 4.73655 ( 2501) SS BOND : bond 0.00120 ( 8) SS BOND : angle 0.62096 ( 16) covalent geometry : bond 0.00213 (10931) covalent geometry : angle 0.42814 (14809) *********************** 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 : 1.133 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 165 average time/residue: 1.1091 time to fit residues: 199.3429 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 : 1.160 ------------------------------------------------------------------------------- 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 111 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4117 r_free = 0.4117 target = 0.194003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.147736 restraints weight = 25360.339| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.72 r_work: 0.3046 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.0677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10939 Z= 0.136 Angle : 0.455 5.966 14825 Z= 0.257 Chirality : 0.036 0.132 1675 Planarity : 0.003 0.032 1810 Dihedral : 4.818 55.958 1479 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.59 % Allowed : 17.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.23), residues: 1339 helix: 3.60 (0.16), residues: 954 sheet: -1.93 (1.46), residues: 10 loop : -0.40 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 606 HIS 0.004 0.001 HIS F 205 PHE 0.019 0.002 PHE E 127 TYR 0.020 0.002 TYR C 549 ARG 0.002 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.05050 ( 862) hydrogen bonds : angle 3.48802 ( 2501) SS BOND : bond 0.00165 ( 8) SS BOND : angle 0.99632 ( 16) covalent geometry : bond 0.00271 (10931) covalent geometry : angle 0.45442 (14809) *********************** 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 194 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: G 131 ARG cc_start: 0.5675 (OUTLIER) cc_final: 0.5216 (mtp-110) REVERT: H 65 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7170 (mtp-110) REVERT: H 130 THR cc_start: 0.7126 (t) cc_final: 0.6810 (m) outliers start: 29 outliers final: 15 residues processed: 178 average time/residue: 1.0565 time to fit residues: 205.2912 Evaluate side-chains 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 11 LEU 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 122 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN D 586 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.192458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.143990 restraints weight = 27127.839| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 4.02 r_work: 0.3046 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0856 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= 0.149 Angle : 0.472 6.081 14825 Z= 0.266 Chirality : 0.037 0.133 1675 Planarity : 0.003 0.036 1810 Dihedral : 4.665 56.467 1476 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.95 % Allowed : 16.44 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.23), residues: 1339 helix: 3.52 (0.16), residues: 952 sheet: -1.82 (1.45), residues: 10 loop : -0.36 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 178 HIS 0.004 0.001 HIS H 205 PHE 0.019 0.002 PHE E 127 TYR 0.019 0.002 TYR C 549 ARG 0.002 0.000 ARG B 594 Details of bonding type rmsd hydrogen bonds : bond 0.05199 ( 862) hydrogen bonds : angle 3.49280 ( 2501) SS BOND : bond 0.00209 ( 8) SS BOND : angle 1.03157 ( 16) covalent geometry : bond 0.00306 (10931) covalent geometry : angle 0.47098 (14809) *********************** 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 192 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 1.084 Fit side-chains REVERT: B 813 GLU cc_start: 0.8375 (tt0) cc_final: 0.7949 (tt0) REVERT: D 813 GLU cc_start: 0.8403 (tt0) cc_final: 0.7911 (tt0) REVERT: E 99 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6991 (mpp80) REVERT: E 131 ARG cc_start: 0.6087 (OUTLIER) cc_final: 0.5498 (mmp-170) REVERT: G 131 ARG cc_start: 0.5726 (OUTLIER) cc_final: 0.5270 (mtp-110) REVERT: F 78 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7268 (ttpt) REVERT: H 65 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7118 (mtp-110) REVERT: H 130 THR cc_start: 0.7206 (t) cc_final: 0.6834 (m) outliers start: 33 outliers final: 16 residues processed: 173 average time/residue: 1.0852 time to fit residues: 204.8171 Evaluate side-chains 174 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 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 14 THR 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 11 LEU Chi-restraints excluded: chain F residue 15 VAL 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 65 ARG Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 205 HIS H 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.193828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.145005 restraints weight = 30814.953| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 4.34 r_work: 0.3066 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.0846 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 : 0.430 6.199 14825 Z= 0.242 Chirality : 0.036 0.134 1675 Planarity : 0.003 0.030 1810 Dihedral : 4.470 56.774 1476 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.32 % Allowed : 17.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (0.23), residues: 1339 helix: 3.68 (0.16), residues: 952 sheet: -1.79 (1.42), residues: 10 loop : -0.35 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 178 HIS 0.004 0.001 HIS F 205 PHE 0.020 0.001 PHE E 127 TYR 0.016 0.002 TYR C 549 ARG 0.001 0.000 ARG E 99 Details of bonding type rmsd hydrogen bonds : bond 0.04681 ( 862) hydrogen bonds : angle 3.34424 ( 2501) SS BOND : bond 0.00197 ( 8) SS BOND : angle 0.95394 ( 16) covalent geometry : bond 0.00236 (10931) covalent geometry : angle 0.42945 (14809) *********************** 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 192 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 1.105 Fit side-chains REVERT: B 570 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7628 (mm-30) REVERT: B 813 GLU cc_start: 0.8395 (tt0) cc_final: 0.7913 (tt0) REVERT: D 570 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7615 (mm-30) REVERT: D 813 GLU cc_start: 0.8410 (tt0) cc_final: 0.7938 (tt0) REVERT: E 99 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.7028 (mpp80) REVERT: E 131 ARG cc_start: 0.5921 (OUTLIER) cc_final: 0.5377 (mmp-170) REVERT: G 131 ARG cc_start: 0.5698 (OUTLIER) cc_final: 0.5171 (mtp-110) REVERT: F 78 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7263 (ttpt) REVERT: H 65 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7139 (mtp-110) REVERT: H 130 THR cc_start: 0.7129 (t) cc_final: 0.6755 (m) outliers start: 26 outliers final: 9 residues processed: 180 average time/residue: 1.0530 time to fit residues: 206.6945 Evaluate side-chains 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 128 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.191555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.145388 restraints weight = 23884.106| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.67 r_work: 0.3013 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1024 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= 0.175 Angle : 0.503 6.433 14825 Z= 0.284 Chirality : 0.039 0.137 1675 Planarity : 0.004 0.043 1810 Dihedral : 4.685 57.840 1474 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.86 % Allowed : 16.35 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.23), residues: 1339 helix: 3.36 (0.16), residues: 950 sheet: 0.38 (0.95), residues: 40 loop : -0.40 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 606 HIS 0.005 0.001 HIS F 205 PHE 0.019 0.002 PHE E 127 TYR 0.022 0.002 TYR H 181 ARG 0.003 0.000 ARG B 594 Details of bonding type rmsd hydrogen bonds : bond 0.05482 ( 862) hydrogen bonds : angle 3.55630 ( 2501) SS BOND : bond 0.00257 ( 8) SS BOND : angle 1.04133 ( 16) covalent geometry : bond 0.00370 (10931) covalent geometry : angle 0.50215 (14809) *********************** 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 193 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 1.173 Fit side-chains REVERT: A 813 GLU cc_start: 0.8056 (tt0) cc_final: 0.7773 (tt0) REVERT: B 813 GLU cc_start: 0.8482 (tt0) cc_final: 0.8016 (tt0) REVERT: B 825 MET cc_start: 0.4793 (tpp) cc_final: 0.4256 (tpp) REVERT: D 813 GLU cc_start: 0.8488 (tt0) cc_final: 0.8047 (tt0) REVERT: E 99 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.7053 (mpp80) REVERT: E 131 ARG cc_start: 0.6031 (OUTLIER) cc_final: 0.5568 (mmp-170) REVERT: G 56 GLU cc_start: 0.5609 (OUTLIER) cc_final: 0.4345 (tp30) REVERT: F 78 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7254 (ttpt) REVERT: H 65 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7015 (mtp-110) REVERT: H 130 THR cc_start: 0.7130 (t) cc_final: 0.6753 (m) outliers start: 32 outliers final: 14 residues processed: 176 average time/residue: 1.0459 time to fit residues: 200.6961 Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 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 56 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.193854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.144394 restraints weight = 29480.774| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 4.32 r_work: 0.3081 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- 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 = 0.22 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 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10939 Z= 0.119 Angle : 0.430 6.417 14825 Z= 0.242 Chirality : 0.036 0.135 1675 Planarity : 0.003 0.029 1810 Dihedral : 4.387 57.399 1474 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.97 % Allowed : 17.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.23), residues: 1339 helix: 3.64 (0.16), residues: 954 sheet: 0.02 (1.29), residues: 20 loop : -0.38 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 178 HIS 0.004 0.001 HIS F 205 PHE 0.020 0.001 PHE E 127 TYR 0.016 0.001 TYR C 549 ARG 0.002 0.000 ARG G 65 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 862) hydrogen bonds : angle 3.33385 ( 2501) SS BOND : bond 0.00179 ( 8) SS BOND : angle 0.96917 ( 16) covalent geometry : bond 0.00230 (10931) covalent geometry : angle 0.42922 (14809) *********************** 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 183 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 813 GLU cc_start: 0.7884 (tt0) cc_final: 0.7640 (tt0) REVERT: B 813 GLU cc_start: 0.8395 (tt0) cc_final: 0.7936 (tt0) REVERT: D 813 GLU cc_start: 0.8408 (tt0) cc_final: 0.7938 (tt0) REVERT: E 99 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.7016 (mpp80) REVERT: E 131 ARG cc_start: 0.6005 (OUTLIER) cc_final: 0.5465 (mmp-170) REVERT: G 131 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.5036 (mtp180) REVERT: F 65 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7227 (mtp-110) REVERT: F 78 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7265 (ttpt) REVERT: H 65 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7135 (mtp-110) outliers start: 22 outliers final: 14 residues processed: 173 average time/residue: 1.1565 time to fit residues: 218.1667 Evaluate side-chains 177 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain E residue 14 THR 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.192979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.143407 restraints weight = 30044.811| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 4.38 r_work: 0.3065 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 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 = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0991 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= 0.135 Angle : 0.454 6.549 14825 Z= 0.256 Chirality : 0.037 0.138 1675 Planarity : 0.003 0.031 1810 Dihedral : 4.445 58.109 1474 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.86 % Allowed : 16.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.23), residues: 1339 helix: 3.52 (0.16), residues: 956 sheet: 0.35 (0.96), residues: 40 loop : -0.34 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 178 HIS 0.004 0.001 HIS F 205 PHE 0.019 0.002 PHE E 127 TYR 0.018 0.002 TYR F 181 ARG 0.002 0.000 ARG D 594 Details of bonding type rmsd hydrogen bonds : bond 0.04934 ( 862) hydrogen bonds : angle 3.40547 ( 2501) SS BOND : bond 0.00169 ( 8) SS BOND : angle 0.97056 ( 16) covalent geometry : bond 0.00273 (10931) covalent geometry : angle 0.45338 (14809) *********************** 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 187 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 813 GLU cc_start: 0.7969 (tt0) cc_final: 0.7673 (tt0) REVERT: B 570 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7719 (mm-30) REVERT: B 813 GLU cc_start: 0.8398 (tt0) cc_final: 0.7943 (tt0) REVERT: D 570 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7701 (mm-30) REVERT: D 813 GLU cc_start: 0.8415 (tt0) cc_final: 0.7961 (tt0) REVERT: E 99 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6903 (mpp80) REVERT: E 131 ARG cc_start: 0.6058 (OUTLIER) cc_final: 0.5545 (mmp-170) REVERT: G 131 ARG cc_start: 0.5757 (OUTLIER) cc_final: 0.5022 (mtp180) REVERT: F 65 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7134 (mtp-110) REVERT: F 78 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7262 (ttpt) REVERT: H 65 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7075 (mtp-110) outliers start: 32 outliers final: 18 residues processed: 171 average time/residue: 1.0873 time to fit residues: 202.1201 Evaluate side-chains 174 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain E residue 14 THR 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 E residue 175 SER 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 86 ASP Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 81 optimal weight: 0.2980 chunk 130 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.192976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.144574 restraints weight = 27580.678| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 4.12 r_work: 0.3051 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10939 Z= 0.138 Angle : 0.462 6.688 14825 Z= 0.260 Chirality : 0.037 0.140 1675 Planarity : 0.003 0.032 1810 Dihedral : 4.457 58.120 1474 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.32 % Allowed : 16.89 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.23), residues: 1339 helix: 3.51 (0.16), residues: 954 sheet: 0.34 (0.96), residues: 40 loop : -0.34 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 178 HIS 0.004 0.001 HIS F 205 PHE 0.019 0.002 PHE E 127 TYR 0.018 0.002 TYR C 549 ARG 0.002 0.000 ARG D 594 Details of bonding type rmsd hydrogen bonds : bond 0.04964 ( 862) hydrogen bonds : angle 3.41546 ( 2501) SS BOND : bond 0.00187 ( 8) SS BOND : angle 0.96451 ( 16) covalent geometry : bond 0.00281 (10931) covalent geometry : angle 0.46071 (14809) *********************** 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 180 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: A 813 GLU cc_start: 0.7989 (tt0) cc_final: 0.7693 (tt0) REVERT: B 570 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7740 (mm-30) REVERT: B 813 GLU cc_start: 0.8437 (tt0) cc_final: 0.7989 (tt0) REVERT: D 570 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7718 (mm-30) REVERT: D 813 GLU cc_start: 0.8446 (tt0) cc_final: 0.7998 (tt0) REVERT: E 99 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6852 (mpp80) REVERT: E 131 ARG cc_start: 0.6060 (OUTLIER) cc_final: 0.5559 (mmp-170) REVERT: G 131 ARG cc_start: 0.5749 (OUTLIER) cc_final: 0.5073 (mtp180) REVERT: F 65 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7104 (mtp-110) REVERT: F 78 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7237 (ttpt) REVERT: H 65 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7050 (mtp-110) outliers start: 26 outliers final: 19 residues processed: 165 average time/residue: 1.1572 time to fit residues: 207.2038 Evaluate side-chains 177 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 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 E residue 175 SER 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 86 ASP Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG 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 40 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.192663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.144051 restraints weight = 28168.156| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 4.13 r_work: 0.3045 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 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 = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10939 Z= 0.145 Angle : 0.470 6.762 14825 Z= 0.265 Chirality : 0.037 0.138 1675 Planarity : 0.003 0.035 1810 Dihedral : 4.499 58.234 1474 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.23 % Allowed : 16.89 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.23), residues: 1339 helix: 3.48 (0.16), residues: 954 sheet: 0.32 (0.95), residues: 40 loop : -0.34 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 178 HIS 0.005 0.001 HIS F 205 PHE 0.019 0.002 PHE E 127 TYR 0.019 0.002 TYR F 181 ARG 0.002 0.000 ARG G 65 Details of bonding type rmsd hydrogen bonds : bond 0.05073 ( 862) hydrogen bonds : angle 3.44535 ( 2501) SS BOND : bond 0.00202 ( 8) SS BOND : angle 0.96056 ( 16) covalent geometry : bond 0.00298 (10931) covalent geometry : angle 0.46969 (14809) *********************** 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 177 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.403 Fit side-chains revert: symmetry clash REVERT: A 813 GLU cc_start: 0.7926 (tt0) cc_final: 0.7666 (tt0) REVERT: B 570 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7734 (mm-30) REVERT: B 813 GLU cc_start: 0.8441 (tt0) cc_final: 0.7991 (tt0) REVERT: D 570 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7718 (mm-30) REVERT: D 813 GLU cc_start: 0.8440 (tt0) cc_final: 0.7992 (tt0) REVERT: E 99 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6843 (mpp80) REVERT: E 131 ARG cc_start: 0.6082 (OUTLIER) cc_final: 0.5582 (mmp-170) REVERT: G 131 ARG cc_start: 0.5859 (OUTLIER) cc_final: 0.5217 (mmp-170) REVERT: F 65 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7085 (mtp-110) REVERT: F 78 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7230 (ttpt) REVERT: H 65 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7083 (mtp-110) outliers start: 25 outliers final: 20 residues processed: 162 average time/residue: 1.1175 time to fit residues: 196.3718 Evaluate side-chains 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 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 E residue 175 SER 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 86 ASP Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG 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 F residue 173 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 9 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.193861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.142602 restraints weight = 29956.613| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 4.57 r_work: 0.3082 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 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 = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10939 Z= 0.127 Angle : 0.448 6.779 14825 Z= 0.252 Chirality : 0.036 0.138 1675 Planarity : 0.003 0.030 1810 Dihedral : 4.428 58.211 1474 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.06 % Allowed : 17.07 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.84 (0.23), residues: 1339 helix: 3.56 (0.16), residues: 956 sheet: 0.35 (0.97), residues: 40 loop : -0.35 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 178 HIS 0.004 0.001 HIS F 205 PHE 0.019 0.001 PHE E 127 TYR 0.018 0.002 TYR C 549 ARG 0.002 0.000 ARG G 65 Details of bonding type rmsd hydrogen bonds : bond 0.04779 ( 862) hydrogen bonds : angle 3.37062 ( 2501) SS BOND : bond 0.00166 ( 8) SS BOND : angle 0.93836 ( 16) covalent geometry : bond 0.00251 (10931) covalent geometry : angle 0.44746 (14809) ********************** 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 179 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: A 813 GLU cc_start: 0.7860 (tt0) cc_final: 0.7599 (tt0) REVERT: B 570 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7690 (mm-30) REVERT: B 585 MET cc_start: 0.9116 (mmt) cc_final: 0.8837 (mmt) REVERT: B 813 GLU cc_start: 0.8373 (tt0) cc_final: 0.7911 (tt0) REVERT: D 570 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7684 (mm-30) REVERT: D 813 GLU cc_start: 0.8390 (tt0) cc_final: 0.7919 (tt0) REVERT: E 99 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6787 (mpp80) REVERT: E 131 ARG cc_start: 0.6097 (OUTLIER) cc_final: 0.5574 (mmp-170) REVERT: G 131 ARG cc_start: 0.5861 (OUTLIER) cc_final: 0.5202 (mmp-170) REVERT: F 65 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7122 (mtp-110) REVERT: F 78 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7255 (ttpt) REVERT: H 65 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7080 (mtp-110) outliers start: 23 outliers final: 17 residues processed: 166 average time/residue: 1.1163 time to fit residues: 201.4640 Evaluate side-chains 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 E residue 175 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG 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 F residue 173 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 0.0050 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.193844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.141448 restraints weight = 34352.666| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 4.93 r_work: 0.3081 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 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 = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10939 Z= 0.128 Angle : 0.452 6.743 14825 Z= 0.253 Chirality : 0.036 0.140 1675 Planarity : 0.003 0.030 1810 Dihedral : 4.419 58.187 1474 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.14 % Allowed : 17.07 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.23), residues: 1339 helix: 3.54 (0.16), residues: 956 sheet: 0.27 (0.96), residues: 40 loop : -0.36 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 178 HIS 0.004 0.001 HIS H 205 PHE 0.019 0.002 PHE E 127 TYR 0.017 0.002 TYR F 181 ARG 0.002 0.000 ARG E 99 Details of bonding type rmsd hydrogen bonds : bond 0.04792 ( 862) hydrogen bonds : angle 3.37501 ( 2501) SS BOND : bond 0.00159 ( 8) SS BOND : angle 0.97551 ( 16) covalent geometry : bond 0.00254 (10931) covalent geometry : angle 0.45158 (14809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8970.24 seconds wall clock time: 155 minutes 0.54 seconds (9300.54 seconds total)