Starting phenix.real_space_refine on Wed Mar 4 04:16:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fqf_29386/03_2026/8fqf_29386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fqf_29386/03_2026/8fqf_29386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fqf_29386/03_2026/8fqf_29386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fqf_29386/03_2026/8fqf_29386.map" model { file = "/net/cci-nas-00/data/ceres_data/8fqf_29386/03_2026/8fqf_29386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fqf_29386/03_2026/8fqf_29386.cif" } resolution = 2.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 77 5.16 5 Cl 2 4.86 5 C 7005 2.51 5 N 1709 2.21 5 O 2102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10895 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1177 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Chain: "B" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 bond proxies already assigned to first conformer: 1253 Chain: "C" Number of atoms: 1183 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Conformer: "C" Number of residues, atoms: 148, 1159 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Chain: "D" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 bond proxies already assigned to first conformer: 1253 Chain: "E" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1451 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1451 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1467 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1467 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 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: 3.65, per 1000 atoms: 0.34 Number of scatterers: 10895 At special positions: 0 Unit cell: (113.98, 113.16, 91.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 77 16.00 O 2102 8.00 N 1709 7.00 C 7005 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 675.0 milliseconds 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2522 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 72.8% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 625 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 826 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 618 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 789 through 791 No H-bonds generated for 'chain 'B' and resid 789 through 791' Processing helix chain 'B' and resid 792 through 826 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 549 No H-bonds generated for 'chain 'C' and resid 547 through 549' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 625 Processing helix chain 'C' and resid 788 through 824 removed outlier: 3.777A pdb=" N VAL C 792 " --> pdb=" O SER C 788 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLY C 794 " --> pdb=" O SER C 790 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 795 " --> pdb=" O ASN C 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 618 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 792 through 826 Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 127 Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.620A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 125 Processing helix chain 'G' and resid 126 through 128 No H-bonds generated for 'chain 'G' and resid 126 through 128' Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.560A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 105 through 129 Processing helix chain 'F' and resid 132 through 162 Processing helix chain 'F' and resid 177 through 216 Processing helix chain 'H' and resid 6 through 30 Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 105 through 129 Processing helix chain 'H' and resid 132 through 162 Processing helix chain 'H' and resid 177 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 551 through 552 Processing sheet with id=AA2, first strand: chain 'B' and resid 509 through 510 Processing sheet with id=AA3, first strand: chain 'C' and resid 551 through 552 Processing sheet with id=AA4, first strand: chain 'D' and resid 509 through 510 Processing sheet with id=AA5, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AA6, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AA7, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AA8, first strand: chain 'H' and resid 77 through 79 862 hydrogen bonds defined for protein. 2501 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.02 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: 4.230 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.130 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.960 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.17 (0.23), residues: 1339 helix: 3.07 (0.16), residues: 948 sheet: -2.38 (1.39), residues: 10 loop : -0.39 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 65 TYR 0.020 0.001 TYR C 549 PHE 0.020 0.001 PHE E 127 TRP 0.006 0.001 TRP F 178 HIS 0.004 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00213 (10931) covalent geometry : angle 0.42814 (14809) SS BOND : bond 0.00120 ( 8) SS BOND : angle 0.62096 ( 16) hydrogen bonds : bond 0.11078 ( 862) hydrogen bonds : angle 4.73655 ( 2501) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.391 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 165 average time/residue: 0.5405 time to fit residues: 96.8019 Evaluate side-chains 164 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 158 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 11 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4121 r_free = 0.4121 target = 0.194419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.145074 restraints weight = 30409.283| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 4.24 r_work: 0.3063 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.0680 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= 0.129 Angle : 0.447 5.942 14825 Z= 0.252 Chirality : 0.036 0.133 1675 Planarity : 0.003 0.029 1810 Dihedral : 4.774 55.891 1479 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.59 % Allowed : 16.89 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.85 (0.23), residues: 1339 helix: 3.64 (0.16), residues: 954 sheet: -1.96 (1.45), residues: 10 loop : -0.41 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 99 TYR 0.019 0.002 TYR C 549 PHE 0.019 0.002 PHE E 127 TRP 0.006 0.001 TRP H 33 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00255 (10931) covalent geometry : angle 0.44607 (14809) SS BOND : bond 0.00147 ( 8) SS BOND : angle 0.98264 ( 16) hydrogen bonds : bond 0.04929 ( 862) hydrogen bonds : angle 3.45217 ( 2501) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: D 825 MET cc_start: 0.4534 (tpp) cc_final: 0.4266 (ptm) REVERT: G 131 ARG cc_start: 0.5689 (OUTLIER) cc_final: 0.5192 (mtp-110) REVERT: H 65 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7166 (mtp-110) REVERT: H 130 THR cc_start: 0.7091 (t) cc_final: 0.6790 (m) outliers start: 29 outliers final: 14 residues processed: 181 average time/residue: 0.4937 time to fit residues: 97.1304 Evaluate side-chains 178 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 126 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.194072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.143868 restraints weight = 33044.534| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 4.70 r_work: 0.3080 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.0781 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= 0.122 Angle : 0.431 5.994 14825 Z= 0.242 Chirality : 0.036 0.134 1675 Planarity : 0.003 0.030 1810 Dihedral : 4.362 56.552 1474 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.77 % Allowed : 17.16 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.93 (0.23), residues: 1339 helix: 3.69 (0.16), residues: 954 sheet: -1.98 (1.39), residues: 10 loop : -0.35 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 65 TYR 0.017 0.001 TYR C 549 PHE 0.020 0.001 PHE E 127 TRP 0.007 0.001 TRP H 178 HIS 0.004 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00238 (10931) covalent geometry : angle 0.43006 (14809) SS BOND : bond 0.00138 ( 8) SS BOND : angle 0.97151 ( 16) hydrogen bonds : bond 0.04719 ( 862) hydrogen bonds : angle 3.35320 ( 2501) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.401 Fit side-chains REVERT: B 813 GLU cc_start: 0.8336 (tt0) cc_final: 0.7884 (tt0) REVERT: D 813 GLU cc_start: 0.8349 (tt0) cc_final: 0.7906 (tt0) REVERT: D 825 MET cc_start: 0.4708 (tpp) cc_final: 0.4443 (ptm) REVERT: E 99 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6803 (mpp80) REVERT: E 131 ARG cc_start: 0.5941 (OUTLIER) cc_final: 0.5349 (mmp-170) REVERT: G 131 ARG cc_start: 0.5710 (OUTLIER) cc_final: 0.5204 (mtp-110) REVERT: F 78 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7314 (ttpt) REVERT: H 65 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7214 (mtp-110) REVERT: H 130 THR cc_start: 0.7204 (t) cc_final: 0.6812 (m) outliers start: 31 outliers final: 11 residues processed: 182 average time/residue: 0.5161 time to fit residues: 102.2942 Evaluate side-chains 178 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 78 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 123 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.192550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141701 restraints weight = 33880.584| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 4.63 r_work: 0.3053 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 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 = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0880 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= 0.148 Angle : 0.468 6.246 14825 Z= 0.264 Chirality : 0.037 0.136 1675 Planarity : 0.003 0.036 1810 Dihedral : 4.495 56.556 1474 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.68 % Allowed : 16.98 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.76 (0.23), residues: 1339 helix: 3.53 (0.16), residues: 954 sheet: -1.71 (1.44), residues: 10 loop : -0.31 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 594 TYR 0.021 0.002 TYR H 181 PHE 0.019 0.002 PHE E 127 TRP 0.008 0.001 TRP F 178 HIS 0.005 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00304 (10931) covalent geometry : angle 0.46732 (14809) SS BOND : bond 0.00218 ( 8) SS BOND : angle 1.04092 ( 16) hydrogen bonds : bond 0.05152 ( 862) hydrogen bonds : angle 3.45955 ( 2501) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.391 Fit side-chains REVERT: B 813 GLU cc_start: 0.8335 (tt0) cc_final: 0.7915 (tt0) REVERT: D 813 GLU cc_start: 0.8372 (tt0) cc_final: 0.7905 (tt0) REVERT: E 99 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.7003 (mpp80) REVERT: E 131 ARG cc_start: 0.6036 (OUTLIER) cc_final: 0.5487 (mmp-170) REVERT: G 131 ARG cc_start: 0.5755 (OUTLIER) cc_final: 0.5262 (mtp-110) REVERT: F 78 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7309 (ttpt) REVERT: H 65 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7070 (mtp-110) REVERT: H 130 THR cc_start: 0.7188 (t) cc_final: 0.6801 (m) outliers start: 30 outliers final: 14 residues processed: 173 average time/residue: 0.5394 time to fit residues: 101.5454 Evaluate side-chains 173 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 69 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.191754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.143081 restraints weight = 28377.460| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 4.14 r_work: 0.3033 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1028 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= 0.167 Angle : 0.495 6.451 14825 Z= 0.279 Chirality : 0.038 0.137 1675 Planarity : 0.004 0.041 1810 Dihedral : 4.624 57.311 1474 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.41 % Allowed : 16.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.61 (0.23), residues: 1339 helix: 3.39 (0.16), residues: 950 sheet: 0.34 (0.96), residues: 40 loop : -0.37 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 99 TYR 0.021 0.002 TYR H 181 PHE 0.020 0.002 PHE E 127 TRP 0.008 0.002 TRP A 606 HIS 0.005 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00351 (10931) covalent geometry : angle 0.49358 (14809) SS BOND : bond 0.00256 ( 8) SS BOND : angle 1.09091 ( 16) hydrogen bonds : bond 0.05384 ( 862) hydrogen bonds : angle 3.53818 ( 2501) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.396 Fit side-chains REVERT: B 813 GLU cc_start: 0.8416 (tt0) cc_final: 0.7942 (tt0) REVERT: B 825 MET cc_start: 0.4893 (tpp) cc_final: 0.4294 (tpp) REVERT: D 813 GLU cc_start: 0.8451 (tt0) cc_final: 0.7982 (tt0) REVERT: E 99 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.7030 (mpp80) REVERT: E 131 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.5546 (mmp-170) REVERT: G 56 GLU cc_start: 0.5586 (OUTLIER) cc_final: 0.4337 (tp30) REVERT: G 131 ARG cc_start: 0.5755 (OUTLIER) cc_final: 0.5309 (mtp-110) REVERT: F 78 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7247 (ttpt) REVERT: H 65 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7024 (mtp-110) REVERT: H 130 THR cc_start: 0.7149 (t) cc_final: 0.6767 (m) outliers start: 27 outliers final: 13 residues processed: 172 average time/residue: 0.5503 time to fit residues: 102.7365 Evaluate side-chains 171 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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 G residue 131 ARG 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 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 101 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 HIS G 205 HIS F 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.194325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.144581 restraints weight = 30307.165| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 4.48 r_work: 0.3089 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10939 Z= 0.114 Angle : 0.422 6.395 14825 Z= 0.237 Chirality : 0.036 0.138 1675 Planarity : 0.003 0.029 1810 Dihedral : 4.317 57.143 1474 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.52 % Allowed : 18.05 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.97 (0.23), residues: 1339 helix: 3.69 (0.16), residues: 954 sheet: 0.00 (1.29), residues: 20 loop : -0.33 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 65 TYR 0.017 0.001 TYR C 549 PHE 0.020 0.001 PHE E 127 TRP 0.009 0.001 TRP F 178 HIS 0.004 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00217 (10931) covalent geometry : angle 0.42054 (14809) SS BOND : bond 0.00281 ( 8) SS BOND : angle 0.97533 ( 16) hydrogen bonds : bond 0.04502 ( 862) hydrogen bonds : angle 3.29969 ( 2501) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: B 570 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7670 (mm-30) REVERT: B 813 GLU cc_start: 0.8371 (tt0) cc_final: 0.7906 (tt0) REVERT: D 570 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7665 (mm-30) REVERT: D 813 GLU cc_start: 0.8385 (tt0) cc_final: 0.7917 (tt0) REVERT: E 31 ASP cc_start: 0.7193 (m-30) cc_final: 0.6967 (m-30) REVERT: E 99 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6999 (mpp80) REVERT: E 131 ARG cc_start: 0.5967 (OUTLIER) cc_final: 0.5422 (mmp-170) REVERT: F 78 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7266 (ttpt) REVERT: H 65 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7193 (mtp-110) outliers start: 17 outliers final: 11 residues processed: 172 average time/residue: 0.5690 time to fit residues: 105.9954 Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 E residue 131 ARG Chi-restraints excluded: chain E residue 175 SER 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 F residue 6 ARG Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 24 optimal weight: 0.0570 chunk 66 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 83 optimal weight: 0.0470 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 HIS G 205 HIS H 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.195576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.147259 restraints weight = 30152.034| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 4.36 r_work: 0.3097 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10939 Z= 0.105 Angle : 0.407 6.389 14825 Z= 0.228 Chirality : 0.035 0.139 1675 Planarity : 0.003 0.030 1810 Dihedral : 4.184 57.241 1474 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.34 % Allowed : 17.96 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.08 (0.23), residues: 1339 helix: 3.80 (0.16), residues: 956 sheet: None (None), residues: 0 loop : -0.36 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 65 TYR 0.016 0.001 TYR C 549 PHE 0.020 0.001 PHE E 127 TRP 0.009 0.001 TRP H 178 HIS 0.005 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00196 (10931) covalent geometry : angle 0.40628 (14809) SS BOND : bond 0.00122 ( 8) SS BOND : angle 0.92552 ( 16) hydrogen bonds : bond 0.04257 ( 862) hydrogen bonds : angle 3.21719 ( 2501) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: B 570 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7604 (mm-30) REVERT: B 813 GLU cc_start: 0.8402 (tt0) cc_final: 0.7960 (tt0) REVERT: D 570 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7592 (mm-30) REVERT: D 813 GLU cc_start: 0.8404 (tt0) cc_final: 0.7966 (tt0) REVERT: E 95 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.5997 (tm-30) REVERT: E 99 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6694 (mpp80) REVERT: F 78 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7266 (ttpt) REVERT: H 65 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7144 (mtp-110) outliers start: 15 outliers final: 10 residues processed: 176 average time/residue: 0.5186 time to fit residues: 98.7763 Evaluate side-chains 171 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 123 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.192345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.143662 restraints weight = 28612.874| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 4.14 r_work: 0.3041 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10939 Z= 0.160 Angle : 0.486 6.766 14825 Z= 0.274 Chirality : 0.038 0.139 1675 Planarity : 0.004 0.038 1810 Dihedral : 4.502 57.693 1473 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.23 % Allowed : 17.43 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.76 (0.23), residues: 1339 helix: 3.51 (0.16), residues: 952 sheet: 0.32 (0.96), residues: 40 loop : -0.34 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 209 TYR 0.021 0.002 TYR H 181 PHE 0.019 0.002 PHE E 127 TRP 0.008 0.002 TRP C 606 HIS 0.005 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00334 (10931) covalent geometry : angle 0.48551 (14809) SS BOND : bond 0.00245 ( 8) SS BOND : angle 0.99465 ( 16) hydrogen bonds : bond 0.05244 ( 862) hydrogen bonds : angle 3.47674 ( 2501) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: B 813 GLU cc_start: 0.8364 (tt0) cc_final: 0.7904 (tt0) REVERT: D 813 GLU cc_start: 0.8399 (tt0) cc_final: 0.7956 (tt0) REVERT: E 95 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6110 (tm-30) REVERT: E 99 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6919 (mpp80) REVERT: E 131 ARG cc_start: 0.6031 (OUTLIER) cc_final: 0.5522 (mmp-170) REVERT: G 131 ARG cc_start: 0.5786 (OUTLIER) cc_final: 0.5279 (mtp-110) REVERT: F 78 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7257 (ttpt) REVERT: H 65 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7054 (mtp-110) outliers start: 25 outliers final: 14 residues processed: 165 average time/residue: 0.5593 time to fit residues: 99.5567 Evaluate side-chains 169 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 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 15 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 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 = 0.4114 r_free = 0.4114 target = 0.193681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.145105 restraints weight = 28146.727| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 4.15 r_work: 0.3064 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0988 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= 0.126 Angle : 0.446 6.690 14825 Z= 0.251 Chirality : 0.036 0.139 1675 Planarity : 0.003 0.030 1810 Dihedral : 4.375 57.833 1473 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.79 % Allowed : 17.96 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.88 (0.23), residues: 1339 helix: 3.59 (0.16), residues: 956 sheet: 0.33 (0.97), residues: 40 loop : -0.32 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 99 TYR 0.018 0.002 TYR C 549 PHE 0.019 0.001 PHE E 127 TRP 0.008 0.001 TRP F 178 HIS 0.005 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00248 (10931) covalent geometry : angle 0.44495 (14809) SS BOND : bond 0.00166 ( 8) SS BOND : angle 0.93096 ( 16) hydrogen bonds : bond 0.04731 ( 862) hydrogen bonds : angle 3.35447 ( 2501) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: B 813 GLU cc_start: 0.8405 (tt0) cc_final: 0.7941 (tt0) REVERT: D 570 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7737 (mm-30) REVERT: D 813 GLU cc_start: 0.8405 (tt0) cc_final: 0.7936 (tt0) REVERT: E 95 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6168 (tm-30) REVERT: E 99 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6803 (mpp80) REVERT: E 131 ARG cc_start: 0.6030 (OUTLIER) cc_final: 0.5502 (mmp-170) REVERT: G 131 ARG cc_start: 0.5748 (OUTLIER) cc_final: 0.5259 (mtp-110) REVERT: F 78 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7246 (ttpt) REVERT: H 65 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7099 (mtp-110) outliers start: 20 outliers final: 12 residues processed: 165 average time/residue: 0.5648 time to fit residues: 100.6059 Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 95 GLU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain F residue 6 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 65 ARG Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.192538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.143756 restraints weight = 28567.115| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 4.15 r_work: 0.3045 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 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 = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 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 0.032 10939 Z= 0.152 Angle : 0.482 6.797 14825 Z= 0.271 Chirality : 0.038 0.139 1675 Planarity : 0.004 0.036 1810 Dihedral : 4.490 57.804 1473 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.79 % Allowed : 17.69 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.70 (0.23), residues: 1339 helix: 3.46 (0.16), residues: 952 sheet: 0.28 (0.95), residues: 40 loop : -0.35 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 594 TYR 0.022 0.002 TYR F 181 PHE 0.019 0.002 PHE E 127 TRP 0.007 0.002 TRP C 606 HIS 0.005 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00315 (10931) covalent geometry : angle 0.48105 (14809) SS BOND : bond 0.00214 ( 8) SS BOND : angle 1.01504 ( 16) hydrogen bonds : bond 0.05140 ( 862) hydrogen bonds : angle 3.46205 ( 2501) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: B 570 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7746 (mm-30) REVERT: B 813 GLU cc_start: 0.8382 (tt0) cc_final: 0.7921 (tt0) REVERT: D 813 GLU cc_start: 0.8397 (tt0) cc_final: 0.7952 (tt0) REVERT: E 95 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6124 (tm-30) REVERT: E 99 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6850 (mpp80) REVERT: E 131 ARG cc_start: 0.6049 (OUTLIER) cc_final: 0.5534 (mmp-170) REVERT: G 131 ARG cc_start: 0.5877 (OUTLIER) cc_final: 0.5370 (mtp-110) REVERT: F 78 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7236 (ttpt) REVERT: H 65 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7045 (mtp-110) outliers start: 20 outliers final: 14 residues processed: 160 average time/residue: 0.5890 time to fit residues: 101.8301 Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 95 GLU Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 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 6 ARG Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 74 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 131 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.193688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.142166 restraints weight = 36971.854| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 4.89 r_work: 0.3086 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0997 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= 0.125 Angle : 0.450 6.785 14825 Z= 0.252 Chirality : 0.036 0.139 1675 Planarity : 0.003 0.029 1810 Dihedral : 4.379 57.320 1473 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.70 % Allowed : 17.87 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.85 (0.23), residues: 1339 helix: 3.57 (0.16), residues: 956 sheet: 0.10 (1.28), residues: 20 loop : -0.31 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 594 TYR 0.018 0.002 TYR C 549 PHE 0.019 0.001 PHE E 127 TRP 0.009 0.001 TRP F 178 HIS 0.005 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00245 (10931) covalent geometry : angle 0.44879 (14809) SS BOND : bond 0.00151 ( 8) SS BOND : angle 0.99424 ( 16) hydrogen bonds : bond 0.04733 ( 862) hydrogen bonds : angle 3.35638 ( 2501) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4620.70 seconds wall clock time: 79 minutes 14.71 seconds (4754.71 seconds total)