Starting phenix.real_space_refine on Wed Feb 4 11:06:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b60_44233/02_2026/9b60_44233.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b60_44233/02_2026/9b60_44233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b60_44233/02_2026/9b60_44233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b60_44233/02_2026/9b60_44233.map" model { file = "/net/cci-nas-00/data/ceres_data/9b60_44233/02_2026/9b60_44233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b60_44233/02_2026/9b60_44233.cif" } resolution = 2.57 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= 0.002 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6909 2.51 5 N 1655 2.21 5 O 1825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10461 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1146 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1154 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 149, 1154 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 1172 Chain: "A" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1141 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 1161 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1150 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 149, 1150 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 1168 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N APHE B 623 " occ=0.41 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.59 residue: pdb=" N APHE D 623 " occ=0.51 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.49 Time building chain proxies: 2.62, per 1000 atoms: 0.25 Number of scatterers: 10461 At special positions: 0 Unit cell: (112.34, 109.88, 98.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1825 8.00 N 1655 7.00 C 6909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 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 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 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 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: 0.65 Conformation dependent library (CDL) restraints added in 584.6 milliseconds 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 74.3% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'H' and resid 5 through 30 Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.664A pdb=" N TYR H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 126 removed outlier: 3.946A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 Processing helix chain 'H' and resid 177 through 214 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.651A pdb=" N TYR F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 126 removed outlier: 3.971A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.538A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 214 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.779A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 572 through 586 Processing helix chain 'C' and resid 595 through 629 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 825 removed outlier: 3.610A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.854A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) 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 626 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 825 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.764A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 629 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 825 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.864A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) 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 626 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 825 removed outlier: 3.513A pdb=" N ALA D 822 " --> pdb=" O SER D 818 " (cutoff:3.500A) 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 removed outlier: 4.072A pdb=" N GLU E 126 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.673A 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 29 Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 126 removed outlier: 4.006A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.654A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 removed outlier: 3.593A pdb=" N MET G 192 " --> pdb=" O ILE G 188 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL G 198 " --> pdb=" O GLY G 194 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 77 through 79 Processing sheet with id=AA2, first strand: chain 'F' and resid 34 through 37 Processing sheet with id=AA3, first strand: chain 'E' and resid 34 through 38 Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 79 847 hydrogen bonds defined for protein. 2471 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: 1.78 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3151 1.35 - 1.47: 3062 1.47 - 1.59: 4398 1.59 - 1.71: 0 1.71 - 1.83: 112 Bond restraints: 10723 Sorted by residual: bond pdb=" CG1 ILE B 798 " pdb=" CD1 ILE B 798 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.63e+00 bond pdb=" CG1 ILE G 140 " pdb=" CD1 ILE G 140 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.36e+00 bond pdb=" CB PHE G 97 " pdb=" CG PHE G 97 " ideal model delta sigma weight residual 1.502 1.522 -0.020 2.30e-02 1.89e+03 7.22e-01 bond pdb=" CB MET B 629 " pdb=" CG MET B 629 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.40e-01 bond pdb=" CB CYS G 77 " pdb=" SG CYS G 77 " ideal model delta sigma weight residual 1.808 1.832 -0.024 3.30e-02 9.18e+02 5.38e-01 ... (remaining 10718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 14435 2.13 - 4.26: 74 4.26 - 6.40: 12 6.40 - 8.53: 5 8.53 - 10.66: 1 Bond angle restraints: 14527 Sorted by residual: angle pdb=" CB MET B 629 " pdb=" CG MET B 629 " pdb=" SD MET B 629 " ideal model delta sigma weight residual 112.70 123.36 -10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" N VAL B 792 " pdb=" CA VAL B 792 " pdb=" C VAL B 792 " ideal model delta sigma weight residual 113.20 110.55 2.65 9.60e-01 1.09e+00 7.62e+00 angle pdb=" CB MET E 192 " pdb=" CG MET E 192 " pdb=" SD MET E 192 " ideal model delta sigma weight residual 112.70 120.03 -7.33 3.00e+00 1.11e-01 5.98e+00 angle pdb=" CB MET D 629 " pdb=" CG MET D 629 " pdb=" SD MET D 629 " ideal model delta sigma weight residual 112.70 119.69 -6.99 3.00e+00 1.11e-01 5.43e+00 angle pdb=" CA MET E 192 " pdb=" CB MET E 192 " pdb=" CG MET E 192 " ideal model delta sigma weight residual 114.10 118.60 -4.50 2.00e+00 2.50e-01 5.07e+00 ... (remaining 14522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 5254 17.63 - 35.27: 621 35.27 - 52.90: 172 52.90 - 70.54: 33 70.54 - 88.17: 7 Dihedral angle restraints: 6087 sinusoidal: 2223 harmonic: 3864 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 -129.75 43.75 1 1.00e+01 1.00e-02 2.67e+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 79.00 15.88 63.12 1 2.00e+01 2.50e-03 1.31e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual 93.00 121.13 -28.13 1 1.00e+01 1.00e-02 1.13e+01 ... (remaining 6084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1102 0.029 - 0.057: 365 0.057 - 0.086: 138 0.086 - 0.114: 37 0.114 - 0.143: 4 Chirality restraints: 1646 Sorted by residual: chirality pdb=" CA VAL E 57 " pdb=" N VAL E 57 " pdb=" C VAL E 57 " pdb=" CB VAL E 57 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA PHE G 107 " pdb=" N PHE G 107 " pdb=" C PHE G 107 " pdb=" CB PHE G 107 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.74e-01 chirality pdb=" CA PHE E 107 " pdb=" N PHE E 107 " pdb=" C PHE E 107 " pdb=" CB PHE E 107 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 1643 not shown) Planarity restraints: 1772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 531 " -0.014 2.00e-02 2.50e+03 1.30e-02 2.96e+00 pdb=" CG PHE D 531 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE D 531 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE D 531 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE D 531 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 531 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE D 531 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE G 107 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.60e+00 pdb=" N PRO G 108 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO G 108 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 108 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 97 " 0.007 2.00e-02 2.50e+03 9.24e-03 1.49e+00 pdb=" CG PHE E 97 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE E 97 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE E 97 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE E 97 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 97 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE E 97 " 0.000 2.00e-02 2.50e+03 ... (remaining 1769 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2188 2.78 - 3.31: 10264 3.31 - 3.84: 18507 3.84 - 4.37: 19897 4.37 - 4.90: 35351 Nonbonded interactions: 86207 Sorted by model distance: nonbonded pdb=" O ILE H 26 " pdb=" OG1 THR H 30 " model vdw 2.245 3.040 nonbonded pdb=" O PHE G 107 " pdb=" OG SER G 148 " model vdw 2.252 3.040 nonbonded pdb=" O PHE F 21 " pdb=" OG1 THR F 25 " model vdw 2.265 3.040 nonbonded pdb=" O SER H 36 " pdb=" OG1 THR H 59 " model vdw 2.268 3.040 nonbonded pdb=" O HIS H 60 " pdb=" ND1 HIS H 60 " model vdw 2.273 3.120 ... (remaining 86202 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 575 or (resid 576 and (name N or name CA or na \ me C or name O or name CB )) or resid 577 through 622 or resid 624 through 626 o \ r (resid 627 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 28 through 629 or resid 784 through 812 or (resid 813 and (name N or name CA or \ name C or name O or name CB )) or resid 814 through 818 or (resid 819 through 82 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 821 through \ 825)) selection = (chain 'B' and ((resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 575 or (resid 576 and (name N or name CA or name C or n \ ame O or name CB )) or resid 577 through 593 or (resid 594 and (name N or name C \ A or name C or name O or name CB )) or resid 595 through 622 or resid 624 throug \ h 626 or (resid 627 and (name N or name CA or name C or name O or name CB )) or \ resid 628 through 629 or (resid 784 and (name N or name CA or name C or name O o \ r name CB )) or resid 785 through 825)) selection = (chain 'C' and (resid 511 through 593 or (resid 594 and (name N or name CA or na \ me C or name O or name CB )) or resid 595 through 622 or resid 624 through 626 o \ r (resid 627 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 28 through 629 or resid 784 through 812 or (resid 813 and (name N or name CA or \ name C or name O or name CB )) or resid 814 through 818 or (resid 819 through 82 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 821 through \ 825)) selection = (chain 'D' and ((resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 575 or (resid 576 and (name N or name CA or name C or n \ ame O or name CB )) or resid 577 through 593 or (resid 594 and (name N or name C \ A or name C or name O or name CB )) or resid 595 through 622 or resid 624 throug \ h 629 or (resid 784 and (name N or name CA or name C or name O or name CB )) or \ resid 785 through 825)) } ncs_group { reference = (chain 'E' and resid 5 through 214) selection = (chain 'F' and (resid 5 through 41 or resid 55 through 214)) selection = (chain 'G' and resid 5 through 214) selection = (chain 'H' and (resid 5 through 41 or resid 55 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=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.190 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 0.050 10731 Z= 0.105 Angle : 0.449 10.660 14543 Z= 0.240 Chirality : 0.035 0.143 1646 Planarity : 0.003 0.035 1772 Dihedral : 16.618 88.171 3587 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.66 % Allowed : 23.92 % Favored : 74.42 % 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: 3.66 (0.23), residues: 1306 helix: 3.46 (0.15), residues: 946 sheet: 0.04 (0.81), residues: 48 loop : -0.71 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 131 TYR 0.013 0.001 TYR F 32 PHE 0.030 0.001 PHE D 531 TRP 0.010 0.001 TRP H 33 HIS 0.002 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00224 (10723) covalent geometry : angle 0.44826 (14527) SS BOND : bond 0.00163 ( 8) SS BOND : angle 0.84873 ( 16) hydrogen bonds : bond 0.14372 ( 847) hydrogen bonds : angle 4.45253 ( 2471) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: H 39 VAL cc_start: 0.6892 (m) cc_final: 0.6514 (t) outliers start: 18 outliers final: 16 residues processed: 172 average time/residue: 0.4562 time to fit residues: 85.6323 Evaluate side-chains 171 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 175 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS H 205 HIS E 132 HIS ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.213510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.162489 restraints weight = 24016.653| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.27 r_work: 0.3364 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10731 Z= 0.137 Angle : 0.471 6.537 14543 Z= 0.259 Chirality : 0.037 0.141 1646 Planarity : 0.003 0.036 1772 Dihedral : 4.937 51.377 1459 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.23 % Allowed : 20.41 % Favored : 76.36 % 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: 3.78 (0.23), residues: 1306 helix: 3.58 (0.15), residues: 942 sheet: 0.54 (0.90), residues: 38 loop : -0.75 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 131 TYR 0.014 0.001 TYR C 523 PHE 0.022 0.002 PHE D 531 TRP 0.009 0.001 TRP B 578 HIS 0.005 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00294 (10723) covalent geometry : angle 0.47019 (14527) SS BOND : bond 0.00187 ( 8) SS BOND : angle 0.82993 ( 16) hydrogen bonds : bond 0.04846 ( 847) hydrogen bonds : angle 3.52694 ( 2471) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: H 39 VAL cc_start: 0.6934 (m) cc_final: 0.6614 (t) REVERT: F 25 THR cc_start: 0.7448 (m) cc_final: 0.7200 (p) REVERT: E 40 CYS cc_start: 0.5853 (OUTLIER) cc_final: 0.4755 (p) REVERT: E 208 LEU cc_start: 0.6975 (mp) cc_final: 0.6596 (tt) outliers start: 35 outliers final: 14 residues processed: 185 average time/residue: 0.4514 time to fit residues: 91.3586 Evaluate side-chains 172 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 175 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 5 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 39 optimal weight: 0.2980 chunk 1 optimal weight: 0.8980 chunk 50 optimal weight: 0.0570 chunk 102 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS E 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.215779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.164726 restraints weight = 22361.703| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.33 r_work: 0.3389 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10731 Z= 0.107 Angle : 0.419 6.639 14543 Z= 0.230 Chirality : 0.035 0.139 1646 Planarity : 0.003 0.035 1772 Dihedral : 4.047 51.691 1445 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.14 % Allowed : 20.78 % Favored : 76.08 % 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: 4.04 (0.23), residues: 1306 helix: 3.76 (0.15), residues: 948 sheet: 0.57 (0.91), residues: 38 loop : -0.73 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 131 TYR 0.009 0.001 TYR G 181 PHE 0.016 0.001 PHE D 531 TRP 0.009 0.001 TRP A 551 HIS 0.003 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00214 (10723) covalent geometry : angle 0.41838 (14527) SS BOND : bond 0.00158 ( 8) SS BOND : angle 0.68604 ( 16) hydrogen bonds : bond 0.04180 ( 847) hydrogen bonds : angle 3.34519 ( 2471) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: H 39 VAL cc_start: 0.7044 (m) cc_final: 0.6714 (t) REVERT: F 25 THR cc_start: 0.7412 (m) cc_final: 0.7166 (p) REVERT: B 524 GLU cc_start: 0.7471 (mp0) cc_final: 0.7210 (mp0) REVERT: D 509 LYS cc_start: 0.5836 (OUTLIER) cc_final: 0.5378 (tttp) REVERT: E 24 MET cc_start: 0.4958 (tpt) cc_final: 0.4692 (tpt) REVERT: E 58 MET cc_start: 0.6080 (tpp) cc_final: 0.5701 (tpp) REVERT: E 149 ASN cc_start: 0.7298 (OUTLIER) cc_final: 0.6843 (t0) REVERT: E 208 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6631 (tt) outliers start: 34 outliers final: 17 residues processed: 187 average time/residue: 0.4706 time to fit residues: 96.0718 Evaluate side-chains 185 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 8 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 78 optimal weight: 0.0670 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.213471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.161692 restraints weight = 26487.760| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 3.56 r_work: 0.3346 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10731 Z= 0.135 Angle : 0.457 6.685 14543 Z= 0.252 Chirality : 0.036 0.135 1646 Planarity : 0.003 0.037 1772 Dihedral : 4.014 51.197 1441 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.69 % Allowed : 20.41 % Favored : 75.90 % 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: 3.81 (0.23), residues: 1306 helix: 3.60 (0.15), residues: 944 sheet: 0.42 (0.89), residues: 38 loop : -0.72 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 131 TYR 0.014 0.001 TYR C 523 PHE 0.016 0.002 PHE D 531 TRP 0.010 0.001 TRP B 578 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00294 (10723) covalent geometry : angle 0.45583 (14527) SS BOND : bond 0.00224 ( 8) SS BOND : angle 1.11680 ( 16) hydrogen bonds : bond 0.04593 ( 847) hydrogen bonds : angle 3.44020 ( 2471) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: D 509 LYS cc_start: 0.5898 (OUTLIER) cc_final: 0.5387 (tttp) REVERT: E 40 CYS cc_start: 0.5947 (OUTLIER) cc_final: 0.4797 (p) REVERT: E 58 MET cc_start: 0.5847 (tpp) cc_final: 0.5558 (tpp) REVERT: E 76 LEU cc_start: 0.5422 (tt) cc_final: 0.4349 (tt) REVERT: E 208 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6580 (tt) outliers start: 40 outliers final: 22 residues processed: 188 average time/residue: 0.4775 time to fit residues: 97.9370 Evaluate side-chains 184 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 121 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 0.0020 chunk 124 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.213688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.161328 restraints weight = 25325.819| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.48 r_work: 0.3367 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10731 Z= 0.131 Angle : 0.455 6.722 14543 Z= 0.249 Chirality : 0.036 0.137 1646 Planarity : 0.003 0.038 1772 Dihedral : 3.993 49.000 1441 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.32 % Allowed : 20.78 % Favored : 75.90 % 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: 3.77 (0.23), residues: 1306 helix: 3.55 (0.15), residues: 944 sheet: 0.48 (0.91), residues: 38 loop : -0.71 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 131 TYR 0.012 0.001 TYR G 181 PHE 0.015 0.001 PHE E 97 TRP 0.011 0.001 TRP A 551 HIS 0.003 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00282 (10723) covalent geometry : angle 0.45425 (14527) SS BOND : bond 0.00278 ( 8) SS BOND : angle 0.87426 ( 16) hydrogen bonds : bond 0.04483 ( 847) hydrogen bonds : angle 3.42836 ( 2471) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: D 509 LYS cc_start: 0.5847 (OUTLIER) cc_final: 0.5330 (tttp) REVERT: E 58 MET cc_start: 0.5944 (tpp) cc_final: 0.5534 (tpp) REVERT: E 76 LEU cc_start: 0.5451 (tt) cc_final: 0.4938 (tt) REVERT: E 208 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6634 (tt) outliers start: 36 outliers final: 24 residues processed: 187 average time/residue: 0.4622 time to fit residues: 94.4546 Evaluate side-chains 188 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 48 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.211102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.159880 restraints weight = 23469.343| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.34 r_work: 0.3340 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10731 Z= 0.193 Angle : 0.544 8.107 14543 Z= 0.298 Chirality : 0.040 0.144 1646 Planarity : 0.004 0.040 1772 Dihedral : 4.149 45.165 1440 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.88 % Allowed : 20.96 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.23 (0.23), residues: 1306 helix: 3.14 (0.15), residues: 938 sheet: 0.48 (0.91), residues: 38 loop : -0.79 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 131 TYR 0.018 0.002 TYR G 181 PHE 0.018 0.002 PHE D 584 TRP 0.015 0.002 TRP H 33 HIS 0.005 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00447 (10723) covalent geometry : angle 0.53750 (14527) SS BOND : bond 0.00394 ( 8) SS BOND : angle 2.48713 ( 16) hydrogen bonds : bond 0.05294 ( 847) hydrogen bonds : angle 3.70471 ( 2471) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 524 GLU cc_start: 0.7744 (mp0) cc_final: 0.7444 (mp0) REVERT: D 509 LYS cc_start: 0.5875 (OUTLIER) cc_final: 0.5355 (tttp) REVERT: E 40 CYS cc_start: 0.6285 (OUTLIER) cc_final: 0.5925 (p) REVERT: E 58 MET cc_start: 0.6055 (tpp) cc_final: 0.5667 (tpp) REVERT: E 208 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6771 (tt) REVERT: G 208 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6552 (mp) outliers start: 42 outliers final: 26 residues processed: 184 average time/residue: 0.4493 time to fit residues: 90.6981 Evaluate side-chains 183 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 523 TYR Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.214411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.162932 restraints weight = 27640.362| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.48 r_work: 0.3376 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10731 Z= 0.119 Angle : 0.459 7.117 14543 Z= 0.250 Chirality : 0.036 0.139 1646 Planarity : 0.003 0.038 1772 Dihedral : 3.859 43.557 1440 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.23 % Allowed : 21.79 % Favored : 74.98 % 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: 3.66 (0.23), residues: 1306 helix: 3.48 (0.16), residues: 946 sheet: 0.28 (0.93), residues: 38 loop : -0.77 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 131 TYR 0.010 0.001 TYR G 181 PHE 0.019 0.001 PHE E 97 TRP 0.015 0.001 TRP A 551 HIS 0.003 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00252 (10723) covalent geometry : angle 0.45479 (14527) SS BOND : bond 0.00254 ( 8) SS BOND : angle 1.82280 ( 16) hydrogen bonds : bond 0.04276 ( 847) hydrogen bonds : angle 3.45673 ( 2471) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 509 LYS cc_start: 0.5753 (OUTLIER) cc_final: 0.5250 (tttp) REVERT: E 76 LEU cc_start: 0.5647 (tt) cc_final: 0.5125 (tt) REVERT: E 175 SER cc_start: 0.7353 (m) cc_final: 0.6865 (p) outliers start: 35 outliers final: 24 residues processed: 187 average time/residue: 0.4496 time to fit residues: 92.0490 Evaluate side-chains 184 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 113 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 22 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.215308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.163594 restraints weight = 28500.868| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 3.72 r_work: 0.3370 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10731 Z= 0.111 Angle : 0.451 10.272 14543 Z= 0.241 Chirality : 0.035 0.145 1646 Planarity : 0.003 0.037 1772 Dihedral : 3.721 39.205 1440 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.77 % Allowed : 22.81 % Favored : 74.42 % 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: 1306 helix: 3.62 (0.15), residues: 948 sheet: 0.21 (0.93), residues: 38 loop : -0.74 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 131 TYR 0.016 0.001 TYR C 523 PHE 0.020 0.001 PHE E 97 TRP 0.012 0.001 TRP E 178 HIS 0.013 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00230 (10723) covalent geometry : angle 0.44876 (14527) SS BOND : bond 0.00254 ( 8) SS BOND : angle 1.46409 ( 16) hydrogen bonds : bond 0.04094 ( 847) hydrogen bonds : angle 3.37580 ( 2471) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 THR cc_start: 0.7423 (m) cc_final: 0.7223 (p) REVERT: D 509 LYS cc_start: 0.5743 (OUTLIER) cc_final: 0.5193 (tttp) REVERT: E 24 MET cc_start: 0.4787 (tpt) cc_final: 0.4132 (tpt) REVERT: E 76 LEU cc_start: 0.5602 (tt) cc_final: 0.5128 (tt) REVERT: G 200 MET cc_start: 0.7145 (mtm) cc_final: 0.6916 (mtm) outliers start: 30 outliers final: 22 residues processed: 186 average time/residue: 0.4678 time to fit residues: 95.1302 Evaluate side-chains 190 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 15 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.213789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.161698 restraints weight = 20109.462| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 3.04 r_work: 0.3393 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10731 Z= 0.135 Angle : 0.483 8.911 14543 Z= 0.260 Chirality : 0.037 0.146 1646 Planarity : 0.003 0.038 1772 Dihedral : 3.814 39.826 1440 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.77 % Allowed : 22.71 % Favored : 74.52 % 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: 3.61 (0.23), residues: 1306 helix: 3.44 (0.15), residues: 946 sheet: 0.17 (0.91), residues: 38 loop : -0.77 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 131 TYR 0.012 0.001 TYR G 181 PHE 0.020 0.002 PHE E 97 TRP 0.014 0.001 TRP H 33 HIS 0.004 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00299 (10723) covalent geometry : angle 0.48115 (14527) SS BOND : bond 0.00254 ( 8) SS BOND : angle 1.36979 ( 16) hydrogen bonds : bond 0.04469 ( 847) hydrogen bonds : angle 3.47711 ( 2471) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.4861 (mmp) REVERT: F 25 THR cc_start: 0.7425 (m) cc_final: 0.7196 (p) REVERT: D 509 LYS cc_start: 0.5756 (OUTLIER) cc_final: 0.5202 (tttp) REVERT: E 24 MET cc_start: 0.4681 (tpt) cc_final: 0.4149 (tpt) REVERT: E 76 LEU cc_start: 0.5594 (tt) cc_final: 0.5088 (tt) REVERT: G 209 ARG cc_start: 0.4929 (OUTLIER) cc_final: 0.4589 (mtp85) outliers start: 30 outliers final: 26 residues processed: 185 average time/residue: 0.4885 time to fit residues: 98.4358 Evaluate side-chains 193 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 209 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 68 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.213341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.161943 restraints weight = 24530.470| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.40 r_work: 0.3364 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10731 Z= 0.145 Angle : 0.498 8.962 14543 Z= 0.268 Chirality : 0.037 0.146 1646 Planarity : 0.003 0.038 1772 Dihedral : 3.871 40.728 1440 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.05 % Allowed : 22.07 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.50 (0.23), residues: 1306 helix: 3.36 (0.15), residues: 944 sheet: 0.12 (0.92), residues: 38 loop : -0.78 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 131 TYR 0.016 0.002 TYR C 523 PHE 0.020 0.002 PHE E 97 TRP 0.016 0.002 TRP A 551 HIS 0.003 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00327 (10723) covalent geometry : angle 0.49591 (14527) SS BOND : bond 0.00268 ( 8) SS BOND : angle 1.38366 ( 16) hydrogen bonds : bond 0.04600 ( 847) hydrogen bonds : angle 3.51170 ( 2471) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 MET cc_start: 0.6345 (OUTLIER) cc_final: 0.4949 (mmp) REVERT: B 524 GLU cc_start: 0.7601 (mp0) cc_final: 0.7299 (mp0) REVERT: D 509 LYS cc_start: 0.5750 (OUTLIER) cc_final: 0.5192 (tttp) REVERT: E 24 MET cc_start: 0.4795 (tpt) cc_final: 0.4309 (tpt) REVERT: E 37 ARG cc_start: 0.6860 (mmt90) cc_final: 0.6554 (mtp85) REVERT: E 76 LEU cc_start: 0.5582 (tt) cc_final: 0.5067 (tt) REVERT: G 209 ARG cc_start: 0.4946 (OUTLIER) cc_final: 0.4600 (mtp85) outliers start: 33 outliers final: 26 residues processed: 183 average time/residue: 0.4968 time to fit residues: 98.9563 Evaluate side-chains 191 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 209 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 121 optimal weight: 6.9990 chunk 116 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.213009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.161329 restraints weight = 19448.401| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.88 r_work: 0.3373 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10731 Z= 0.136 Angle : 0.494 8.906 14543 Z= 0.264 Chirality : 0.037 0.146 1646 Planarity : 0.003 0.049 1772 Dihedral : 3.871 41.094 1440 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.86 % Allowed : 22.62 % Favored : 74.52 % 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: 3.55 (0.23), residues: 1306 helix: 3.39 (0.15), residues: 944 sheet: 0.08 (0.81), residues: 48 loop : -0.79 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 131 TYR 0.012 0.001 TYR G 181 PHE 0.020 0.002 PHE E 97 TRP 0.016 0.001 TRP H 33 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00301 (10723) covalent geometry : angle 0.49224 (14527) SS BOND : bond 0.00256 ( 8) SS BOND : angle 1.33514 ( 16) hydrogen bonds : bond 0.04493 ( 847) hydrogen bonds : angle 3.49307 ( 2471) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4480.24 seconds wall clock time: 76 minutes 59.82 seconds (4619.82 seconds total)