Starting phenix.real_space_refine on Mon Jul 28 13:09:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b60_44233/07_2025/9b60_44233.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b60_44233/07_2025/9b60_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_44233/07_2025/9b60_44233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b60_44233/07_2025/9b60_44233.map" model { file = "/net/cci-nas-00/data/ceres_data/9b60_44233/07_2025/9b60_44233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b60_44233/07_2025/9b60_44233.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.54, per 1000 atoms: 0.82 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: 3.81 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.09 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: 3.73 Time building geometry restraints manager: 3.99 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: 22.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 31.080 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.150 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: 0.030 Load rotamer database and sin/cos tables:14.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.720 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (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 TRP 0.010 0.001 TRP H 33 HIS 0.002 0.001 HIS F 60 PHE 0.030 0.001 PHE D 531 TYR 0.013 0.001 TYR F 32 ARG 0.010 0.000 ARG F 131 Details of bonding type rmsd hydrogen bonds : bond 0.14372 ( 847) hydrogen bonds : angle 4.45253 ( 2471) SS BOND : bond 0.00163 ( 8) SS BOND : angle 0.84873 ( 16) covalent geometry : bond 0.00224 (10723) covalent geometry : angle 0.44826 (14527) *********************** 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 : 1.178 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: 0.9849 time to fit residues: 185.7613 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 : 1.101 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.6980 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.215213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.163056 restraints weight = 27892.235| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.48 r_work: 0.3403 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10731 Z= 0.117 Angle : 0.441 6.538 14543 Z= 0.243 Chirality : 0.035 0.136 1646 Planarity : 0.003 0.035 1772 Dihedral : 4.771 53.531 1459 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.86 % Allowed : 20.96 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.23), residues: 1306 helix: 3.76 (0.15), residues: 946 sheet: 0.49 (0.89), residues: 38 loop : -0.70 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 178 HIS 0.004 0.001 HIS H 205 PHE 0.021 0.001 PHE D 531 TYR 0.014 0.001 TYR C 523 ARG 0.007 0.000 ARG F 131 Details of bonding type rmsd hydrogen bonds : bond 0.04488 ( 847) hydrogen bonds : angle 3.43060 ( 2471) SS BOND : bond 0.00153 ( 8) SS BOND : angle 0.78094 ( 16) covalent geometry : bond 0.00234 (10723) covalent geometry : angle 0.44008 (14527) *********************** 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 196 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: H 39 VAL cc_start: 0.6906 (m) cc_final: 0.6565 (t) REVERT: F 25 THR cc_start: 0.7428 (m) cc_final: 0.7209 (p) REVERT: B 524 GLU cc_start: 0.7500 (mp0) cc_final: 0.7202 (mp0) REVERT: E 40 CYS cc_start: 0.5775 (OUTLIER) cc_final: 0.4688 (p) REVERT: E 58 MET cc_start: 0.6047 (tpp) cc_final: 0.5658 (tpp) REVERT: E 208 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6598 (tt) outliers start: 31 outliers final: 12 residues processed: 182 average time/residue: 1.1901 time to fit residues: 239.1961 Evaluate side-chains 172 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 E residue 8 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 196 LEU Chi-restraints excluded: chain E residue 208 LEU 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 84 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.212269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.160057 restraints weight = 22928.541| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.48 r_work: 0.3336 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10731 Z= 0.162 Angle : 0.494 6.491 14543 Z= 0.272 Chirality : 0.038 0.140 1646 Planarity : 0.003 0.038 1772 Dihedral : 4.205 47.697 1443 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.79 % Allowed : 19.76 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.23), residues: 1306 helix: 3.42 (0.15), residues: 940 sheet: 0.58 (0.91), residues: 38 loop : -0.79 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 578 HIS 0.005 0.001 HIS E 205 PHE 0.017 0.002 PHE D 531 TYR 0.015 0.002 TYR G 181 ARG 0.006 0.000 ARG F 131 Details of bonding type rmsd hydrogen bonds : bond 0.05079 ( 847) hydrogen bonds : angle 3.58896 ( 2471) SS BOND : bond 0.00333 ( 8) SS BOND : angle 0.78071 ( 16) covalent geometry : bond 0.00364 (10723) covalent geometry : angle 0.49326 (14527) *********************** 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 207 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: H 39 VAL cc_start: 0.7007 (m) cc_final: 0.6680 (t) REVERT: D 509 LYS cc_start: 0.5885 (OUTLIER) cc_final: 0.5363 (tttp) REVERT: E 40 CYS cc_start: 0.5934 (OUTLIER) cc_final: 0.4826 (p) REVERT: E 58 MET cc_start: 0.6006 (tpp) cc_final: 0.5580 (tpp) REVERT: E 76 LEU cc_start: 0.5444 (tt) cc_final: 0.4346 (tt) REVERT: E 149 ASN cc_start: 0.7360 (OUTLIER) cc_final: 0.6903 (t0) REVERT: E 208 LEU cc_start: 0.7019 (mp) cc_final: 0.6623 (tt) outliers start: 41 outliers final: 20 residues processed: 190 average time/residue: 1.0590 time to fit residues: 220.6891 Evaluate side-chains 182 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain F residue 67 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 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 67 CYS Chi-restraints excluded: chain E residue 149 ASN 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 G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 70 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.213747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.163769 restraints weight = 25712.323| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 3.58 r_work: 0.3349 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 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 = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10731 Z= 0.128 Angle : 0.452 6.778 14543 Z= 0.249 Chirality : 0.036 0.136 1646 Planarity : 0.003 0.038 1772 Dihedral : 4.014 46.859 1441 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.51 % Allowed : 21.14 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.23), residues: 1306 helix: 3.54 (0.15), residues: 944 sheet: 0.30 (0.89), residues: 38 loop : -0.75 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 33 HIS 0.003 0.001 HIS H 205 PHE 0.015 0.001 PHE D 584 TYR 0.015 0.001 TYR C 523 ARG 0.007 0.000 ARG F 131 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 847) hydrogen bonds : angle 3.45039 ( 2471) SS BOND : bond 0.00279 ( 8) SS BOND : angle 1.09995 ( 16) covalent geometry : bond 0.00273 (10723) covalent geometry : angle 0.45119 (14527) *********************** 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 203 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 1.496 Fit side-chains revert: symmetry clash REVERT: H 39 VAL cc_start: 0.6972 (m) cc_final: 0.6606 (t) REVERT: H 199 HIS cc_start: 0.7418 (OUTLIER) cc_final: 0.7091 (t-90) REVERT: E 58 MET cc_start: 0.6020 (tpp) cc_final: 0.5631 (tpp) REVERT: E 76 LEU cc_start: 0.5397 (tt) cc_final: 0.4928 (tt) REVERT: E 149 ASN cc_start: 0.7364 (OUTLIER) cc_final: 0.6922 (t0) REVERT: E 192 MET cc_start: 0.5984 (tpp) cc_final: 0.5783 (tpp) REVERT: E 208 LEU cc_start: 0.6867 (mp) cc_final: 0.6578 (tt) outliers start: 38 outliers final: 21 residues processed: 184 average time/residue: 1.1687 time to fit residues: 235.9187 Evaluate side-chains 186 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 67 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 629 MET Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 811 LEU 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 67 CYS Chi-restraints excluded: chain E residue 149 ASN 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 203 ASP 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 107 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4318 r_free = 0.4318 target = 0.213454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.162201 restraints weight = 26329.336| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.67 r_work: 0.3345 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 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 = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10731 Z= 0.129 Angle : 0.459 6.884 14543 Z= 0.252 Chirality : 0.036 0.134 1646 Planarity : 0.003 0.038 1772 Dihedral : 3.821 42.152 1440 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.69 % Allowed : 20.50 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.72 (0.23), residues: 1306 helix: 3.51 (0.15), residues: 946 sheet: 0.22 (0.89), residues: 38 loop : -0.70 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 551 HIS 0.003 0.001 HIS H 205 PHE 0.014 0.001 PHE D 584 TYR 0.012 0.001 TYR G 181 ARG 0.007 0.000 ARG F 131 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 847) hydrogen bonds : angle 3.43972 ( 2471) SS BOND : bond 0.00236 ( 8) SS BOND : angle 2.18776 ( 16) covalent geometry : bond 0.00277 (10723) covalent geometry : angle 0.45343 (14527) *********************** 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 203 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 199 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.7148 (t-90) REVERT: D 509 LYS cc_start: 0.5859 (OUTLIER) cc_final: 0.5340 (tttp) REVERT: E 58 MET cc_start: 0.5978 (tpp) cc_final: 0.5581 (tpp) REVERT: E 76 LEU cc_start: 0.5412 (tt) cc_final: 0.4909 (tt) REVERT: E 149 ASN cc_start: 0.7360 (OUTLIER) cc_final: 0.6942 (t0) outliers start: 40 outliers final: 23 residues processed: 186 average time/residue: 1.1052 time to fit residues: 225.4891 Evaluate side-chains 186 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 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 629 MET 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 67 CYS Chi-restraints excluded: chain E residue 149 ASN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 13 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4327 r_free = 0.4327 target = 0.214437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.164420 restraints weight = 29590.670| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 3.65 r_work: 0.3364 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 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 = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10731 Z= 0.117 Angle : 0.440 7.024 14543 Z= 0.240 Chirality : 0.036 0.134 1646 Planarity : 0.003 0.038 1772 Dihedral : 3.733 40.331 1440 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.32 % Allowed : 21.14 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.85 (0.23), residues: 1306 helix: 3.61 (0.15), residues: 946 sheet: 0.35 (0.90), residues: 38 loop : -0.69 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 551 HIS 0.003 0.001 HIS H 205 PHE 0.014 0.001 PHE D 584 TYR 0.016 0.001 TYR C 523 ARG 0.008 0.000 ARG F 131 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 847) hydrogen bonds : angle 3.37267 ( 2471) SS BOND : bond 0.00197 ( 8) SS BOND : angle 1.15135 ( 16) covalent geometry : bond 0.00244 (10723) covalent geometry : angle 0.43901 (14527) *********************** 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 204 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 199 HIS cc_start: 0.7501 (OUTLIER) cc_final: 0.7191 (t-90) REVERT: D 509 LYS cc_start: 0.5803 (OUTLIER) cc_final: 0.5304 (tttp) REVERT: E 58 MET cc_start: 0.6038 (tpp) cc_final: 0.5632 (tpp) REVERT: E 76 LEU cc_start: 0.5524 (tt) cc_final: 0.5005 (tt) REVERT: E 149 ASN cc_start: 0.7341 (OUTLIER) cc_final: 0.6953 (t0) outliers start: 36 outliers final: 23 residues processed: 189 average time/residue: 0.9507 time to fit residues: 197.5349 Evaluate side-chains 191 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 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 86 ASP 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 67 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 149 ASN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 95 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4332 r_free = 0.4332 target = 0.214935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.162552 restraints weight = 25408.583| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.44 r_work: 0.3391 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 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 = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10731 Z= 0.112 Angle : 0.436 7.309 14543 Z= 0.238 Chirality : 0.035 0.134 1646 Planarity : 0.003 0.037 1772 Dihedral : 3.673 38.834 1440 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.23 % Allowed : 21.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.90 (0.23), residues: 1306 helix: 3.64 (0.16), residues: 948 sheet: 0.43 (0.91), residues: 38 loop : -0.68 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 551 HIS 0.011 0.001 HIS F 60 PHE 0.014 0.001 PHE D 584 TYR 0.009 0.001 TYR G 181 ARG 0.009 0.000 ARG F 131 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 847) hydrogen bonds : angle 3.36250 ( 2471) SS BOND : bond 0.00161 ( 8) SS BOND : angle 1.00404 ( 16) covalent geometry : bond 0.00233 (10723) covalent geometry : angle 0.43521 (14527) *********************** 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 202 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 199 HIS cc_start: 0.7420 (OUTLIER) cc_final: 0.7114 (t-90) REVERT: F 25 THR cc_start: 0.7429 (m) cc_final: 0.7205 (p) REVERT: D 509 LYS cc_start: 0.5793 (OUTLIER) cc_final: 0.5307 (tttp) REVERT: E 58 MET cc_start: 0.5847 (tpp) cc_final: 0.5590 (tpp) REVERT: E 76 LEU cc_start: 0.5462 (tt) cc_final: 0.4939 (tt) REVERT: E 149 ASN cc_start: 0.7319 (OUTLIER) cc_final: 0.6939 (t0) REVERT: E 175 SER cc_start: 0.7153 (m) cc_final: 0.6698 (p) REVERT: E 200 MET cc_start: 0.7361 (mtt) cc_final: 0.7151 (mtm) outliers start: 35 outliers final: 23 residues processed: 187 average time/residue: 0.8931 time to fit residues: 184.0354 Evaluate side-chains 191 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS 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 86 ASP 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 795 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 67 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 186 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 107 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 89 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4332 r_free = 0.4332 target = 0.215026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.161992 restraints weight = 18649.857| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.59 r_work: 0.3433 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1414 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= 0.113 Angle : 0.439 7.196 14543 Z= 0.238 Chirality : 0.035 0.135 1646 Planarity : 0.003 0.037 1772 Dihedral : 3.649 37.302 1440 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.95 % Allowed : 22.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.90 (0.23), residues: 1306 helix: 3.64 (0.15), residues: 948 sheet: 0.46 (0.90), residues: 38 loop : -0.67 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 551 HIS 0.003 0.001 HIS F 60 PHE 0.017 0.001 PHE E 97 TYR 0.015 0.001 TYR C 523 ARG 0.009 0.000 ARG F 131 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 847) hydrogen bonds : angle 3.35297 ( 2471) SS BOND : bond 0.00161 ( 8) SS BOND : angle 0.94048 ( 16) covalent geometry : bond 0.00235 (10723) covalent geometry : angle 0.43846 (14527) *********************** 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 201 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 10 MET cc_start: 0.7080 (tpt) cc_final: 0.6820 (mmm) REVERT: H 99 ARG cc_start: 0.6754 (mpt90) cc_final: 0.6502 (mpt90) REVERT: H 199 HIS cc_start: 0.7302 (OUTLIER) cc_final: 0.6982 (t-90) REVERT: F 25 THR cc_start: 0.7408 (m) cc_final: 0.7169 (p) REVERT: D 509 LYS cc_start: 0.5808 (OUTLIER) cc_final: 0.5373 (tttp) REVERT: E 76 LEU cc_start: 0.5499 (tt) cc_final: 0.4962 (tt) REVERT: E 149 ASN cc_start: 0.7138 (OUTLIER) cc_final: 0.6769 (t0) REVERT: E 175 SER cc_start: 0.7118 (m) cc_final: 0.6658 (p) outliers start: 32 outliers final: 26 residues processed: 189 average time/residue: 0.8851 time to fit residues: 184.8464 Evaluate side-chains 195 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS 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 86 ASP 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 812 ILE 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 8 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 149 ASN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 99 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 96 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.214332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.165193 restraints weight = 27497.136| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 3.63 r_work: 0.3350 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1438 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= 0.125 Angle : 0.461 8.132 14543 Z= 0.249 Chirality : 0.036 0.137 1646 Planarity : 0.003 0.037 1772 Dihedral : 3.704 36.956 1440 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.05 % Allowed : 22.90 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.23), residues: 1306 helix: 3.56 (0.15), residues: 946 sheet: 0.52 (0.91), residues: 38 loop : -0.66 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 551 HIS 0.003 0.001 HIS H 205 PHE 0.018 0.001 PHE E 97 TYR 0.011 0.001 TYR A 523 ARG 0.010 0.000 ARG F 131 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 847) hydrogen bonds : angle 3.40120 ( 2471) SS BOND : bond 0.00172 ( 8) SS BOND : angle 0.93242 ( 16) covalent geometry : bond 0.00269 (10723) covalent geometry : angle 0.45982 (14527) *********************** 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 200 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 99 ARG cc_start: 0.6828 (mpt90) cc_final: 0.6533 (mpt90) REVERT: H 199 HIS cc_start: 0.7457 (OUTLIER) cc_final: 0.7167 (t-90) REVERT: F 25 THR cc_start: 0.7423 (m) cc_final: 0.7168 (p) REVERT: D 509 LYS cc_start: 0.5786 (OUTLIER) cc_final: 0.5295 (tttp) REVERT: E 76 LEU cc_start: 0.5397 (tt) cc_final: 0.4849 (tt) REVERT: E 149 ASN cc_start: 0.7247 (OUTLIER) cc_final: 0.6852 (t0) REVERT: E 175 SER cc_start: 0.7193 (m) cc_final: 0.6726 (p) REVERT: G 208 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6524 (mp) outliers start: 33 outliers final: 23 residues processed: 187 average time/residue: 0.9381 time to fit residues: 194.0048 Evaluate side-chains 189 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 86 ASP 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 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 67 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 149 ASN 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 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 Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 12 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 82 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.4342 r_free = 0.4342 target = 0.216188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.165307 restraints weight = 22902.626| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 3.44 r_work: 0.3401 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10731 Z= 0.104 Angle : 0.441 8.136 14543 Z= 0.236 Chirality : 0.035 0.136 1646 Planarity : 0.003 0.037 1772 Dihedral : 3.584 34.790 1440 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.40 % Allowed : 23.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.05 (0.23), residues: 1306 helix: 3.75 (0.16), residues: 948 sheet: 0.42 (0.90), residues: 38 loop : -0.63 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 551 HIS 0.014 0.001 HIS F 60 PHE 0.021 0.001 PHE E 97 TYR 0.017 0.001 TYR C 523 ARG 0.010 0.000 ARG F 131 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 847) hydrogen bonds : angle 3.30596 ( 2471) SS BOND : bond 0.00155 ( 8) SS BOND : angle 0.85626 ( 16) covalent geometry : bond 0.00207 (10723) covalent geometry : angle 0.44036 (14527) ********************** 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: 26 poor density : 169 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 99 ARG cc_start: 0.6855 (mpt90) cc_final: 0.6545 (mpt90) REVERT: H 199 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.7180 (t70) REVERT: F 25 THR cc_start: 0.7394 (m) cc_final: 0.7173 (p) REVERT: B 524 GLU cc_start: 0.7430 (mp0) cc_final: 0.7172 (mp0) REVERT: D 509 LYS cc_start: 0.5798 (OUTLIER) cc_final: 0.5262 (tttp) REVERT: E 76 LEU cc_start: 0.5483 (tt) cc_final: 0.4952 (tt) REVERT: E 175 SER cc_start: 0.7151 (m) cc_final: 0.6698 (p) REVERT: E 200 MET cc_start: 0.7295 (mtt) cc_final: 0.7090 (mtm) REVERT: G 208 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6575 (mp) outliers start: 26 outliers final: 18 residues processed: 185 average time/residue: 0.8946 time to fit residues: 181.9250 Evaluate side-chains 186 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain C residue 542 LEU 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 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 186 SER 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 Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 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 = 0.4296 r_free = 0.4296 target = 0.211144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.157785 restraints weight = 17774.931| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.53 r_work: 0.3372 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10731 Z= 0.195 Angle : 0.554 9.099 14543 Z= 0.298 Chirality : 0.040 0.154 1646 Planarity : 0.003 0.038 1772 Dihedral : 4.018 41.648 1440 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.86 % Allowed : 22.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.23), residues: 1306 helix: 3.19 (0.15), residues: 940 sheet: 0.59 (0.91), residues: 38 loop : -0.72 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 578 HIS 0.005 0.001 HIS E 205 PHE 0.020 0.002 PHE C 531 TYR 0.016 0.002 TYR G 181 ARG 0.011 0.001 ARG F 131 Details of bonding type rmsd hydrogen bonds : bond 0.05182 ( 847) hydrogen bonds : angle 3.61982 ( 2471) SS BOND : bond 0.00258 ( 8) SS BOND : angle 1.03991 ( 16) covalent geometry : bond 0.00451 (10723) covalent geometry : angle 0.55351 (14527) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9349.92 seconds wall clock time: 163 minutes 43.37 seconds (9823.37 seconds total)