Starting phenix.real_space_refine on Sun Aug 4 11:18:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b60_44233/08_2024/9b60_44233.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b60_44233/08_2024/9b60_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b60_44233/08_2024/9b60_44233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b60_44233/08_2024/9b60_44233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b60_44233/08_2024/9b60_44233.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b60_44233/08_2024/9b60_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 Residue "H ASP 31": "OD1" <-> "OD2" Residue "H PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 70": "OE1" <-> "OE2" Residue "C GLU 524": "OE1" <-> "OE2" Residue "C PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 570": "OE1" <-> "OE2" Residue "B ASP 590": "OD1" <-> "OD2" Residue "A PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 813": "OE1" <-> "OE2" Residue "D PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 8.03, per 1000 atoms: 0.77 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 - 3.50 Amino acid : False - 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: 4.28 Conformation dependent library (CDL) restraints added in 2.4 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: 1.02 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: 3.53 Time building geometry restraints manager: 4.70 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: 98.45 - 105.56: 112 105.56 - 112.68: 5614 112.68 - 119.79: 3238 119.79 - 126.91: 5431 126.91 - 134.02: 132 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: 2.360 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: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 35.670 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:21.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.390 ------------------------------------------------------------------------------- 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 10723 Z= 0.143 Angle : 0.448 10.660 14527 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 *********************** 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 fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 1.074 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: 0.9395 time to fit residues: 177.1921 Evaluate side-chains 171 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 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 10723 Z= 0.151 Angle : 0.440 6.538 14527 Z= 0.242 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 *********************** 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 fitting. rotamer outliers: 31 poor density : 165 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: H 39 VAL cc_start: 0.6907 (m) cc_final: 0.6567 (t) REVERT: B 524 GLU cc_start: 0.7537 (mp0) cc_final: 0.7304 (mp0) REVERT: E 40 CYS cc_start: 0.5372 (OUTLIER) cc_final: 0.4520 (p) REVERT: E 58 MET cc_start: 0.6219 (tpp) cc_final: 0.6012 (tpp) REVERT: E 208 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6932 (tt) outliers start: 31 outliers final: 12 residues processed: 182 average time/residue: 0.9317 time to fit residues: 186.0769 Evaluate side-chains 172 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 158 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 64 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 116 optimal weight: 40.0000 chunk 125 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 39 optimal weight: 0.0570 chunk 93 optimal weight: 0.9980 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10723 Z= 0.142 Angle : 0.419 6.656 14527 Z= 0.231 Chirality : 0.035 0.138 1646 Planarity : 0.003 0.035 1772 Dihedral : 3.944 53.756 1443 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.14 % Allowed : 21.05 % 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: 4.08 (0.23), residues: 1306 helix: 3.78 (0.15), residues: 948 sheet: 0.49 (0.90), residues: 38 loop : -0.66 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 551 HIS 0.003 0.001 HIS H 205 PHE 0.018 0.001 PHE D 531 TYR 0.010 0.001 TYR F 32 ARG 0.006 0.000 ARG F 131 *********************** 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 201 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 167 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: H 39 VAL cc_start: 0.7008 (m) cc_final: 0.6679 (t) REVERT: E 149 ASN cc_start: 0.7062 (OUTLIER) cc_final: 0.6663 (t0) REVERT: E 208 LEU cc_start: 0.7425 (mp) cc_final: 0.6975 (tt) outliers start: 34 outliers final: 19 residues processed: 185 average time/residue: 0.9383 time to fit residues: 190.8490 Evaluate side-chains 184 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 570 GLU 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 149 ASN 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 115 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10723 Z= 0.168 Angle : 0.437 6.755 14527 Z= 0.240 Chirality : 0.036 0.136 1646 Planarity : 0.003 0.036 1772 Dihedral : 3.986 54.258 1442 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.32 % Allowed : 20.50 % 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: 3.98 (0.23), residues: 1306 helix: 3.71 (0.15), residues: 948 sheet: 0.38 (0.90), residues: 38 loop : -0.68 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 551 HIS 0.004 0.001 HIS H 205 PHE 0.016 0.001 PHE D 531 TYR 0.014 0.001 TYR C 523 ARG 0.007 0.000 ARG F 131 *********************** 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 201 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 165 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: H 39 VAL cc_start: 0.6989 (m) cc_final: 0.6654 (t) REVERT: H 199 HIS cc_start: 0.7370 (OUTLIER) cc_final: 0.7039 (t-90) REVERT: D 509 LYS cc_start: 0.5868 (OUTLIER) cc_final: 0.5426 (tttp) REVERT: E 76 LEU cc_start: 0.5944 (tt) cc_final: 0.5695 (tt) REVERT: E 149 ASN cc_start: 0.7090 (OUTLIER) cc_final: 0.6728 (t0) REVERT: E 208 LEU cc_start: 0.7323 (mp) cc_final: 0.6935 (tt) outliers start: 36 outliers final: 23 residues processed: 183 average time/residue: 0.9376 time to fit residues: 188.4237 Evaluate side-chains 186 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 795 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 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 103 optimal weight: 0.3980 chunk 70 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 0.0670 chunk 105 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10723 Z= 0.137 Angle : 0.419 6.913 14527 Z= 0.229 Chirality : 0.035 0.134 1646 Planarity : 0.003 0.036 1772 Dihedral : 3.856 54.961 1441 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.23 % Allowed : 21.05 % Favored : 75.72 % 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: 4.09 (0.23), residues: 1306 helix: 3.80 (0.15), residues: 948 sheet: 0.74 (1.19), residues: 20 loop : -0.67 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 551 HIS 0.003 0.001 HIS H 205 PHE 0.014 0.001 PHE D 531 TYR 0.009 0.001 TYR G 181 ARG 0.007 0.000 ARG F 131 *********************** 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 204 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 169 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: H 199 HIS cc_start: 0.7360 (OUTLIER) cc_final: 0.7046 (t-90) REVERT: D 509 LYS cc_start: 0.5845 (OUTLIER) cc_final: 0.5406 (tttp) REVERT: E 40 CYS cc_start: 0.5474 (OUTLIER) cc_final: 0.4537 (p) REVERT: E 76 LEU cc_start: 0.5892 (tt) cc_final: 0.5094 (tt) REVERT: E 149 ASN cc_start: 0.7035 (OUTLIER) cc_final: 0.6754 (t0) REVERT: E 208 LEU cc_start: 0.7295 (mp) cc_final: 0.7001 (tt) outliers start: 35 outliers final: 21 residues processed: 189 average time/residue: 0.9774 time to fit residues: 202.1296 Evaluate side-chains 188 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 795 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 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 41 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 0.0010 chunk 65 optimal weight: 0.8980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS E 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10723 Z= 0.152 Angle : 0.431 7.209 14527 Z= 0.236 Chirality : 0.035 0.137 1646 Planarity : 0.003 0.036 1772 Dihedral : 3.616 38.028 1440 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.51 % Allowed : 21.61 % 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: 4.02 (0.23), residues: 1306 helix: 3.75 (0.15), residues: 948 sheet: 0.75 (1.20), residues: 20 loop : -0.66 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 551 HIS 0.003 0.001 HIS H 205 PHE 0.013 0.001 PHE D 531 TYR 0.015 0.001 TYR C 523 ARG 0.008 0.000 ARG F 131 *********************** 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 fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: F 6 ARG cc_start: 0.5061 (OUTLIER) cc_final: 0.4609 (tpt90) REVERT: B 524 GLU cc_start: 0.7532 (mp0) cc_final: 0.7320 (mp0) REVERT: D 509 LYS cc_start: 0.5851 (OUTLIER) cc_final: 0.5413 (tttp) REVERT: E 40 CYS cc_start: 0.5342 (OUTLIER) cc_final: 0.4898 (p) REVERT: E 76 LEU cc_start: 0.5974 (tt) cc_final: 0.5399 (tt) REVERT: E 149 ASN cc_start: 0.7002 (OUTLIER) cc_final: 0.6713 (t0) REVERT: E 208 LEU cc_start: 0.7263 (mp) cc_final: 0.7008 (tt) outliers start: 38 outliers final: 24 residues processed: 189 average time/residue: 0.9250 time to fit residues: 191.8866 Evaluate side-chains 191 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 163 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 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 196 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 70 optimal weight: 0.0030 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS E 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10723 Z= 0.149 Angle : 0.438 7.279 14527 Z= 0.239 Chirality : 0.036 0.140 1646 Planarity : 0.003 0.036 1772 Dihedral : 3.595 36.754 1440 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.32 % Allowed : 21.51 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.75 (0.15), residues: 948 sheet: 0.91 (1.20), residues: 20 loop : -0.65 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 178 HIS 0.003 0.001 HIS H 205 PHE 0.016 0.001 PHE E 73 TYR 0.013 0.001 TYR F 32 ARG 0.009 0.000 ARG F 131 *********************** 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 205 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 169 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 6 ARG cc_start: 0.5023 (OUTLIER) cc_final: 0.4602 (tpt90) REVERT: B 524 GLU cc_start: 0.7535 (mp0) cc_final: 0.7325 (mp0) REVERT: D 509 LYS cc_start: 0.5844 (OUTLIER) cc_final: 0.5404 (tttp) REVERT: E 76 LEU cc_start: 0.6127 (tt) cc_final: 0.5821 (tt) REVERT: E 149 ASN cc_start: 0.7049 (OUTLIER) cc_final: 0.6688 (t0) outliers start: 36 outliers final: 26 residues processed: 191 average time/residue: 0.9326 time to fit residues: 195.3683 Evaluate side-chains 197 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 F residue 6 ARG Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 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 G residue 8 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10723 Z= 0.246 Angle : 0.517 7.451 14527 Z= 0.282 Chirality : 0.038 0.147 1646 Planarity : 0.003 0.037 1772 Dihedral : 3.915 41.438 1440 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.69 % Allowed : 21.14 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.36 (0.15), residues: 942 sheet: 0.63 (0.82), residues: 48 loop : -0.67 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 33 HIS 0.004 0.001 HIS E 205 PHE 0.016 0.002 PHE A 584 TYR 0.016 0.002 TYR G 181 ARG 0.010 0.001 ARG F 131 *********************** 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 203 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 163 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 509 LYS cc_start: 0.5880 (OUTLIER) cc_final: 0.5426 (tttp) REVERT: E 76 LEU cc_start: 0.6102 (tt) cc_final: 0.5720 (tt) REVERT: E 149 ASN cc_start: 0.7104 (OUTLIER) cc_final: 0.6678 (t0) REVERT: G 208 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6630 (mp) outliers start: 40 outliers final: 24 residues processed: 185 average time/residue: 0.9470 time to fit residues: 192.2095 Evaluate side-chains 184 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 523 TYR Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 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 57 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 121 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10723 Z= 0.166 Angle : 0.467 8.686 14527 Z= 0.252 Chirality : 0.036 0.145 1646 Planarity : 0.003 0.037 1772 Dihedral : 3.780 40.700 1440 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.68 % Allowed : 22.35 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.23), residues: 1306 helix: 3.56 (0.15), residues: 946 sheet: 0.60 (1.01), residues: 30 loop : -0.70 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 551 HIS 0.003 0.001 HIS H 205 PHE 0.013 0.001 PHE D 584 TYR 0.016 0.001 TYR F 32 ARG 0.010 0.000 ARG F 131 *********************** 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 193 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 164 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 509 LYS cc_start: 0.5832 (OUTLIER) cc_final: 0.5386 (tttp) REVERT: E 76 LEU cc_start: 0.6027 (tt) cc_final: 0.5702 (tt) REVERT: E 149 ASN cc_start: 0.7049 (OUTLIER) cc_final: 0.6727 (t0) REVERT: G 208 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6720 (mp) outliers start: 29 outliers final: 22 residues processed: 181 average time/residue: 0.9492 time to fit residues: 188.5046 Evaluate side-chains 187 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 812 ILE 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 28 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 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 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.0010 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 117 optimal weight: 0.0270 chunk 101 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10723 Z= 0.143 Angle : 0.457 8.874 14527 Z= 0.245 Chirality : 0.035 0.151 1646 Planarity : 0.003 0.036 1772 Dihedral : 3.696 38.662 1440 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.22 % Allowed : 22.81 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.92 (0.23), residues: 1306 helix: 3.66 (0.16), residues: 948 sheet: 0.49 (1.02), residues: 30 loop : -0.68 (0.34), residues: 328 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 0.019 0.001 PHE C 531 TYR 0.017 0.001 TYR C 523 ARG 0.010 0.000 ARG F 131 ********************** 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 190 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 10 MET cc_start: 0.7627 (tpt) cc_final: 0.7347 (mmm) REVERT: D 509 LYS cc_start: 0.5842 (OUTLIER) cc_final: 0.5402 (tttp) REVERT: E 76 LEU cc_start: 0.6007 (tt) cc_final: 0.5707 (tt) outliers start: 24 outliers final: 20 residues processed: 181 average time/residue: 0.9162 time to fit residues: 182.4113 Evaluate side-chains 184 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 812 ILE 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 36 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.214458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.162131 restraints weight = 28301.675| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.57 r_work: 0.3399 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10723 Z= 0.194 Angle : 0.489 8.887 14527 Z= 0.263 Chirality : 0.037 0.152 1646 Planarity : 0.003 0.037 1772 Dihedral : 3.784 38.559 1440 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.49 % Allowed : 22.81 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.23), residues: 1306 helix: 3.48 (0.15), residues: 946 sheet: 0.37 (0.86), residues: 48 loop : -0.67 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 551 HIS 0.003 0.001 HIS E 205 PHE 0.016 0.002 PHE D 531 TYR 0.012 0.001 TYR A 523 ARG 0.010 0.000 ARG F 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3973.36 seconds wall clock time: 70 minutes 8.41 seconds (4208.41 seconds total)