Starting phenix.real_space_refine on Mon Mar 11 13:39:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwk_21419/03_2024/6vwk_21419_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwk_21419/03_2024/6vwk_21419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwk_21419/03_2024/6vwk_21419.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwk_21419/03_2024/6vwk_21419.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwk_21419/03_2024/6vwk_21419_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwk_21419/03_2024/6vwk_21419_neut.pdb" } resolution = 3.3 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= 1.000 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 86 5.16 5 C 5615 2.51 5 N 1328 2.21 5 O 1394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I ASP 7": "OD1" <-> "OD2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "J TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "L TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 37": "OE1" <-> "OE2" Residue "L ASP 44": "OD1" <-> "OD2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "M ASP 7": "OD1" <-> "OD2" Residue "M TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "N ASP 7": "OD1" <-> "OD2" Residue "N TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ASP 61": "OD1" <-> "OD2" Residue "O TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "P ASP 7": "OD1" <-> "OD2" Residue "P TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 37": "OE1" <-> "OE2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "R TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R ARG 41": "NH1" <-> "NH2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "S TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 44": "OD1" <-> "OD2" Residue "S ARG 50": "NH1" <-> "NH2" Residue "X PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 39": "OE1" <-> "OE2" Residue "X ASP 42": "OD1" <-> "OD2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Y GLU 48": "OE1" <-> "OE2" Residue "a TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 80": "OE1" <-> "OE2" Residue "a PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 177": "OE1" <-> "OE2" Residue "a GLU 219": "OE1" <-> "OE2" Residue "a PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 269": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8423 Number of models: 1 Model: "" Number of chains: 13 Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "X" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 362 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Time building chain proxies: 4.85, per 1000 atoms: 0.58 Number of scatterers: 8423 At special positions: 0 Unit cell: (89.557, 99.268, 102.505, 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 86 16.00 O 1394 8.00 N 1328 7.00 C 5615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.23 Conformation dependent library (CDL) restraints added in 1.8 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 1 sheets defined 90.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'I' and resid 3 through 42 removed outlier: 3.703A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 77 removed outlier: 3.722A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'J' and resid 4 through 42 Processing helix chain 'J' and resid 45 through 77 removed outlier: 3.750A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'L' and resid 4 through 42 Processing helix chain 'L' and resid 45 through 77 removed outlier: 3.716A pdb=" N LEU L 59 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) Proline residue: L 64 - end of helix Processing helix chain 'M' and resid 4 through 42 removed outlier: 3.743A pdb=" N GLN M 42 " --> pdb=" O GLY M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 77 removed outlier: 3.789A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) Proline residue: M 64 - end of helix Processing helix chain 'N' and resid 4 through 42 removed outlier: 3.589A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA N 40 " --> pdb=" O LEU N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 77 removed outlier: 3.837A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE N 63 " --> pdb=" O LEU N 59 " (cutoff:3.500A) Proline residue: N 64 - end of helix Processing helix chain 'O' and resid 4 through 42 removed outlier: 3.628A pdb=" N LEU O 8 " --> pdb=" O LEU O 4 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 77 removed outlier: 3.861A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) Proline residue: O 64 - end of helix Processing helix chain 'P' and resid 4 through 42 Processing helix chain 'P' and resid 45 through 77 removed outlier: 3.789A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.671A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 42 Processing helix chain 'Q' and resid 45 through 77 removed outlier: 3.602A pdb=" N LEU Q 59 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Proline residue: Q 64 - end of helix Processing helix chain 'R' and resid 4 through 42 Processing helix chain 'R' and resid 45 through 77 removed outlier: 3.811A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'S' and resid 4 through 42 removed outlier: 3.808A pdb=" N LEU S 8 " --> pdb=" O LEU S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 3.767A pdb=" N LEU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 77 removed outlier: 3.541A pdb=" N ALA S 67 " --> pdb=" O ILE S 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 25 Processing helix chain 'X' and resid 25 through 46 Processing helix chain 'Y' and resid 2 through 50 Proline residue: Y 27 - end of helix Processing helix chain 'a' and resid 7 through 16 Processing helix chain 'a' and resid 43 through 67 Processing helix chain 'a' and resid 73 through 94 Processing helix chain 'a' and resid 100 through 118 Processing helix chain 'a' and resid 119 through 121 No H-bonds generated for 'chain 'a' and resid 119 through 121' Processing helix chain 'a' and resid 124 through 133 Processing helix chain 'a' and resid 146 through 169 removed outlier: 3.878A pdb=" N THR a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) Processing helix chain 'a' and resid 172 through 180 Processing helix chain 'a' and resid 185 through 187 No H-bonds generated for 'chain 'a' and resid 185 through 187' Processing helix chain 'a' and resid 188 through 229 Proline residue: a 204 - end of helix removed outlier: 3.568A pdb=" N PHE a 222 " --> pdb=" O GLY a 218 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 269 removed outlier: 4.692A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.892A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR a 250 " --> pdb=" O ILE a 246 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 20 through 22 813 hydrogen bonds defined for protein. 2439 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: 2.61 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1336 1.32 - 1.44: 2020 1.44 - 1.57: 5049 1.57 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 8577 Sorted by residual: bond pdb=" C ARG a 210 " pdb=" O ARG a 210 " ideal model delta sigma weight residual 1.236 1.196 0.041 1.15e-02 7.56e+03 1.24e+01 bond pdb=" N VAL S 60 " pdb=" CA VAL S 60 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.31e+00 bond pdb=" C LEU S 8 " pdb=" O LEU S 8 " ideal model delta sigma weight residual 1.236 1.202 0.034 1.26e-02 6.30e+03 7.37e+00 bond pdb=" N MET S 11 " pdb=" CA MET S 11 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.33e-02 5.65e+03 6.72e+00 bond pdb=" C ASP S 7 " pdb=" O ASP S 7 " ideal model delta sigma weight residual 1.237 1.267 -0.031 1.19e-02 7.06e+03 6.61e+00 ... (remaining 8572 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.62: 270 105.62 - 112.76: 3930 112.76 - 119.89: 3607 119.89 - 127.02: 3739 127.02 - 134.15: 80 Bond angle restraints: 11626 Sorted by residual: angle pdb=" N ALA M 62 " pdb=" CA ALA M 62 " pdb=" C ALA M 62 " ideal model delta sigma weight residual 111.07 116.01 -4.94 1.07e+00 8.73e-01 2.13e+01 angle pdb=" N ALA Q 62 " pdb=" CA ALA Q 62 " pdb=" C ALA Q 62 " ideal model delta sigma weight residual 111.28 116.29 -5.01 1.09e+00 8.42e-01 2.11e+01 angle pdb=" CA VAL S 60 " pdb=" C VAL S 60 " pdb=" O VAL S 60 " ideal model delta sigma weight residual 121.17 116.64 4.53 1.06e+00 8.90e-01 1.83e+01 angle pdb=" N PRO X 27 " pdb=" CA PRO X 27 " pdb=" C PRO X 27 " ideal model delta sigma weight residual 110.70 115.88 -5.18 1.22e+00 6.72e-01 1.80e+01 angle pdb=" N PHE R 76 " pdb=" CA PHE R 76 " pdb=" C PHE R 76 " ideal model delta sigma weight residual 111.40 116.56 -5.16 1.22e+00 6.72e-01 1.79e+01 ... (remaining 11621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 4676 17.07 - 34.15: 306 34.15 - 51.22: 55 51.22 - 68.29: 14 68.29 - 85.36: 5 Dihedral angle restraints: 5056 sinusoidal: 1884 harmonic: 3172 Sorted by residual: dihedral pdb=" CA LEU X 3 " pdb=" C LEU X 3 " pdb=" N ASN X 4 " pdb=" CA ASN X 4 " ideal model delta harmonic sigma weight residual -180.00 -151.82 -28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA MET a 6 " pdb=" C MET a 6 " pdb=" N THR a 7 " pdb=" CA THR a 7 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ARG a 140 " pdb=" C ARG a 140 " pdb=" N VAL a 141 " pdb=" CA VAL a 141 " ideal model delta harmonic sigma weight residual -180.00 -152.75 -27.25 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 5053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1148 0.078 - 0.157: 213 0.157 - 0.235: 33 0.235 - 0.314: 17 0.314 - 0.392: 4 Chirality restraints: 1415 Sorted by residual: chirality pdb=" CA PHE S 76 " pdb=" N PHE S 76 " pdb=" C PHE S 76 " pdb=" CB PHE S 76 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA PHE P 76 " pdb=" N PHE P 76 " pdb=" C PHE P 76 " pdb=" CB PHE P 76 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA PHE J 76 " pdb=" N PHE J 76 " pdb=" C PHE J 76 " pdb=" CB PHE J 76 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 1412 not shown) Planarity restraints: 1434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU O 8 " -0.027 2.00e-02 2.50e+03 5.49e-02 3.02e+01 pdb=" C LEU O 8 " 0.095 2.00e-02 2.50e+03 pdb=" O LEU O 8 " -0.036 2.00e-02 2.50e+03 pdb=" N LEU O 9 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET Y 22 " 0.024 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C MET Y 22 " -0.081 2.00e-02 2.50e+03 pdb=" O MET Y 22 " 0.030 2.00e-02 2.50e+03 pdb=" N LYS Y 23 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 21 " -0.022 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C ALA J 21 " 0.075 2.00e-02 2.50e+03 pdb=" O ALA J 21 " -0.028 2.00e-02 2.50e+03 pdb=" N ILE J 22 " -0.026 2.00e-02 2.50e+03 ... (remaining 1431 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 2295 2.86 - 3.37: 8720 3.37 - 3.88: 14108 3.88 - 4.39: 15509 4.39 - 4.90: 27755 Nonbonded interactions: 68387 Sorted by model distance: nonbonded pdb=" O ASN a 33 " pdb=" OD1 ASN a 33 " model vdw 2.355 3.040 nonbonded pdb=" O SER a 165 " pdb=" O LYS a 169 " model vdw 2.367 3.040 nonbonded pdb=" O ASN N 5 " pdb=" OD2 ASP O 7 " model vdw 2.395 3.040 nonbonded pdb=" O LEU L 4 " pdb=" OD1 ASP L 7 " model vdw 2.418 3.040 nonbonded pdb=" OD1 ASN O 5 " pdb=" N MET O 6 " model vdw 2.510 2.520 ... (remaining 68382 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'X' selection = (chain 'Y' and resid 1 through 47) } 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=1.00 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: 2.660 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: 9.110 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.990 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 : 0.010 0.064 8577 Z= 0.640 Angle : 1.305 7.796 11626 Z= 0.848 Chirality : 0.069 0.392 1415 Planarity : 0.013 0.063 1434 Dihedral : 12.707 85.363 3032 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.59 % Allowed : 5.19 % Favored : 94.21 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 2.04 % 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: -0.35 (0.22), residues: 1107 helix: 0.01 (0.14), residues: 974 sheet: None (None), residues: 0 loop : -0.96 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.006 TRP Y 26 HIS 0.020 0.007 HIS a 15 PHE 0.032 0.004 PHE L 76 TYR 0.052 0.007 TYR O 10 ARG 0.047 0.009 ARG Y 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 168 time to evaluate : 0.882 Fit side-chains REVERT: I 6 MET cc_start: 0.5274 (mtm) cc_final: 0.4821 (mmp) REVERT: J 11 MET cc_start: 0.8069 (tpp) cc_final: 0.7832 (tpt) REVERT: L 11 MET cc_start: 0.8456 (tpt) cc_final: 0.7974 (tpt) REVERT: M 6 MET cc_start: 0.5909 (mtt) cc_final: 0.5557 (mtm) REVERT: Q 28 ILE cc_start: 0.9184 (mt) cc_final: 0.8977 (mp) REVERT: S 6 MET cc_start: 0.5895 (mmt) cc_final: 0.5233 (mmt) REVERT: S 11 MET cc_start: 0.8581 (tpp) cc_final: 0.8263 (tpt) REVERT: S 65 MET cc_start: 0.8400 (mmt) cc_final: 0.8186 (mmt) REVERT: Y 16 LEU cc_start: 0.8865 (mp) cc_final: 0.8557 (mp) REVERT: a 257 MET cc_start: 0.8137 (ttp) cc_final: 0.7927 (ttt) outliers start: 5 outliers final: 2 residues processed: 172 average time/residue: 0.2208 time to fit residues: 51.2190 Evaluate side-chains 133 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain a residue 149 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 5 ASN R 52 GLN S 3 ASN a 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8577 Z= 0.290 Angle : 0.714 7.936 11626 Z= 0.368 Chirality : 0.045 0.345 1415 Planarity : 0.006 0.048 1434 Dihedral : 4.975 35.004 1178 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.65 % Allowed : 9.21 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 2.28 (0.24), residues: 1107 helix: 1.78 (0.15), residues: 977 sheet: None (None), residues: 0 loop : -0.40 (0.56), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP a 111 HIS 0.007 0.002 HIS a 132 PHE 0.017 0.002 PHE a 75 TYR 0.024 0.002 TYR M 10 ARG 0.006 0.001 ARG Q 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 0.884 Fit side-chains REVERT: J 11 MET cc_start: 0.7964 (tpp) cc_final: 0.7704 (tpt) REVERT: L 11 MET cc_start: 0.8309 (tpt) cc_final: 0.7651 (tpt) REVERT: M 6 MET cc_start: 0.5567 (mtt) cc_final: 0.5307 (mtt) REVERT: Q 41 ARG cc_start: 0.8093 (ttm110) cc_final: 0.7696 (ttm-80) REVERT: S 6 MET cc_start: 0.5668 (mmt) cc_final: 0.5209 (mmt) REVERT: X 2 ASN cc_start: 0.6397 (t0) cc_final: 0.6176 (p0) REVERT: Y 18 VAL cc_start: 0.8013 (t) cc_final: 0.7757 (t) REVERT: a 116 ASN cc_start: 0.8553 (m-40) cc_final: 0.7993 (m110) outliers start: 14 outliers final: 7 residues processed: 151 average time/residue: 0.2191 time to fit residues: 45.7118 Evaluate side-chains 136 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 246 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 0.0980 chunk 103 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 14 HIS a 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8577 Z= 0.236 Angle : 0.623 7.702 11626 Z= 0.316 Chirality : 0.041 0.302 1415 Planarity : 0.005 0.047 1434 Dihedral : 4.490 39.142 1176 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.13 % Allowed : 9.68 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 2.94 (0.24), residues: 1107 helix: 2.24 (0.15), residues: 978 sheet: None (None), residues: 0 loop : -0.38 (0.56), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 111 HIS 0.002 0.001 HIS a 14 PHE 0.012 0.001 PHE a 75 TYR 0.024 0.001 TYR M 10 ARG 0.006 0.000 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 0.890 Fit side-chains REVERT: J 11 MET cc_start: 0.7900 (tpp) cc_final: 0.7641 (tpt) REVERT: J 57 MET cc_start: 0.8337 (tmm) cc_final: 0.7759 (ttp) REVERT: L 11 MET cc_start: 0.8281 (tpt) cc_final: 0.7599 (tpt) REVERT: M 6 MET cc_start: 0.5325 (mtt) cc_final: 0.4997 (mtt) REVERT: S 6 MET cc_start: 0.5563 (mmt) cc_final: 0.5117 (mmt) REVERT: X 2 ASN cc_start: 0.6717 (t0) cc_final: 0.6355 (p0) REVERT: X 23 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7454 (mttt) REVERT: X 24 TYR cc_start: 0.7892 (m-10) cc_final: 0.7557 (m-10) REVERT: Y 18 VAL cc_start: 0.7934 (t) cc_final: 0.7670 (t) REVERT: a 116 ASN cc_start: 0.8507 (m-40) cc_final: 0.8043 (m110) outliers start: 18 outliers final: 10 residues processed: 143 average time/residue: 0.1910 time to fit residues: 38.6373 Evaluate side-chains 140 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain O residue 16 MET Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain a residue 265 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 95 optimal weight: 0.0870 chunk 101 optimal weight: 0.0670 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8577 Z= 0.223 Angle : 0.604 8.358 11626 Z= 0.302 Chirality : 0.040 0.340 1415 Planarity : 0.005 0.047 1434 Dihedral : 4.334 45.334 1176 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.83 % Allowed : 10.86 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 3.33 (0.24), residues: 1107 helix: 2.59 (0.15), residues: 957 sheet: None (None), residues: 0 loop : -0.49 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 111 HIS 0.001 0.001 HIS a 245 PHE 0.011 0.001 PHE a 85 TYR 0.023 0.001 TYR M 10 ARG 0.004 0.000 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: J 11 MET cc_start: 0.7829 (tpp) cc_final: 0.7546 (tpt) REVERT: J 57 MET cc_start: 0.8271 (tmm) cc_final: 0.7878 (ttp) REVERT: L 11 MET cc_start: 0.8265 (tpt) cc_final: 0.7585 (tpt) REVERT: M 6 MET cc_start: 0.5312 (mtt) cc_final: 0.5071 (mtt) REVERT: O 57 MET cc_start: 0.8486 (tmm) cc_final: 0.8204 (ttp) REVERT: Q 65 MET cc_start: 0.7176 (mmm) cc_final: 0.6849 (mmt) REVERT: R 3 ASN cc_start: 0.1257 (OUTLIER) cc_final: 0.0717 (t0) REVERT: R 17 MET cc_start: 0.7917 (mmm) cc_final: 0.7479 (mmm) REVERT: S 6 MET cc_start: 0.5527 (mmt) cc_final: 0.5076 (mmt) REVERT: X 1 MET cc_start: 0.4894 (mtt) cc_final: 0.4435 (ttm) REVERT: X 24 TYR cc_start: 0.7898 (m-10) cc_final: 0.7540 (m-10) REVERT: Y 18 VAL cc_start: 0.7900 (t) cc_final: 0.7633 (t) REVERT: a 46 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.6340 (mtp) REVERT: a 116 ASN cc_start: 0.8471 (m-40) cc_final: 0.8036 (m110) outliers start: 24 outliers final: 10 residues processed: 150 average time/residue: 0.1801 time to fit residues: 38.5768 Evaluate side-chains 143 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain R residue 3 ASN Chi-restraints excluded: chain a residue 46 MET Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain a residue 265 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8577 Z= 0.329 Angle : 0.650 8.513 11626 Z= 0.321 Chirality : 0.042 0.327 1415 Planarity : 0.005 0.048 1434 Dihedral : 4.396 51.203 1176 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.60 % Allowed : 10.98 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 3.14 (0.23), residues: 1107 helix: 2.43 (0.15), residues: 961 sheet: None (None), residues: 0 loop : -0.35 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 241 HIS 0.002 0.001 HIS a 95 PHE 0.016 0.001 PHE a 85 TYR 0.014 0.001 TYR M 10 ARG 0.002 0.000 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: I 57 MET cc_start: 0.7854 (tmm) cc_final: 0.7585 (ttp) REVERT: J 11 MET cc_start: 0.7972 (tpp) cc_final: 0.7696 (tpt) REVERT: J 41 ARG cc_start: 0.7069 (ttm-80) cc_final: 0.6750 (ttm-80) REVERT: O 42 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7133 (mm-40) REVERT: R 57 MET cc_start: 0.8240 (ttp) cc_final: 0.7832 (ttt) REVERT: S 6 MET cc_start: 0.5627 (mmt) cc_final: 0.5207 (mmt) REVERT: X 24 TYR cc_start: 0.7813 (m-10) cc_final: 0.7436 (m-10) REVERT: Y 18 VAL cc_start: 0.7967 (t) cc_final: 0.7702 (t) REVERT: a 46 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6412 (mtp) REVERT: a 116 ASN cc_start: 0.8525 (m-40) cc_final: 0.8081 (m110) outliers start: 22 outliers final: 15 residues processed: 145 average time/residue: 0.1937 time to fit residues: 39.2355 Evaluate side-chains 149 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain O residue 16 MET Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain R residue 3 ASN Chi-restraints excluded: chain R residue 44 ASP Chi-restraints excluded: chain a residue 46 MET Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 245 HIS Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain a residue 259 LEU Chi-restraints excluded: chain a residue 265 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.4980 chunk 91 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 101 optimal weight: 0.4980 chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 ASN R 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8577 Z= 0.249 Angle : 0.614 8.588 11626 Z= 0.302 Chirality : 0.040 0.319 1415 Planarity : 0.005 0.047 1434 Dihedral : 4.340 52.043 1176 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.83 % Allowed : 11.92 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 3.33 (0.23), residues: 1107 helix: 2.57 (0.15), residues: 961 sheet: None (None), residues: 0 loop : -0.44 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 231 HIS 0.002 0.001 HIS a 245 PHE 0.012 0.001 PHE a 85 TYR 0.013 0.001 TYR M 10 ARG 0.007 0.000 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: I 57 MET cc_start: 0.7807 (tmm) cc_final: 0.7543 (ttp) REVERT: J 11 MET cc_start: 0.7973 (tpp) cc_final: 0.7705 (tpt) REVERT: L 75 MET cc_start: 0.7549 (ttt) cc_final: 0.7039 (ttt) REVERT: N 16 MET cc_start: 0.7955 (ttm) cc_final: 0.7698 (ttp) REVERT: O 42 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7067 (mm-40) REVERT: O 57 MET cc_start: 0.8425 (tmm) cc_final: 0.7572 (ttt) REVERT: Q 65 MET cc_start: 0.7215 (mmm) cc_final: 0.6945 (mmt) REVERT: R 17 MET cc_start: 0.7944 (mmm) cc_final: 0.7469 (mmm) REVERT: R 57 MET cc_start: 0.8127 (ttp) cc_final: 0.7797 (ttt) REVERT: R 75 MET cc_start: 0.8639 (ttp) cc_final: 0.8121 (mtp) REVERT: S 6 MET cc_start: 0.5576 (mmt) cc_final: 0.5177 (mmt) REVERT: X 1 MET cc_start: 0.4654 (mtt) cc_final: 0.4402 (ttm) REVERT: X 24 TYR cc_start: 0.7757 (m-10) cc_final: 0.7381 (m-10) REVERT: Y 18 VAL cc_start: 0.7973 (t) cc_final: 0.7702 (t) REVERT: a 6 MET cc_start: 0.6959 (mmp) cc_final: 0.6692 (mmt) REVERT: a 46 MET cc_start: 0.6743 (OUTLIER) cc_final: 0.6397 (mtp) REVERT: a 116 ASN cc_start: 0.8487 (m-40) cc_final: 0.8025 (m110) outliers start: 24 outliers final: 18 residues processed: 148 average time/residue: 0.2180 time to fit residues: 45.0192 Evaluate side-chains 152 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain O residue 16 MET Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain R residue 3 ASN Chi-restraints excluded: chain a residue 46 MET Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 245 HIS Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain a residue 259 LEU Chi-restraints excluded: chain a residue 265 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 chunk 57 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 101 optimal weight: 0.0970 chunk 63 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 46 optimal weight: 0.0980 chunk 62 optimal weight: 0.3980 overall best weight: 0.1578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 5 ASN M 3 ASN R 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8577 Z= 0.164 Angle : 0.572 8.530 11626 Z= 0.282 Chirality : 0.037 0.314 1415 Planarity : 0.004 0.048 1434 Dihedral : 4.248 54.052 1176 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.36 % Allowed : 12.51 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.24), residues: 1107 helix: 2.90 (0.15), residues: 961 sheet: None (None), residues: 0 loop : -0.54 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 231 HIS 0.002 0.001 HIS a 15 PHE 0.008 0.001 PHE a 38 TYR 0.017 0.001 TYR M 10 ARG 0.005 0.000 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: I 16 MET cc_start: 0.8134 (ttm) cc_final: 0.7786 (ttp) REVERT: I 57 MET cc_start: 0.7766 (tmm) cc_final: 0.7498 (ttp) REVERT: J 11 MET cc_start: 0.7856 (tpp) cc_final: 0.7602 (tpt) REVERT: L 75 MET cc_start: 0.7348 (ttt) cc_final: 0.6622 (ttt) REVERT: O 57 MET cc_start: 0.8409 (tmm) cc_final: 0.8148 (ttp) REVERT: R 75 MET cc_start: 0.8642 (ttp) cc_final: 0.8154 (mtp) REVERT: S 57 MET cc_start: 0.8196 (tmt) cc_final: 0.7967 (tmt) REVERT: X 1 MET cc_start: 0.5033 (mtt) cc_final: 0.4799 (ttm) REVERT: X 24 TYR cc_start: 0.7746 (m-10) cc_final: 0.7375 (m-10) REVERT: Y 18 VAL cc_start: 0.7911 (t) cc_final: 0.7630 (t) REVERT: a 6 MET cc_start: 0.6975 (mmp) cc_final: 0.6556 (tpt) REVERT: a 116 ASN cc_start: 0.8475 (m-40) cc_final: 0.7891 (m110) outliers start: 20 outliers final: 13 residues processed: 151 average time/residue: 0.1897 time to fit residues: 40.6926 Evaluate side-chains 145 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain R residue 3 ASN Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 245 HIS Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain a residue 259 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 79 optimal weight: 0.0050 chunk 92 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 5 ASN R 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8577 Z= 0.269 Angle : 0.625 8.238 11626 Z= 0.306 Chirality : 0.040 0.292 1415 Planarity : 0.005 0.048 1434 Dihedral : 4.292 54.627 1176 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.13 % Allowed : 13.46 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 3.59 (0.23), residues: 1107 helix: 2.77 (0.15), residues: 961 sheet: None (None), residues: 0 loop : -0.54 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 241 HIS 0.002 0.001 HIS a 245 PHE 0.012 0.001 PHE a 85 TYR 0.013 0.001 TYR M 10 ARG 0.004 0.000 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: I 6 MET cc_start: 0.4796 (ppp) cc_final: 0.3710 (mtm) REVERT: I 16 MET cc_start: 0.8190 (ttm) cc_final: 0.7851 (ttp) REVERT: I 57 MET cc_start: 0.7821 (tmm) cc_final: 0.7546 (ttp) REVERT: J 11 MET cc_start: 0.7886 (tpp) cc_final: 0.7613 (tpt) REVERT: L 75 MET cc_start: 0.7540 (ttt) cc_final: 0.7108 (ttt) REVERT: R 57 MET cc_start: 0.8091 (ttp) cc_final: 0.7762 (ttp) REVERT: R 75 MET cc_start: 0.8658 (ttp) cc_final: 0.8195 (mtp) REVERT: X 24 TYR cc_start: 0.7723 (m-10) cc_final: 0.7360 (m-10) REVERT: Y 18 VAL cc_start: 0.7976 (t) cc_final: 0.7713 (t) REVERT: a 116 ASN cc_start: 0.8557 (m-40) cc_final: 0.7983 (m110) outliers start: 18 outliers final: 18 residues processed: 141 average time/residue: 0.1855 time to fit residues: 37.2451 Evaluate side-chains 146 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain R residue 3 ASN Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 245 HIS Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain a residue 259 LEU Chi-restraints excluded: chain a residue 265 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 61 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8577 Z= 0.235 Angle : 0.611 8.084 11626 Z= 0.300 Chirality : 0.039 0.298 1415 Planarity : 0.005 0.049 1434 Dihedral : 4.281 54.487 1176 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.89 % Allowed : 14.05 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 3.64 (0.23), residues: 1107 helix: 2.80 (0.15), residues: 961 sheet: None (None), residues: 0 loop : -0.57 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 241 HIS 0.002 0.001 HIS a 245 PHE 0.011 0.001 PHE a 85 TYR 0.012 0.001 TYR M 10 ARG 0.004 0.000 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: I 6 MET cc_start: 0.4821 (ppp) cc_final: 0.3620 (mtm) REVERT: I 16 MET cc_start: 0.8169 (ttm) cc_final: 0.7831 (ttp) REVERT: I 57 MET cc_start: 0.7816 (tmm) cc_final: 0.7540 (ttp) REVERT: J 11 MET cc_start: 0.7961 (tpp) cc_final: 0.7694 (tpt) REVERT: L 75 MET cc_start: 0.7518 (ttt) cc_final: 0.7122 (ttt) REVERT: O 57 MET cc_start: 0.8297 (tmm) cc_final: 0.8014 (ttp) REVERT: R 17 MET cc_start: 0.7871 (mmm) cc_final: 0.7584 (mtp) REVERT: R 57 MET cc_start: 0.8062 (ttp) cc_final: 0.7744 (ttp) REVERT: R 75 MET cc_start: 0.8678 (ttp) cc_final: 0.8177 (mtp) REVERT: X 24 TYR cc_start: 0.7706 (m-10) cc_final: 0.7364 (m-10) REVERT: Y 18 VAL cc_start: 0.7976 (t) cc_final: 0.7703 (t) REVERT: a 6 MET cc_start: 0.7069 (mmt) cc_final: 0.6463 (tpt) REVERT: a 116 ASN cc_start: 0.8565 (m-40) cc_final: 0.7990 (m110) outliers start: 16 outliers final: 16 residues processed: 142 average time/residue: 0.1851 time to fit residues: 37.4777 Evaluate side-chains 147 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain R residue 3 ASN Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 245 HIS Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain a residue 259 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.5980 chunk 60 optimal weight: 0.0470 chunk 47 optimal weight: 0.0970 chunk 69 optimal weight: 0.5980 chunk 104 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8577 Z= 0.203 Angle : 0.602 9.100 11626 Z= 0.294 Chirality : 0.038 0.295 1415 Planarity : 0.004 0.049 1434 Dihedral : 4.259 55.203 1176 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.01 % Allowed : 13.81 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 3.74 (0.23), residues: 1107 helix: 2.88 (0.15), residues: 961 sheet: None (None), residues: 0 loop : -0.61 (0.46), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 231 HIS 0.002 0.001 HIS a 245 PHE 0.009 0.001 PHE a 85 TYR 0.011 0.001 TYR M 10 ARG 0.004 0.000 ARG I 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: I 6 MET cc_start: 0.4798 (ppp) cc_final: 0.3569 (mtm) REVERT: I 16 MET cc_start: 0.8139 (ttm) cc_final: 0.7777 (ttp) REVERT: I 57 MET cc_start: 0.7799 (tmm) cc_final: 0.7524 (ttp) REVERT: J 11 MET cc_start: 0.7852 (tpp) cc_final: 0.7551 (tpt) REVERT: L 11 MET cc_start: 0.8268 (tpt) cc_final: 0.7489 (tpt) REVERT: L 75 MET cc_start: 0.7425 (ttt) cc_final: 0.7040 (ttt) REVERT: O 57 MET cc_start: 0.8305 (tmm) cc_final: 0.8040 (ttp) REVERT: R 6 MET cc_start: 0.6092 (ptt) cc_final: 0.5877 (ptm) REVERT: R 17 MET cc_start: 0.7859 (mmm) cc_final: 0.7566 (mtp) REVERT: R 57 MET cc_start: 0.8033 (ttp) cc_final: 0.7709 (ttp) REVERT: R 75 MET cc_start: 0.8661 (ttp) cc_final: 0.8164 (mtp) REVERT: X 24 TYR cc_start: 0.7722 (m-10) cc_final: 0.7301 (m-10) REVERT: Y 18 VAL cc_start: 0.7959 (t) cc_final: 0.7683 (t) REVERT: a 6 MET cc_start: 0.7034 (mmt) cc_final: 0.6471 (tpt) REVERT: a 116 ASN cc_start: 0.8555 (m-40) cc_final: 0.8013 (m110) outliers start: 17 outliers final: 17 residues processed: 147 average time/residue: 0.1826 time to fit residues: 38.3706 Evaluate side-chains 152 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 245 HIS Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain a residue 259 LEU Chi-restraints excluded: chain a residue 265 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.8980 chunk 25 optimal weight: 0.0980 chunk 76 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 0.0020 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.111129 restraints weight = 10156.229| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.27 r_work: 0.3102 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8577 Z= 0.205 Angle : 0.597 10.101 11626 Z= 0.291 Chirality : 0.038 0.288 1415 Planarity : 0.005 0.049 1434 Dihedral : 4.222 56.992 1176 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.13 % Allowed : 13.93 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.23), residues: 1107 helix: 2.93 (0.15), residues: 959 sheet: None (None), residues: 0 loop : -0.75 (0.46), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 39 HIS 0.001 0.001 HIS a 245 PHE 0.010 0.001 PHE a 85 TYR 0.010 0.001 TYR a 11 ARG 0.004 0.000 ARG I 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2014.41 seconds wall clock time: 36 minutes 49.65 seconds (2209.65 seconds total)