Starting phenix.real_space_refine on Sun May 12 09:39:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/05_2024/8ump_42381.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/05_2024/8ump_42381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/05_2024/8ump_42381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/05_2024/8ump_42381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/05_2024/8ump_42381.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/05_2024/8ump_42381.pdb" } resolution = 2.92 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= 0.003 sd= 0.046 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 24 5.16 5 C 13764 2.51 5 N 3564 2.21 5 O 4080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 21432 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "B" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "C" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "E" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "F" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "G" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "H" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "I" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "J" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "K" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "M" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "N" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "O" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "P" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "Q" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "R" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "S" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "T" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "U" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "V" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "W" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "X" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Time building chain proxies: 11.19, per 1000 atoms: 0.52 Number of scatterers: 21432 At special positions: 0 Unit cell: (138.938, 131.625, 126.75, 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 24 16.00 O 4080 8.00 N 3564 7.00 C 13764 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: 8.05 Conformation dependent library (CDL) restraints added in 3.8 seconds 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5232 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 24 sheets defined 66.1% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 Processing helix chain 'A' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 52 Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 112 through 121 Processing helix chain 'C' and resid 2 through 17 Processing helix chain 'C' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 52 Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'C' and resid 71 through 85 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 105 through 121 Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 83 through 95 Processing helix chain 'D' and resid 112 through 121 Processing helix chain 'E' and resid 2 through 17 Processing helix chain 'E' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 52 Processing helix chain 'E' and resid 53 through 68 Processing helix chain 'E' and resid 71 through 85 Processing helix chain 'E' and resid 87 through 102 Processing helix chain 'E' and resid 105 through 121 Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 83 through 95 Processing helix chain 'F' and resid 112 through 121 Processing helix chain 'G' and resid 2 through 17 Processing helix chain 'G' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 52 Processing helix chain 'G' and resid 53 through 68 Processing helix chain 'G' and resid 71 through 85 Processing helix chain 'G' and resid 87 through 102 Processing helix chain 'G' and resid 105 through 121 Processing helix chain 'H' and resid 32 through 46 Processing helix chain 'H' and resid 83 through 95 Processing helix chain 'H' and resid 112 through 121 Processing helix chain 'I' and resid 2 through 17 Processing helix chain 'I' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS I 33 " --> pdb=" O LEU I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 52 Processing helix chain 'I' and resid 53 through 68 Processing helix chain 'I' and resid 71 through 85 Processing helix chain 'I' and resid 87 through 102 Processing helix chain 'I' and resid 105 through 121 Processing helix chain 'J' and resid 32 through 46 Processing helix chain 'J' and resid 83 through 95 Processing helix chain 'J' and resid 112 through 121 Processing helix chain 'K' and resid 2 through 17 Processing helix chain 'K' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 52 Processing helix chain 'K' and resid 53 through 68 Processing helix chain 'K' and resid 71 through 85 Processing helix chain 'K' and resid 87 through 102 Processing helix chain 'K' and resid 105 through 121 Processing helix chain 'L' and resid 32 through 46 Processing helix chain 'L' and resid 83 through 95 Processing helix chain 'L' and resid 112 through 121 Processing helix chain 'M' and resid 2 through 17 Processing helix chain 'M' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS M 33 " --> pdb=" O LEU M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 52 Processing helix chain 'M' and resid 53 through 68 Processing helix chain 'M' and resid 71 through 85 Processing helix chain 'M' and resid 87 through 102 Processing helix chain 'M' and resid 105 through 121 Processing helix chain 'N' and resid 32 through 46 Processing helix chain 'N' and resid 83 through 95 Processing helix chain 'N' and resid 112 through 121 Processing helix chain 'O' and resid 2 through 17 Processing helix chain 'O' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS O 33 " --> pdb=" O LEU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 52 Processing helix chain 'O' and resid 53 through 68 Processing helix chain 'O' and resid 71 through 85 Processing helix chain 'O' and resid 87 through 102 Processing helix chain 'O' and resid 105 through 121 Processing helix chain 'P' and resid 32 through 46 Processing helix chain 'P' and resid 83 through 95 Processing helix chain 'P' and resid 112 through 121 Processing helix chain 'Q' and resid 2 through 17 Processing helix chain 'Q' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS Q 33 " --> pdb=" O LEU Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 52 Processing helix chain 'Q' and resid 53 through 68 Processing helix chain 'Q' and resid 71 through 85 Processing helix chain 'Q' and resid 87 through 102 Processing helix chain 'Q' and resid 105 through 121 Processing helix chain 'R' and resid 32 through 46 Processing helix chain 'R' and resid 83 through 95 Processing helix chain 'R' and resid 112 through 121 Processing helix chain 'S' and resid 2 through 17 Processing helix chain 'S' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS S 33 " --> pdb=" O LEU S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 52 Processing helix chain 'S' and resid 53 through 68 Processing helix chain 'S' and resid 71 through 85 Processing helix chain 'S' and resid 87 through 102 Processing helix chain 'S' and resid 105 through 121 Processing helix chain 'T' and resid 32 through 46 Processing helix chain 'T' and resid 83 through 95 Processing helix chain 'T' and resid 112 through 121 Processing helix chain 'U' and resid 2 through 17 Processing helix chain 'U' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS U 33 " --> pdb=" O LEU U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 52 Processing helix chain 'U' and resid 53 through 68 Processing helix chain 'U' and resid 71 through 85 Processing helix chain 'U' and resid 87 through 102 Processing helix chain 'U' and resid 105 through 121 Processing helix chain 'V' and resid 32 through 46 Processing helix chain 'V' and resid 83 through 95 Processing helix chain 'V' and resid 112 through 121 Processing helix chain 'W' and resid 2 through 17 Processing helix chain 'W' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS W 33 " --> pdb=" O LEU W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 52 Processing helix chain 'W' and resid 53 through 68 Processing helix chain 'W' and resid 71 through 85 Processing helix chain 'W' and resid 87 through 102 Processing helix chain 'W' and resid 105 through 121 Processing helix chain 'X' and resid 32 through 46 Processing helix chain 'X' and resid 83 through 95 Processing helix chain 'X' and resid 112 through 121 Processing sheet with id= 1, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= 2, first strand: chain 'B' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU B 51 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 17 through 19 Processing sheet with id= 4, first strand: chain 'D' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU D 51 " --> pdb=" O LYS D 78 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'F' and resid 17 through 19 Processing sheet with id= 6, first strand: chain 'F' and resid 51 through 63 removed outlier: 3.796A pdb=" N GLU F 51 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'H' and resid 17 through 19 Processing sheet with id= 8, first strand: chain 'H' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU H 51 " --> pdb=" O LYS H 78 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'J' and resid 17 through 19 Processing sheet with id= 10, first strand: chain 'J' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU J 51 " --> pdb=" O LYS J 78 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'L' and resid 17 through 19 Processing sheet with id= 12, first strand: chain 'L' and resid 51 through 63 removed outlier: 3.798A pdb=" N GLU L 51 " --> pdb=" O LYS L 78 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'N' and resid 17 through 19 Processing sheet with id= 14, first strand: chain 'N' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU N 51 " --> pdb=" O LYS N 78 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'P' and resid 17 through 19 Processing sheet with id= 16, first strand: chain 'P' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU P 51 " --> pdb=" O LYS P 78 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'R' and resid 17 through 19 Processing sheet with id= 18, first strand: chain 'R' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU R 51 " --> pdb=" O LYS R 78 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'T' and resid 17 through 19 Processing sheet with id= 20, first strand: chain 'T' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU T 51 " --> pdb=" O LYS T 78 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'V' and resid 17 through 19 Processing sheet with id= 22, first strand: chain 'V' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU V 51 " --> pdb=" O LYS V 78 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'X' and resid 17 through 19 Processing sheet with id= 24, first strand: chain 'X' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU X 51 " --> pdb=" O LYS X 78 " (cutoff:3.500A) 1632 hydrogen bonds defined for protein. 4824 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: 7.07 Time building geometry restraints manager: 8.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6996 1.34 - 1.46: 4834 1.46 - 1.58: 9926 1.58 - 1.70: 12 1.70 - 1.82: 36 Bond restraints: 21804 Sorted by residual: bond pdb=" CB PRO X 100 " pdb=" CG PRO X 100 " ideal model delta sigma weight residual 1.492 1.656 -0.164 5.00e-02 4.00e+02 1.07e+01 bond pdb=" CB PRO R 100 " pdb=" CG PRO R 100 " ideal model delta sigma weight residual 1.492 1.656 -0.164 5.00e-02 4.00e+02 1.07e+01 bond pdb=" CB PRO P 100 " pdb=" CG PRO P 100 " ideal model delta sigma weight residual 1.492 1.655 -0.163 5.00e-02 4.00e+02 1.07e+01 bond pdb=" CB PRO D 100 " pdb=" CG PRO D 100 " ideal model delta sigma weight residual 1.492 1.655 -0.163 5.00e-02 4.00e+02 1.07e+01 bond pdb=" CB PRO L 100 " pdb=" CG PRO L 100 " ideal model delta sigma weight residual 1.492 1.655 -0.163 5.00e-02 4.00e+02 1.07e+01 ... (remaining 21799 not shown) Histogram of bond angle deviations from ideal: 95.17 - 103.42: 214 103.42 - 111.66: 10646 111.66 - 119.91: 8690 119.91 - 128.15: 9970 128.15 - 136.39: 132 Bond angle restraints: 29652 Sorted by residual: angle pdb=" CA PRO L 100 " pdb=" N PRO L 100 " pdb=" CD PRO L 100 " ideal model delta sigma weight residual 112.00 96.97 15.03 1.40e+00 5.10e-01 1.15e+02 angle pdb=" CA PRO P 100 " pdb=" N PRO P 100 " pdb=" CD PRO P 100 " ideal model delta sigma weight residual 112.00 96.97 15.03 1.40e+00 5.10e-01 1.15e+02 angle pdb=" CA PRO X 100 " pdb=" N PRO X 100 " pdb=" CD PRO X 100 " ideal model delta sigma weight residual 112.00 96.97 15.03 1.40e+00 5.10e-01 1.15e+02 angle pdb=" CA PRO N 100 " pdb=" N PRO N 100 " pdb=" CD PRO N 100 " ideal model delta sigma weight residual 112.00 96.97 15.03 1.40e+00 5.10e-01 1.15e+02 angle pdb=" CA PRO R 100 " pdb=" N PRO R 100 " pdb=" CD PRO R 100 " ideal model delta sigma weight residual 112.00 96.98 15.02 1.40e+00 5.10e-01 1.15e+02 ... (remaining 29647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 11030 17.47 - 34.93: 1570 34.93 - 52.40: 480 52.40 - 69.86: 132 69.86 - 87.33: 36 Dihedral angle restraints: 13248 sinusoidal: 5160 harmonic: 8088 Sorted by residual: dihedral pdb=" CA ASN W 37 " pdb=" CB ASN W 37 " pdb=" CG ASN W 37 " pdb=" OD1 ASN W 37 " ideal model delta sinusoidal sigma weight residual 120.00 -172.87 -67.13 2 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASN G 37 " pdb=" CB ASN G 37 " pdb=" CG ASN G 37 " pdb=" OD1 ASN G 37 " ideal model delta sinusoidal sigma weight residual 120.00 -172.88 -67.12 2 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASN M 37 " pdb=" CB ASN M 37 " pdb=" CG ASN M 37 " pdb=" OD1 ASN M 37 " ideal model delta sinusoidal sigma weight residual 120.00 -172.88 -67.12 2 2.00e+01 2.50e-03 1.02e+01 ... (remaining 13245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3057 0.055 - 0.109: 367 0.109 - 0.163: 32 0.163 - 0.218: 0 0.218 - 0.272: 12 Chirality restraints: 3468 Sorted by residual: chirality pdb=" CA PRO X 100 " pdb=" N PRO X 100 " pdb=" C PRO X 100 " pdb=" CB PRO X 100 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA PRO P 100 " pdb=" N PRO P 100 " pdb=" C PRO P 100 " pdb=" CB PRO P 100 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA PRO F 100 " pdb=" N PRO F 100 " pdb=" C PRO F 100 " pdb=" CB PRO F 100 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3465 not shown) Planarity restraints: 3756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 99 " 0.060 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO F 100 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO F 100 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 100 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU X 99 " -0.060 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO X 100 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO X 100 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO X 100 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU L 99 " -0.060 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO L 100 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO L 100 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 100 " -0.045 5.00e-02 4.00e+02 ... (remaining 3753 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3606 2.76 - 3.30: 19381 3.30 - 3.83: 35712 3.83 - 4.37: 44013 4.37 - 4.90: 78614 Nonbonded interactions: 181326 Sorted by model distance: nonbonded pdb=" OH TYR U 76 " pdb=" OE2 GLU V 45 " model vdw 2.226 2.440 nonbonded pdb=" OH TYR I 76 " pdb=" OE2 GLU J 45 " model vdw 2.227 2.440 nonbonded pdb=" OH TYR G 76 " pdb=" OE2 GLU H 45 " model vdw 2.227 2.440 nonbonded pdb=" OH TYR S 76 " pdb=" OE2 GLU T 45 " model vdw 2.227 2.440 nonbonded pdb=" OH TYR C 76 " pdb=" OE2 GLU D 45 " model vdw 2.227 2.440 ... (remaining 181321 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 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } 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: 0.850 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: 4.800 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 56.230 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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 : 0.007 0.164 21804 Z= 0.445 Angle : 0.736 15.033 29652 Z= 0.390 Chirality : 0.041 0.272 3468 Planarity : 0.006 0.081 3756 Dihedral : 19.060 87.331 8016 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.69 % Allowed : 32.88 % Favored : 66.44 % 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: 1.18 (0.15), residues: 2676 helix: 1.38 (0.11), residues: 1764 sheet: -0.63 (0.25), residues: 348 loop : 0.14 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 90 HIS 0.002 0.001 HIS F 95 PHE 0.008 0.001 PHE D 77 TYR 0.016 0.002 TYR X 73 ARG 0.011 0.001 ARG P 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 260 time to evaluate : 2.393 Fit side-chains REVERT: G 5 GLU cc_start: 0.7655 (mp0) cc_final: 0.7157 (mm-30) REVERT: K 5 GLU cc_start: 0.7585 (mp0) cc_final: 0.7253 (mm-30) REVERT: N 115 ARG cc_start: 0.7073 (ttt-90) cc_final: 0.6760 (ttt-90) REVERT: O 5 GLU cc_start: 0.7624 (mp0) cc_final: 0.7250 (mm-30) REVERT: P 81 ARG cc_start: 0.7986 (ptp90) cc_final: 0.7771 (ptt-90) REVERT: V 83 ARG cc_start: 0.8663 (mtp180) cc_final: 0.8373 (mmt180) outliers start: 15 outliers final: 2 residues processed: 261 average time/residue: 1.5798 time to fit residues: 464.5257 Evaluate side-chains 226 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 224 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain U residue 89 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.6980 chunk 200 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 239 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN C 19 ASN C 37 ASN E 37 ASN G 37 ASN G 90 ASN I 37 ASN I 90 ASN K 37 ASN M 37 ASN M 90 ASN O 37 ASN Q 37 ASN S 37 ASN U 37 ASN U 90 ASN W 37 ASN W 90 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21804 Z= 0.191 Angle : 0.459 5.437 29652 Z= 0.237 Chirality : 0.035 0.129 3468 Planarity : 0.003 0.040 3756 Dihedral : 3.706 25.808 2992 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 3.07 % Allowed : 25.96 % Favored : 70.97 % 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: 2.37 (0.16), residues: 2676 helix: 2.25 (0.11), residues: 1824 sheet: 0.14 (0.27), residues: 324 loop : 0.17 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 75 HIS 0.001 0.000 HIS P 95 PHE 0.012 0.001 PHE J 77 TYR 0.016 0.001 TYR Q 27 ARG 0.006 0.001 ARG N 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 248 time to evaluate : 2.510 Fit side-chains REVERT: F 100 PRO cc_start: 0.8010 (Cg_endo) cc_final: 0.7616 (Cg_exo) REVERT: G 5 GLU cc_start: 0.7725 (mp0) cc_final: 0.7242 (mm-30) REVERT: H 100 PRO cc_start: 0.7954 (Cg_endo) cc_final: 0.7593 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7652 (mp0) cc_final: 0.7222 (mm-30) REVERT: N 115 ARG cc_start: 0.6974 (ttt-90) cc_final: 0.6516 (ttt-90) REVERT: N 119 ARG cc_start: 0.6721 (mtm180) cc_final: 0.6495 (mtm110) REVERT: O 5 GLU cc_start: 0.7578 (mp0) cc_final: 0.7180 (mm-30) REVERT: P 81 ARG cc_start: 0.7966 (ptp90) cc_final: 0.7743 (ptt-90) REVERT: P 83 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7999 (mtp180) REVERT: P 100 PRO cc_start: 0.8027 (Cg_endo) cc_final: 0.7598 (Cg_exo) REVERT: V 92 GLN cc_start: 0.8046 (mt0) cc_final: 0.7817 (mm110) REVERT: W 32 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7585 (mp) REVERT: X 100 PRO cc_start: 0.7903 (Cg_endo) cc_final: 0.7529 (Cg_exo) outliers start: 67 outliers final: 20 residues processed: 265 average time/residue: 1.8602 time to fit residues: 543.6550 Evaluate side-chains 238 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 217 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain T residue 70 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 240 optimal weight: 0.0980 chunk 259 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 238 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN C 90 ASN E 90 ASN K 90 ASN O 90 ASN Q 90 ASN S 90 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21804 Z= 0.187 Angle : 0.434 5.704 29652 Z= 0.222 Chirality : 0.036 0.133 3468 Planarity : 0.004 0.045 3756 Dihedral : 3.495 14.875 2988 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.62 % Allowed : 25.69 % Favored : 70.70 % 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: 2.79 (0.16), residues: 2676 helix: 2.60 (0.11), residues: 1824 sheet: -0.00 (0.28), residues: 348 loop : 0.43 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 117 HIS 0.001 0.001 HIS F 95 PHE 0.012 0.001 PHE P 77 TYR 0.009 0.001 TYR M 76 ARG 0.005 0.001 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 244 time to evaluate : 2.377 Fit side-chains REVERT: F 100 PRO cc_start: 0.8006 (Cg_endo) cc_final: 0.7685 (Cg_exo) REVERT: H 100 PRO cc_start: 0.7981 (Cg_endo) cc_final: 0.7676 (Cg_exo) REVERT: P 81 ARG cc_start: 0.8013 (ptp90) cc_final: 0.7807 (ptt-90) REVERT: P 100 PRO cc_start: 0.8074 (Cg_endo) cc_final: 0.7775 (Cg_exo) REVERT: X 100 PRO cc_start: 0.7935 (Cg_endo) cc_final: 0.7634 (Cg_exo) outliers start: 79 outliers final: 34 residues processed: 278 average time/residue: 1.5563 time to fit residues: 484.4509 Evaluate side-chains 245 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 211 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 70 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 55 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 255 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21804 Z= 0.246 Angle : 0.456 7.186 29652 Z= 0.231 Chirality : 0.037 0.137 3468 Planarity : 0.004 0.043 3756 Dihedral : 3.581 15.840 2988 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 3.94 % Allowed : 26.19 % Favored : 69.87 % 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: 2.84 (0.16), residues: 2676 helix: 2.68 (0.11), residues: 1824 sheet: -0.03 (0.28), residues: 348 loop : 0.31 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 90 HIS 0.002 0.001 HIS F 95 PHE 0.013 0.001 PHE J 77 TYR 0.011 0.001 TYR P 73 ARG 0.007 0.001 ARG F 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 238 time to evaluate : 2.419 Fit side-chains REVERT: A 33 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6750 (tptp) REVERT: F 100 PRO cc_start: 0.8091 (Cg_endo) cc_final: 0.7866 (Cg_exo) REVERT: F 115 ARG cc_start: 0.6985 (ttt-90) cc_final: 0.6704 (ttt90) REVERT: G 33 LYS cc_start: 0.7653 (mptt) cc_final: 0.7179 (mmmm) REVERT: H 100 PRO cc_start: 0.8054 (Cg_endo) cc_final: 0.7809 (Cg_exo) REVERT: J 61 ARG cc_start: 0.8055 (ptt-90) cc_final: 0.7731 (ptt-90) REVERT: P 61 ARG cc_start: 0.8086 (ptt-90) cc_final: 0.7767 (ptt-90) REVERT: P 81 ARG cc_start: 0.8128 (ptp90) cc_final: 0.7918 (ptt-90) REVERT: P 100 PRO cc_start: 0.8128 (Cg_endo) cc_final: 0.7864 (Cg_exo) REVERT: V 92 GLN cc_start: 0.7988 (mt0) cc_final: 0.7700 (mm110) REVERT: X 100 PRO cc_start: 0.7994 (Cg_endo) cc_final: 0.7750 (Cg_exo) outliers start: 86 outliers final: 52 residues processed: 283 average time/residue: 1.7047 time to fit residues: 535.3628 Evaluate side-chains 267 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 214 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 70 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain V residue 121 SER Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 121 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 190 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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: 0.8307 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21804 Z= 0.145 Angle : 0.405 7.163 29652 Z= 0.208 Chirality : 0.035 0.132 3468 Planarity : 0.004 0.044 3756 Dihedral : 3.443 15.377 2988 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.88 % Allowed : 28.53 % Favored : 68.59 % 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: 3.10 (0.16), residues: 2676 helix: 2.89 (0.11), residues: 1824 sheet: 0.08 (0.28), residues: 348 loop : 0.34 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP W 75 HIS 0.001 0.000 HIS X 95 PHE 0.010 0.001 PHE T 77 TYR 0.013 0.001 TYR U 76 ARG 0.008 0.001 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 242 time to evaluate : 2.447 Fit side-chains REVERT: D 51 GLU cc_start: 0.8502 (tt0) cc_final: 0.7985 (tt0) REVERT: E 33 LYS cc_start: 0.7858 (mmmm) cc_final: 0.7648 (tptp) REVERT: F 100 PRO cc_start: 0.8068 (Cg_endo) cc_final: 0.7828 (Cg_exo) REVERT: F 115 ARG cc_start: 0.7020 (ttt-90) cc_final: 0.6723 (ttt90) REVERT: G 33 LYS cc_start: 0.7361 (mptt) cc_final: 0.7102 (mmmm) REVERT: H 100 PRO cc_start: 0.8031 (Cg_endo) cc_final: 0.7792 (Cg_exo) REVERT: N 100 PRO cc_start: 0.8182 (Cg_endo) cc_final: 0.7812 (Cg_exo) REVERT: P 51 GLU cc_start: 0.8695 (tt0) cc_final: 0.8491 (tt0) REVERT: P 81 ARG cc_start: 0.8054 (ptp90) cc_final: 0.7839 (ptt-90) REVERT: P 100 PRO cc_start: 0.8110 (Cg_endo) cc_final: 0.7839 (Cg_exo) REVERT: R 51 GLU cc_start: 0.8673 (tt0) cc_final: 0.8467 (tt0) REVERT: V 92 GLN cc_start: 0.7985 (mt0) cc_final: 0.7750 (mm110) REVERT: X 100 PRO cc_start: 0.8016 (Cg_endo) cc_final: 0.7788 (Cg_exo) REVERT: X 119 ARG cc_start: 0.6573 (mtm110) cc_final: 0.6327 (mtm110) outliers start: 63 outliers final: 39 residues processed: 270 average time/residue: 1.6410 time to fit residues: 497.1334 Evaluate side-chains 265 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 226 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 70 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain V residue 45 GLU Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain X residue 121 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.3980 chunk 229 optimal weight: 5.9990 chunk 50 optimal weight: 0.0170 chunk 149 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 255 optimal weight: 2.9990 chunk 212 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- 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: 0.8286 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21804 Z= 0.132 Angle : 0.403 7.874 29652 Z= 0.204 Chirality : 0.035 0.131 3468 Planarity : 0.003 0.045 3756 Dihedral : 3.339 15.413 2988 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 3.07 % Allowed : 29.12 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.16), residues: 2676 helix: 3.07 (0.11), residues: 1824 sheet: 0.34 (0.29), residues: 348 loop : 0.38 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP V 117 HIS 0.000 0.000 HIS R 95 PHE 0.010 0.001 PHE B 77 TYR 0.011 0.001 TYR U 76 ARG 0.007 0.000 ARG H 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 241 time to evaluate : 2.284 Fit side-chains REVERT: A 33 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6708 (tptp) REVERT: C 33 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.7054 (mmmm) REVERT: D 51 GLU cc_start: 0.8486 (tt0) cc_final: 0.8025 (tt0) REVERT: F 100 PRO cc_start: 0.8059 (Cg_endo) cc_final: 0.7827 (Cg_exo) REVERT: F 115 ARG cc_start: 0.6989 (ttt-90) cc_final: 0.6683 (ttt90) REVERT: G 33 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.7114 (mmmm) REVERT: H 100 PRO cc_start: 0.8034 (Cg_endo) cc_final: 0.7819 (Cg_exo) REVERT: J 51 GLU cc_start: 0.8839 (tt0) cc_final: 0.8538 (tt0) REVERT: J 100 PRO cc_start: 0.8134 (Cg_endo) cc_final: 0.7730 (Cg_exo) REVERT: K 33 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.7079 (mmmm) REVERT: N 100 PRO cc_start: 0.8137 (Cg_endo) cc_final: 0.7791 (Cg_exo) REVERT: P 81 ARG cc_start: 0.8037 (ptp90) cc_final: 0.7828 (ptt-90) REVERT: P 100 PRO cc_start: 0.8101 (Cg_endo) cc_final: 0.7844 (Cg_exo) REVERT: V 92 GLN cc_start: 0.7972 (mt0) cc_final: 0.7759 (mm110) REVERT: V 100 PRO cc_start: 0.8169 (Cg_endo) cc_final: 0.7847 (Cg_exo) REVERT: X 100 PRO cc_start: 0.8001 (Cg_endo) cc_final: 0.7778 (Cg_exo) REVERT: X 119 ARG cc_start: 0.6549 (mtm110) cc_final: 0.6264 (mtm110) outliers start: 67 outliers final: 42 residues processed: 269 average time/residue: 1.6255 time to fit residues: 487.8084 Evaluate side-chains 274 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 228 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 70 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 121 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 254 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.8324 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21804 Z= 0.206 Angle : 0.443 7.654 29652 Z= 0.222 Chirality : 0.036 0.134 3468 Planarity : 0.004 0.046 3756 Dihedral : 3.422 15.077 2988 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.53 % Allowed : 29.17 % Favored : 67.31 % 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: 3.35 (0.16), residues: 2676 helix: 3.08 (0.11), residues: 1824 sheet: 0.26 (0.29), residues: 348 loop : 0.38 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP X 117 HIS 0.001 0.001 HIS T 95 PHE 0.012 0.001 PHE J 77 TYR 0.014 0.001 TYR P 73 ARG 0.009 0.001 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 233 time to evaluate : 2.426 Fit side-chains REVERT: C 33 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7109 (mmmm) REVERT: F 100 PRO cc_start: 0.8090 (Cg_endo) cc_final: 0.7888 (Cg_exo) REVERT: F 115 ARG cc_start: 0.7037 (ttt-90) cc_final: 0.6729 (ttt90) REVERT: G 33 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.7154 (mmmm) REVERT: H 61 ARG cc_start: 0.8030 (ptt-90) cc_final: 0.7413 (ptt-90) REVERT: H 100 PRO cc_start: 0.8058 (Cg_endo) cc_final: 0.7855 (Cg_exo) REVERT: J 51 GLU cc_start: 0.8928 (tt0) cc_final: 0.8687 (tt0) REVERT: J 61 ARG cc_start: 0.7987 (ptt-90) cc_final: 0.7700 (ptt-90) REVERT: N 100 PRO cc_start: 0.8177 (Cg_endo) cc_final: 0.7836 (Cg_exo) REVERT: P 61 ARG cc_start: 0.8061 (ptt-90) cc_final: 0.7838 (ptt-90) REVERT: P 81 ARG cc_start: 0.8100 (ptp90) cc_final: 0.7886 (ptt-90) REVERT: P 100 PRO cc_start: 0.8119 (Cg_endo) cc_final: 0.7895 (Cg_exo) REVERT: V 92 GLN cc_start: 0.8003 (mt0) cc_final: 0.7734 (mm110) REVERT: V 100 PRO cc_start: 0.8178 (Cg_endo) cc_final: 0.7876 (Cg_exo) REVERT: X 100 PRO cc_start: 0.8010 (Cg_endo) cc_final: 0.7801 (Cg_exo) REVERT: X 119 ARG cc_start: 0.6584 (mtm110) cc_final: 0.6312 (mtm110) outliers start: 77 outliers final: 55 residues processed: 272 average time/residue: 1.6423 time to fit residues: 498.7736 Evaluate side-chains 275 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 218 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 70 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 45 GLU Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain V residue 121 SER Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 121 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.8296 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21804 Z= 0.149 Angle : 0.425 8.177 29652 Z= 0.214 Chirality : 0.035 0.132 3468 Planarity : 0.003 0.048 3756 Dihedral : 3.360 15.084 2988 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 3.30 % Allowed : 29.85 % Favored : 66.85 % 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: 3.46 (0.16), residues: 2676 helix: 3.16 (0.11), residues: 1824 sheet: 0.36 (0.29), residues: 348 loop : 0.38 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP O 75 HIS 0.001 0.000 HIS H 95 PHE 0.010 0.001 PHE J 77 TYR 0.012 0.001 TYR P 73 ARG 0.008 0.000 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 234 time to evaluate : 2.433 Fit side-chains REVERT: C 33 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.7072 (mmmm) REVERT: F 46 LYS cc_start: 0.8561 (ptpt) cc_final: 0.8305 (ptpt) REVERT: F 100 PRO cc_start: 0.8098 (Cg_endo) cc_final: 0.7894 (Cg_exo) REVERT: H 100 PRO cc_start: 0.8042 (Cg_endo) cc_final: 0.7840 (Cg_exo) REVERT: J 51 GLU cc_start: 0.8904 (tt0) cc_final: 0.8652 (tt0) REVERT: J 100 PRO cc_start: 0.8135 (Cg_endo) cc_final: 0.7750 (Cg_exo) REVERT: L 46 LYS cc_start: 0.8706 (ptpp) cc_final: 0.8366 (ptmt) REVERT: M 5 GLU cc_start: 0.7750 (mp0) cc_final: 0.7250 (mm-30) REVERT: N 100 PRO cc_start: 0.8126 (Cg_endo) cc_final: 0.7790 (Cg_exo) REVERT: P 81 ARG cc_start: 0.8055 (ptp90) cc_final: 0.7848 (ptt-90) REVERT: P 100 PRO cc_start: 0.8102 (Cg_endo) cc_final: 0.7881 (Cg_exo) REVERT: R 51 GLU cc_start: 0.8811 (tt0) cc_final: 0.8587 (tt0) REVERT: V 92 GLN cc_start: 0.8004 (mt0) cc_final: 0.7742 (mm110) REVERT: V 100 PRO cc_start: 0.8176 (Cg_endo) cc_final: 0.7866 (Cg_exo) REVERT: X 119 ARG cc_start: 0.6586 (mtm110) cc_final: 0.6325 (mtm110) outliers start: 72 outliers final: 57 residues processed: 267 average time/residue: 1.5822 time to fit residues: 474.0275 Evaluate side-chains 290 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 232 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 70 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 45 GLU Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 121 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 7.9990 chunk 222 optimal weight: 0.9990 chunk 237 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 103 optimal weight: 0.1980 chunk 186 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 214 optimal weight: 0.6980 chunk 224 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21804 Z= 0.152 Angle : 0.427 8.415 29652 Z= 0.213 Chirality : 0.035 0.132 3468 Planarity : 0.004 0.068 3756 Dihedral : 3.347 15.164 2988 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.98 % Allowed : 30.08 % Favored : 66.94 % 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: 3.53 (0.16), residues: 2676 helix: 3.20 (0.11), residues: 1824 sheet: 0.40 (0.30), residues: 348 loop : 0.40 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP L 117 HIS 0.001 0.000 HIS X 95 PHE 0.011 0.001 PHE B 77 TYR 0.013 0.001 TYR P 73 ARG 0.009 0.000 ARG B 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 241 time to evaluate : 2.380 Fit side-chains REVERT: C 33 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.7066 (mmmm) REVERT: F 46 LYS cc_start: 0.8544 (ptpt) cc_final: 0.8321 (ptpt) REVERT: F 100 PRO cc_start: 0.8084 (Cg_endo) cc_final: 0.7879 (Cg_exo) REVERT: H 61 ARG cc_start: 0.7952 (ptt-90) cc_final: 0.7417 (ptt-90) REVERT: J 51 GLU cc_start: 0.8868 (tt0) cc_final: 0.8581 (tt0) REVERT: J 100 PRO cc_start: 0.8136 (Cg_endo) cc_final: 0.7755 (Cg_exo) REVERT: L 46 LYS cc_start: 0.8702 (ptpp) cc_final: 0.8374 (ptmt) REVERT: M 5 GLU cc_start: 0.7800 (mp0) cc_final: 0.7276 (mm-30) REVERT: N 100 PRO cc_start: 0.8134 (Cg_endo) cc_final: 0.7810 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7703 (mp0) cc_final: 0.7273 (mm-30) REVERT: P 81 ARG cc_start: 0.8064 (ptp90) cc_final: 0.7848 (ptt-90) REVERT: P 100 PRO cc_start: 0.8101 (Cg_endo) cc_final: 0.7893 (Cg_exo) REVERT: R 51 GLU cc_start: 0.8828 (tt0) cc_final: 0.8494 (tt0) REVERT: U 32 LEU cc_start: 0.8129 (mm) cc_final: 0.7903 (mp) REVERT: V 92 GLN cc_start: 0.8010 (mt0) cc_final: 0.7748 (mm110) REVERT: V 100 PRO cc_start: 0.8176 (Cg_endo) cc_final: 0.7873 (Cg_exo) REVERT: X 119 ARG cc_start: 0.6581 (mtm110) cc_final: 0.6290 (mtm110) outliers start: 65 outliers final: 53 residues processed: 272 average time/residue: 1.6077 time to fit residues: 489.4103 Evaluate side-chains 290 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 236 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 70 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain V residue 121 SER Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 121 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 263 optimal weight: 0.5980 chunk 242 optimal weight: 0.9980 chunk 209 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 161 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 166 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21804 Z= 0.135 Angle : 0.423 8.689 29652 Z= 0.210 Chirality : 0.035 0.132 3468 Planarity : 0.004 0.068 3756 Dihedral : 3.319 15.260 2988 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.70 % Allowed : 30.49 % Favored : 66.80 % 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: 3.61 (0.16), residues: 2676 helix: 3.25 (0.11), residues: 1824 sheet: 0.46 (0.30), residues: 348 loop : 0.44 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP P 117 HIS 0.001 0.000 HIS H 95 PHE 0.011 0.001 PHE B 77 TYR 0.013 0.001 TYR P 73 ARG 0.009 0.000 ARG B 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 236 time to evaluate : 2.396 Fit side-chains REVERT: B 100 PRO cc_start: 0.8071 (Cg_endo) cc_final: 0.7683 (Cg_exo) REVERT: D 100 PRO cc_start: 0.8041 (Cg_endo) cc_final: 0.7663 (Cg_exo) REVERT: F 100 PRO cc_start: 0.8078 (Cg_endo) cc_final: 0.7870 (Cg_exo) REVERT: H 61 ARG cc_start: 0.7916 (ptt-90) cc_final: 0.7381 (ptt-90) REVERT: J 51 GLU cc_start: 0.8832 (tt0) cc_final: 0.8590 (tt0) REVERT: J 100 PRO cc_start: 0.8127 (Cg_endo) cc_final: 0.7754 (Cg_exo) REVERT: L 46 LYS cc_start: 0.8676 (ptpp) cc_final: 0.8355 (ptmt) REVERT: M 5 GLU cc_start: 0.7810 (mp0) cc_final: 0.7276 (mm-30) REVERT: N 100 PRO cc_start: 0.8148 (Cg_endo) cc_final: 0.7818 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7691 (mp0) cc_final: 0.7259 (mm-30) REVERT: P 81 ARG cc_start: 0.8044 (ptp90) cc_final: 0.7843 (ptt-90) REVERT: Q 33 LYS cc_start: 0.7422 (mptt) cc_final: 0.7192 (mmmm) REVERT: T 51 GLU cc_start: 0.8745 (tt0) cc_final: 0.8465 (tt0) REVERT: U 32 LEU cc_start: 0.8086 (mm) cc_final: 0.7864 (mp) REVERT: V 92 GLN cc_start: 0.7998 (mt0) cc_final: 0.7713 (mm110) REVERT: V 100 PRO cc_start: 0.8156 (Cg_endo) cc_final: 0.7878 (Cg_exo) outliers start: 59 outliers final: 50 residues processed: 264 average time/residue: 1.6156 time to fit residues: 476.7430 Evaluate side-chains 280 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 230 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 70 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain V residue 121 SER Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 121 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 193 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 0.0670 chunk 184 optimal weight: 4.9990 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.116046 restraints weight = 25640.904| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.63 r_work: 0.3246 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21804 Z= 0.159 Angle : 0.438 8.483 29652 Z= 0.217 Chirality : 0.035 0.132 3468 Planarity : 0.004 0.073 3756 Dihedral : 3.347 15.258 2988 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.75 % Allowed : 30.27 % Favored : 66.99 % 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: 3.61 (0.16), residues: 2676 helix: 3.25 (0.11), residues: 1824 sheet: 0.44 (0.30), residues: 348 loop : 0.48 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP L 117 HIS 0.001 0.000 HIS H 95 PHE 0.014 0.001 PHE B 77 TYR 0.015 0.001 TYR P 73 ARG 0.009 0.001 ARG B 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7639.28 seconds wall clock time: 137 minutes 57.64 seconds (8277.64 seconds total)