Starting phenix.real_space_refine on Tue Dec 12 13:44:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/12_2023/8ump_42381.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/12_2023/8ump_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_42381/12_2023/8ump_42381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/12_2023/8ump_42381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/12_2023/8ump_42381.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/12_2023/8ump_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-1.21rc1-5172/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: 12.00, per 1000 atoms: 0.56 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: 8.10 Conformation dependent library (CDL) restraints added in 4.1 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: 2.02 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: 6.52 Time building geometry restraints manager: 8.75 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.050 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 56.540 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.200 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:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.660 ------------------------------------------------------------------------------- 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 : 2.453 Fit side-chains outliers start: 15 outliers final: 2 residues processed: 261 average time/residue: 1.5489 time to fit residues: 456.5127 Evaluate side-chains 223 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 221 time to evaluate : 2.895 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3311 time to fit residues: 4.1089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 239 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN C 19 ASN C 37 ASN C 90 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21804 Z= 0.203 Angle : 0.467 5.253 29652 Z= 0.241 Chirality : 0.036 0.131 3468 Planarity : 0.003 0.040 3756 Dihedral : 3.624 14.139 2988 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 3.07 % Allowed : 25.78 % Favored : 71.15 % 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: 2.31 (0.16), residues: 2676 helix: 2.24 (0.11), residues: 1824 sheet: -0.33 (0.27), residues: 348 loop : 0.40 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 75 HIS 0.001 0.001 HIS N 95 PHE 0.012 0.001 PHE J 77 TYR 0.016 0.001 TYR Q 27 ARG 0.005 0.001 ARG H 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 310 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 243 time to evaluate : 2.592 Fit side-chains outliers start: 67 outliers final: 21 residues processed: 259 average time/residue: 1.8021 time to fit residues: 516.3643 Evaluate side-chains 236 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 215 time to evaluate : 2.342 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 1.1049 time to fit residues: 29.8599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 163 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 259 optimal weight: 6.9990 chunk 213 optimal weight: 5.9990 chunk 238 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 90 ASN S 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 21804 Z= 0.229 Angle : 0.452 5.493 29652 Z= 0.231 Chirality : 0.036 0.134 3468 Planarity : 0.004 0.061 3756 Dihedral : 3.581 14.964 2988 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.66 % Allowed : 25.96 % Favored : 70.38 % 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: 2.69 (0.16), residues: 2676 helix: 2.55 (0.11), residues: 1824 sheet: -0.14 (0.27), residues: 348 loop : 0.39 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 117 HIS 0.002 0.001 HIS B 95 PHE 0.012 0.001 PHE J 77 TYR 0.011 0.001 TYR H 38 ARG 0.007 0.001 ARG N 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 316 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 236 time to evaluate : 2.719 Fit side-chains revert: symmetry clash outliers start: 80 outliers final: 39 residues processed: 271 average time/residue: 1.5949 time to fit residues: 483.7271 Evaluate side-chains 250 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 211 time to evaluate : 2.443 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 16 residues processed: 24 average time/residue: 0.9524 time to fit residues: 30.2641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 161 optimal weight: 0.9980 chunk 241 optimal weight: 10.0000 chunk 255 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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: 0.8358 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21804 Z= 0.276 Angle : 0.466 6.921 29652 Z= 0.235 Chirality : 0.037 0.137 3468 Planarity : 0.004 0.049 3756 Dihedral : 3.641 15.357 2988 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 4.26 % Allowed : 26.42 % Favored : 69.32 % 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: 2.74 (0.16), residues: 2676 helix: 2.62 (0.11), residues: 1824 sheet: -0.19 (0.27), residues: 348 loop : 0.31 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 90 HIS 0.002 0.001 HIS F 95 PHE 0.013 0.001 PHE J 77 TYR 0.012 0.002 TYR P 73 ARG 0.007 0.001 ARG N 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 331 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 238 time to evaluate : 2.629 Fit side-chains outliers start: 93 outliers final: 53 residues processed: 292 average time/residue: 1.6899 time to fit residues: 547.5038 Evaluate side-chains 274 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 221 time to evaluate : 2.481 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 29 residues processed: 24 average time/residue: 0.9487 time to fit residues: 30.0956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 190 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 229 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 90 ASN W 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 21804 Z= 0.146 Angle : 0.406 7.001 29652 Z= 0.210 Chirality : 0.035 0.133 3468 Planarity : 0.004 0.045 3756 Dihedral : 3.473 15.080 2988 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.43 % Allowed : 27.70 % Favored : 68.86 % 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: 3.06 (0.16), residues: 2676 helix: 2.87 (0.11), residues: 1824 sheet: -0.01 (0.28), residues: 348 loop : 0.36 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP W 75 HIS 0.001 0.000 HIS X 95 PHE 0.010 0.001 PHE P 77 TYR 0.012 0.001 TYR W 76 ARG 0.008 0.000 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 324 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 249 time to evaluate : 2.587 Fit side-chains outliers start: 75 outliers final: 46 residues processed: 295 average time/residue: 1.5411 time to fit residues: 510.8308 Evaluate side-chains 272 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 226 time to evaluate : 2.492 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 24 residues processed: 22 average time/residue: 0.7508 time to fit residues: 23.8548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 62 optimal weight: 0.0040 chunk 255 optimal weight: 2.9990 chunk 212 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.2996 ------------------------------------------------------------------------------- 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: 0.8319 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 21804 Z= 0.172 Angle : 0.425 7.246 29652 Z= 0.215 Chirality : 0.035 0.135 3468 Planarity : 0.004 0.052 3756 Dihedral : 3.450 15.240 2988 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 3.07 % Allowed : 28.89 % Favored : 68.04 % 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: 3.24 (0.16), residues: 2676 helix: 2.98 (0.11), residues: 1824 sheet: 0.13 (0.28), residues: 348 loop : 0.46 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP X 117 HIS 0.001 0.001 HIS X 95 PHE 0.011 0.001 PHE B 77 TYR 0.011 0.001 TYR P 73 ARG 0.009 0.001 ARG V 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 307 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 240 time to evaluate : 2.502 Fit side-chains outliers start: 67 outliers final: 48 residues processed: 279 average time/residue: 1.5810 time to fit residues: 492.6476 Evaluate side-chains 269 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 221 time to evaluate : 2.502 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 26 residues processed: 22 average time/residue: 0.8823 time to fit residues: 26.4632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 254 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.8313 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21804 Z= 0.165 Angle : 0.422 7.612 29652 Z= 0.214 Chirality : 0.035 0.133 3468 Planarity : 0.004 0.051 3756 Dihedral : 3.425 15.562 2988 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.88 % Allowed : 29.35 % Favored : 67.77 % 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: 3.06 (0.11), residues: 1824 sheet: 0.16 (0.29), residues: 348 loop : 0.51 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP X 117 HIS 0.001 0.001 HIS N 95 PHE 0.011 0.001 PHE B 77 TYR 0.012 0.001 TYR P 73 ARG 0.009 0.000 ARG X 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 298 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 235 time to evaluate : 2.488 Fit side-chains outliers start: 63 outliers final: 48 residues processed: 271 average time/residue: 1.5386 time to fit residues: 467.4207 Evaluate side-chains 276 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 228 time to evaluate : 2.457 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 27 residues processed: 21 average time/residue: 0.8158 time to fit residues: 23.6765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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: 0.8332 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21804 Z= 0.210 Angle : 0.449 7.888 29652 Z= 0.225 Chirality : 0.036 0.134 3468 Planarity : 0.004 0.047 3756 Dihedral : 3.484 15.455 2988 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.79 % Allowed : 29.90 % 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: 3.33 (0.16), residues: 2676 helix: 3.06 (0.11), residues: 1824 sheet: 0.10 (0.28), residues: 348 loop : 0.53 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP V 90 HIS 0.001 0.001 HIS X 95 PHE 0.012 0.001 PHE J 77 TYR 0.015 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 289 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 228 time to evaluate : 2.321 Fit side-chains outliers start: 61 outliers final: 43 residues processed: 262 average time/residue: 1.5877 time to fit residues: 465.0985 Evaluate side-chains 264 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 221 time to evaluate : 2.322 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 26 residues processed: 17 average time/residue: 1.0351 time to fit residues: 23.9511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 237 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 224 optimal weight: 7.9990 chunk 236 optimal weight: 0.0670 chunk 155 optimal weight: 1.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- 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: 0.8327 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21804 Z= 0.197 Angle : 0.448 8.209 29652 Z= 0.223 Chirality : 0.036 0.134 3468 Planarity : 0.004 0.047 3756 Dihedral : 3.481 15.504 2988 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.20 % Allowed : 30.77 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.16), residues: 2676 helix: 3.07 (0.11), residues: 1824 sheet: 0.10 (0.29), residues: 348 loop : 0.53 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP V 90 HIS 0.001 0.001 HIS X 95 PHE 0.011 0.001 PHE F 77 TYR 0.015 0.001 TYR P 73 ARG 0.009 0.001 ARG V 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 279 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 231 time to evaluate : 2.559 Fit side-chains outliers start: 48 outliers final: 40 residues processed: 260 average time/residue: 1.6167 time to fit residues: 469.9140 Evaluate side-chains 264 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 224 time to evaluate : 2.420 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 26 residues processed: 14 average time/residue: 0.9416 time to fit residues: 18.7857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.0060 chunk 153 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 242 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 161 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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: 0.8294 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21804 Z= 0.138 Angle : 0.432 8.494 29652 Z= 0.215 Chirality : 0.035 0.133 3468 Planarity : 0.004 0.047 3756 Dihedral : 3.387 15.629 2988 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.56 % Allowed : 31.50 % 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: 3.50 (0.16), residues: 2676 helix: 3.18 (0.11), residues: 1824 sheet: 0.24 (0.29), residues: 348 loop : 0.55 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 117 HIS 0.001 0.000 HIS X 95 PHE 0.010 0.001 PHE D 77 TYR 0.013 0.001 TYR P 73 ARG 0.009 0.000 ARG V 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 269 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 235 time to evaluate : 2.478 Fit side-chains outliers start: 34 outliers final: 32 residues processed: 262 average time/residue: 1.5307 time to fit residues: 452.0079 Evaluate side-chains 257 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 225 time to evaluate : 2.686 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 26 residues processed: 6 average time/residue: 0.6490 time to fit residues: 9.3223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.0970 chunk 64 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.134971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.116526 restraints weight = 25712.343| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.60 r_work: 0.3258 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21804 Z= 0.151 Angle : 0.441 8.490 29652 Z= 0.218 Chirality : 0.035 0.133 3468 Planarity : 0.004 0.063 3756 Dihedral : 3.390 15.736 2988 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.79 % Allowed : 31.18 % Favored : 67.03 % 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: 3.55 (0.16), residues: 2676 helix: 3.20 (0.11), residues: 1824 sheet: 0.31 (0.29), residues: 348 loop : 0.59 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP H 117 HIS 0.001 0.000 HIS X 95 PHE 0.012 0.001 PHE B 77 TYR 0.014 0.001 TYR H 73 ARG 0.009 0.001 ARG D 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7692.30 seconds wall clock time: 137 minutes 29.37 seconds (8249.37 seconds total)