Starting phenix.real_space_refine on Fri Dec 8 20:39:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx5_24725/12_2023/7rx5_24725.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx5_24725/12_2023/7rx5_24725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx5_24725/12_2023/7rx5_24725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx5_24725/12_2023/7rx5_24725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx5_24725/12_2023/7rx5_24725.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx5_24725/12_2023/7rx5_24725.pdb" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 0.068 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: 3 Type Number sf(0) Gaussians C 5640 2.51 5 N 1720 2.21 5 O 1760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9120 Number of models: 1 Model: "" Number of chains: 40 Chain: "B" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "C" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "D" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "E" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "F" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "G" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "H" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "J" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "K" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "L" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "M" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "N" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "O" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "P" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "Q" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "S" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "T" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "U" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "V" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "W" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "X" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "Y" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "Z" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "0" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "1" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "2" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "3" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "4" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "5" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "6" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "7" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "8" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "9" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "a" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "b" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "c" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "d" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 228 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Time building chain proxies: 4.77, per 1000 atoms: 0.52 Number of scatterers: 9120 At special positions: 0 Unit cell: (89.64, 89.64, 105.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1760 8.00 N 1720 7.00 C 5640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.8 seconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 100.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA A 7 " --> pdb=" O GLU A 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA C 7 " --> pdb=" O GLU C 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA D 7 " --> pdb=" O GLU D 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA E 7 " --> pdb=" O GLU E 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA F 7 " --> pdb=" O GLU F 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA G 7 " --> pdb=" O GLU G 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA H 7 " --> pdb=" O GLU H 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA I 7 " --> pdb=" O GLU I 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA J 7 " --> pdb=" O GLU J 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA L 7 " --> pdb=" O GLU L 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA M 7 " --> pdb=" O GLU M 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA N 7 " --> pdb=" O GLU N 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA O 7 " --> pdb=" O GLU O 3 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA P 7 " --> pdb=" O GLU P 3 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA Q 7 " --> pdb=" O GLU Q 3 " (cutoff:3.500A) Processing helix chain 'R' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA R 7 " --> pdb=" O GLU R 3 " (cutoff:3.500A) Processing helix chain 'S' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA S 7 " --> pdb=" O GLU S 3 " (cutoff:3.500A) Processing helix chain 'T' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA T 7 " --> pdb=" O GLU T 3 " (cutoff:3.500A) Processing helix chain 'U' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA U 7 " --> pdb=" O GLU U 3 " (cutoff:3.500A) Processing helix chain 'V' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA V 7 " --> pdb=" O GLU V 3 " (cutoff:3.500A) Processing helix chain 'W' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA W 7 " --> pdb=" O GLU W 3 " (cutoff:3.500A) Processing helix chain 'X' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA X 7 " --> pdb=" O GLU X 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA Y 7 " --> pdb=" O GLU Y 3 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA Z 7 " --> pdb=" O GLU Z 3 " (cutoff:3.500A) Processing helix chain '0' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA 0 7 " --> pdb=" O GLU 0 3 " (cutoff:3.500A) Processing helix chain '1' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA 1 7 " --> pdb=" O GLU 1 3 " (cutoff:3.500A) Processing helix chain '2' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA 2 7 " --> pdb=" O GLU 2 3 " (cutoff:3.500A) Processing helix chain '3' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA 3 7 " --> pdb=" O GLU 3 3 " (cutoff:3.500A) Processing helix chain '4' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA 4 7 " --> pdb=" O GLU 4 3 " (cutoff:3.500A) Processing helix chain '5' and resid 1 through 29 removed outlier: 3.912A pdb=" N ALA 5 7 " --> pdb=" O GLU 5 3 " (cutoff:3.500A) Processing helix chain '6' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA 6 7 " --> pdb=" O GLU 6 3 " (cutoff:3.500A) Processing helix chain '7' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA 7 7 " --> pdb=" O GLU 7 3 " (cutoff:3.500A) Processing helix chain '8' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA 8 7 " --> pdb=" O GLU 8 3 " (cutoff:3.500A) Processing helix chain '9' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA 9 7 " --> pdb=" O GLU 9 3 " (cutoff:3.500A) Processing helix chain 'a' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA a 7 " --> pdb=" O GLU a 3 " (cutoff:3.500A) Processing helix chain 'b' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA b 7 " --> pdb=" O GLU b 3 " (cutoff:3.500A) Processing helix chain 'c' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA c 7 " --> pdb=" O GLU c 3 " (cutoff:3.500A) Processing helix chain 'd' and resid 1 through 29 removed outlier: 3.911A pdb=" N ALA d 7 " --> pdb=" O GLU d 3 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2880 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 1720 1.29 - 1.35: 1626 1.35 - 1.42: 374 1.42 - 1.48: 1240 1.48 - 1.54: 4200 Bond restraints: 9160 Sorted by residual: bond pdb=" N ILE B 18 " pdb=" CA ILE B 18 " ideal model delta sigma weight residual 1.461 1.466 -0.005 1.19e-02 7.06e+03 1.74e-01 bond pdb=" N ILE C 18 " pdb=" CA ILE C 18 " ideal model delta sigma weight residual 1.461 1.466 -0.005 1.19e-02 7.06e+03 1.74e-01 bond pdb=" N HIS F 22 " pdb=" CA HIS F 22 " ideal model delta sigma weight residual 1.459 1.464 -0.005 1.21e-02 6.83e+03 1.50e-01 bond pdb=" N HIS G 22 " pdb=" CA HIS G 22 " ideal model delta sigma weight residual 1.459 1.464 -0.005 1.21e-02 6.83e+03 1.50e-01 bond pdb=" N ILE N 18 " pdb=" CA ILE N 18 " ideal model delta sigma weight residual 1.461 1.465 -0.004 1.19e-02 7.06e+03 1.33e-01 ... (remaining 9155 not shown) Histogram of bond angle deviations from ideal: 106.11 - 111.13: 3562 111.13 - 116.15: 2330 116.15 - 121.18: 4508 121.18 - 126.20: 1840 126.20 - 131.22: 40 Bond angle restraints: 12280 Sorted by residual: angle pdb=" C ILE N 25 " pdb=" CA ILE N 25 " pdb=" CB ILE N 25 " ideal model delta sigma weight residual 111.97 110.97 1.00 1.28e+00 6.10e-01 6.07e-01 angle pdb=" C ILE O 25 " pdb=" CA ILE O 25 " pdb=" CB ILE O 25 " ideal model delta sigma weight residual 111.97 110.97 1.00 1.28e+00 6.10e-01 6.07e-01 angle pdb=" C ILE 8 25 " pdb=" CA ILE 8 25 " pdb=" CB ILE 8 25 " ideal model delta sigma weight residual 111.97 110.98 0.99 1.28e+00 6.10e-01 5.95e-01 angle pdb=" C ILE 9 25 " pdb=" CA ILE 9 25 " pdb=" CB ILE 9 25 " ideal model delta sigma weight residual 111.97 110.98 0.99 1.28e+00 6.10e-01 5.95e-01 angle pdb=" C ILE c 25 " pdb=" CA ILE c 25 " pdb=" CB ILE c 25 " ideal model delta sigma weight residual 111.97 110.99 0.98 1.28e+00 6.10e-01 5.82e-01 ... (remaining 12275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.23: 4440 7.23 - 14.46: 680 14.46 - 21.69: 320 21.69 - 28.91: 200 28.91 - 36.14: 160 Dihedral angle restraints: 5800 sinusoidal: 2320 harmonic: 3480 Sorted by residual: dihedral pdb=" CB ARG H 13 " pdb=" CG ARG H 13 " pdb=" CD ARG H 13 " pdb=" NE ARG H 13 " ideal model delta sinusoidal sigma weight residual -180.00 -143.86 -36.14 3 1.50e+01 4.44e-03 6.24e+00 dihedral pdb=" CB ARG I 13 " pdb=" CG ARG I 13 " pdb=" CD ARG I 13 " pdb=" NE ARG I 13 " ideal model delta sinusoidal sigma weight residual -180.00 -143.86 -36.14 3 1.50e+01 4.44e-03 6.24e+00 dihedral pdb=" CB ARG 7 13 " pdb=" CG ARG 7 13 " pdb=" CD ARG 7 13 " pdb=" NE ARG 7 13 " ideal model delta sinusoidal sigma weight residual -180.00 -143.86 -36.14 3 1.50e+01 4.44e-03 6.24e+00 ... (remaining 5797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.017: 782 0.017 - 0.035: 440 0.035 - 0.052: 58 0.052 - 0.070: 40 0.070 - 0.087: 80 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CA ILE H 25 " pdb=" N ILE H 25 " pdb=" C ILE H 25 " pdb=" CB ILE H 25 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.09 2.00e-01 2.50e+01 1.89e-01 chirality pdb=" CA ILE I 25 " pdb=" N ILE I 25 " pdb=" C ILE I 25 " pdb=" CB ILE I 25 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.09 2.00e-01 2.50e+01 1.89e-01 chirality pdb=" CA ILE O 25 " pdb=" N ILE O 25 " pdb=" C ILE O 25 " pdb=" CB ILE O 25 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.09 2.00e-01 2.50e+01 1.86e-01 ... (remaining 1397 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 22 " 0.003 2.00e-02 2.50e+03 2.68e-03 1.07e-01 pdb=" CG HIS D 22 " -0.006 2.00e-02 2.50e+03 pdb=" ND1 HIS D 22 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS D 22 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS D 22 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS D 22 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 22 " 0.003 2.00e-02 2.50e+03 2.68e-03 1.07e-01 pdb=" CG HIS E 22 " -0.006 2.00e-02 2.50e+03 pdb=" ND1 HIS E 22 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS E 22 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS E 22 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS E 22 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS Y 22 " 0.002 2.00e-02 2.50e+03 2.65e-03 1.05e-01 pdb=" CG HIS Y 22 " -0.006 2.00e-02 2.50e+03 pdb=" ND1 HIS Y 22 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS Y 22 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS Y 22 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS Y 22 " 0.000 2.00e-02 2.50e+03 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2424 2.81 - 3.33: 9756 3.33 - 3.86: 15358 3.86 - 4.38: 18176 4.38 - 4.90: 29488 Nonbonded interactions: 75202 Sorted by model distance: nonbonded pdb=" OE1 GLN Y 29 " pdb=" NH1 ARG 0 13 " model vdw 2.288 2.520 nonbonded pdb=" OE1 GLN Z 29 " pdb=" NH1 ARG 1 13 " model vdw 2.288 2.520 nonbonded pdb=" OE1 GLN S 29 " pdb=" NH1 ARG U 13 " model vdw 2.288 2.520 nonbonded pdb=" OE1 GLN R 29 " pdb=" NH1 ARG T 13 " model vdw 2.288 2.520 nonbonded pdb=" OE1 GLN U 29 " pdb=" NH1 ARG V 13 " model vdw 2.288 2.520 ... (remaining 75197 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 '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 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: 6.910 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 26.540 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.008 9160 Z= 0.117 Angle : 0.246 1.318 12280 Z= 0.156 Chirality : 0.029 0.087 1400 Planarity : 0.001 0.006 1640 Dihedral : 11.982 36.141 3480 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.54 (0.24), residues: 1080 helix: 2.95 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS Y 22 TYR 0.002 0.001 TYR T 15 ARG 0.001 0.000 ARG P 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.025 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.4302 time to fit residues: 41.9688 Evaluate side-chains 80 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.8345 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.059 9160 Z= 0.892 Angle : 0.725 4.125 12280 Z= 0.412 Chirality : 0.050 0.102 1400 Planarity : 0.007 0.056 1640 Dihedral : 3.773 7.287 1240 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: 1.10 (0.24), residues: 1080 helix: 0.82 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS K 22 TYR 0.013 0.003 TYR b 15 ARG 0.009 0.002 ARG T 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.085 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.5305 time to fit residues: 36.8022 Evaluate side-chains 58 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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: 0.8298 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.036 9160 Z= 0.517 Angle : 0.485 2.591 12280 Z= 0.278 Chirality : 0.038 0.097 1400 Planarity : 0.005 0.035 1640 Dihedral : 3.610 7.341 1240 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % 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: 1.52 (0.24), residues: 1080 helix: 1.08 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS J 22 TYR 0.008 0.002 TYR a 15 ARG 0.005 0.001 ARG T 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.076 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.5207 time to fit residues: 38.9026 Evaluate side-chains 62 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.8250 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 9160 Z= 0.299 Angle : 0.353 3.553 12280 Z= 0.205 Chirality : 0.032 0.095 1400 Planarity : 0.003 0.021 1640 Dihedral : 3.451 7.067 1240 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % 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: 2.63 (0.23), residues: 1080 helix: 1.77 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 22 TYR 0.005 0.001 TYR b 15 ARG 0.003 0.000 ARG U 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.962 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.4754 time to fit residues: 39.1904 Evaluate side-chains 68 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.955 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.8194 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 9160 Z= 0.165 Angle : 0.277 2.855 12280 Z= 0.164 Chirality : 0.030 0.097 1400 Planarity : 0.002 0.012 1640 Dihedral : 3.340 6.582 1240 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % 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: 3.87 (0.23), residues: 1080 helix: 2.53 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS S 22 TYR 0.003 0.001 TYR a 15 ARG 0.001 0.000 ARG U 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.279 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.4497 time to fit residues: 40.4357 Evaluate side-chains 74 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8164 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9160 Z= 0.136 Angle : 0.284 3.952 12280 Z= 0.166 Chirality : 0.029 0.099 1400 Planarity : 0.001 0.008 1640 Dihedral : 3.242 6.489 1240 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.72 (0.22), residues: 1080 helix: 3.06 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS 0 22 TYR 0.002 0.000 TYR a 15 ARG 0.001 0.000 ARG S 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.4270 time to fit residues: 40.6690 Evaluate side-chains 78 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.8222 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 9160 Z= 0.254 Angle : 0.327 3.255 12280 Z= 0.188 Chirality : 0.032 0.100 1400 Planarity : 0.002 0.016 1640 Dihedral : 3.252 7.423 1240 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.34 (0.22), residues: 1080 helix: 2.83 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 22 TYR 0.003 0.001 TYR b 15 ARG 0.002 0.000 ARG 4 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.4583 time to fit residues: 39.9269 Evaluate side-chains 72 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.8223 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 9160 Z= 0.255 Angle : 0.325 2.880 12280 Z= 0.188 Chirality : 0.032 0.100 1400 Planarity : 0.002 0.017 1640 Dihedral : 3.282 8.644 1240 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.24 (0.22), residues: 1080 helix: 2.77 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS R 22 TYR 0.003 0.001 TYR b 15 ARG 0.002 0.000 ARG U 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.927 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.4540 time to fit residues: 39.5941 Evaluate side-chains 72 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8175 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 9160 Z= 0.150 Angle : 0.275 2.944 12280 Z= 0.162 Chirality : 0.030 0.101 1400 Planarity : 0.002 0.012 1640 Dihedral : 3.255 8.806 1240 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.85 (0.22), residues: 1080 helix: 3.14 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS a 22 TYR 0.003 0.001 TYR b 15 ARG 0.001 0.000 ARG 4 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.107 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.4352 time to fit residues: 41.6093 Evaluate side-chains 78 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 63 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8150 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9160 Z= 0.131 Angle : 0.285 5.683 12280 Z= 0.167 Chirality : 0.029 0.104 1400 Planarity : 0.001 0.009 1640 Dihedral : 3.211 9.066 1240 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: 5.26 (0.22), residues: 1080 helix: 3.39 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS b 22 TYR 0.002 0.000 TYR b 15 ARG 0.001 0.000 ARG 4 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.199 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.4465 time to fit residues: 42.5101 Evaluate side-chains 78 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 26 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.166270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.138056 restraints weight = 8605.283| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.12 r_work: 0.2866 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9160 Z= 0.199 Angle : 0.317 3.575 12280 Z= 0.182 Chirality : 0.031 0.102 1400 Planarity : 0.002 0.012 1640 Dihedral : 3.211 9.421 1240 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % 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: 5.01 (0.22), residues: 1080 helix: 3.24 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS I 22 TYR 0.003 0.000 TYR b 15 ARG 0.001 0.000 ARG T 13 =============================================================================== Job complete usr+sys time: 1732.87 seconds wall clock time: 32 minutes 27.04 seconds (1947.04 seconds total)