Starting phenix.real_space_refine on Mon Mar 11 00:12:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q65_13852/03_2024/7q65_13852.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q65_13852/03_2024/7q65_13852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q65_13852/03_2024/7q65_13852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q65_13852/03_2024/7q65_13852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q65_13852/03_2024/7q65_13852.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q65_13852/03_2024/7q65_13852.pdb" } resolution = 3.32 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= 0.001 sd= 0.008 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 3806 2.51 5 N 1056 2.21 5 O 1342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6204 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "B" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "C" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "D" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "E" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "F" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "G" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "H" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "I" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "K" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "M" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "N" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "O" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "P" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "Q" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "R" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "S" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "T" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "U" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "V" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Time building chain proxies: 3.84, per 1000 atoms: 0.62 Number of scatterers: 6204 At special positions: 0 Unit cell: (79.8, 65.1, 77.7, 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 1342 8.00 N 1056 7.00 C 3806 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: 2.72 Conformation dependent library (CDL) restraints added in 1.6 seconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 103 removed outlier: 6.526A pdb=" N THR A 99 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE C 102 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU A 101 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR C 99 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE E 102 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU C 101 " --> pdb=" O PHE E 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR E 99 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE G 102 " --> pdb=" O THR E 99 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU E 101 " --> pdb=" O PHE G 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR G 99 " --> pdb=" O SER I 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE I 102 " --> pdb=" O THR G 99 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU G 101 " --> pdb=" O PHE I 102 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR I 99 " --> pdb=" O SER K 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE K 102 " --> pdb=" O THR I 99 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU I 101 " --> pdb=" O PHE K 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR K 99 " --> pdb=" O SER M 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE M 102 " --> pdb=" O THR K 99 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU K 101 " --> pdb=" O PHE M 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR M 99 " --> pdb=" O SER O 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE O 102 " --> pdb=" O THR M 99 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU M 101 " --> pdb=" O PHE O 102 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR O 99 " --> pdb=" O SER Q 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE Q 102 " --> pdb=" O THR O 99 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU O 101 " --> pdb=" O PHE Q 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR Q 99 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N PHE S 102 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU Q 101 " --> pdb=" O PHE S 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR S 99 " --> pdb=" O SER U 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE U 102 " --> pdb=" O THR S 99 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU S 101 " --> pdb=" O PHE U 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.805A pdb=" N GLY C 121 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY E 121 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY G 121 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY I 121 " --> pdb=" O PHE G 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY K 121 " --> pdb=" O PHE I 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY M 121 " --> pdb=" O PHE K 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY O 121 " --> pdb=" O PHE M 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY Q 121 " --> pdb=" O PHE O 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY S 121 " --> pdb=" O PHE Q 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY U 121 " --> pdb=" O PHE S 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 88 through 89 Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 101 removed outlier: 6.544A pdb=" N SER B 100 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER D 100 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER F 100 " --> pdb=" O LEU H 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER H 100 " --> pdb=" O LEU J 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER J 100 " --> pdb=" O LEU L 101 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER L 100 " --> pdb=" O LEU N 101 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER N 100 " --> pdb=" O LEU P 101 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER P 100 " --> pdb=" O LEU R 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER R 100 " --> pdb=" O LEU T 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER T 100 " --> pdb=" O LEU V 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 104 through 106 removed outlier: 6.323A pdb=" N SER B 104 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER D 104 " --> pdb=" O GLN F 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER F 104 " --> pdb=" O GLN H 105 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER H 104 " --> pdb=" O GLN J 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER J 104 " --> pdb=" O GLN L 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER L 104 " --> pdb=" O GLN N 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER N 104 " --> pdb=" O GLN P 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER P 104 " --> pdb=" O GLN R 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER R 104 " --> pdb=" O GLN T 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER T 104 " --> pdb=" O GLN V 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 111 through 112 Processing sheet with id=AA8, first strand: chain 'B' and resid 118 through 123 removed outlier: 6.843A pdb=" N ASN D 119 " --> pdb=" O GLY B 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE B 120 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY D 121 " --> pdb=" O PHE B 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN F 119 " --> pdb=" O GLY D 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE D 120 " --> pdb=" O ASN F 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY F 121 " --> pdb=" O PHE D 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN H 119 " --> pdb=" O GLY F 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE F 120 " --> pdb=" O ASN H 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY H 121 " --> pdb=" O PHE F 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN J 119 " --> pdb=" O GLY H 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE H 120 " --> pdb=" O ASN J 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY J 121 " --> pdb=" O PHE H 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN L 119 " --> pdb=" O GLY J 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE J 120 " --> pdb=" O ASN L 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY L 121 " --> pdb=" O PHE J 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN N 119 " --> pdb=" O GLY L 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE L 120 " --> pdb=" O ASN N 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY N 121 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN P 119 " --> pdb=" O GLY N 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE N 120 " --> pdb=" O ASN P 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY P 121 " --> pdb=" O PHE N 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN R 119 " --> pdb=" O GLY P 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE P 120 " --> pdb=" O ASN R 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY R 121 " --> pdb=" O PHE P 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN T 119 " --> pdb=" O GLY R 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE R 120 " --> pdb=" O ASN T 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY T 121 " --> pdb=" O PHE R 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN V 119 " --> pdb=" O GLY T 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE T 120 " --> pdb=" O ASN V 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY V 121 " --> pdb=" O PHE T 120 " (cutoff:3.500A) 60 hydrogen bonds defined for protein. 180 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: 1.60 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.28: 1034 1.28 - 1.35: 1023 1.35 - 1.42: 766 1.42 - 1.49: 1544 1.49 - 1.57: 1947 Bond restraints: 6314 Sorted by residual: bond pdb=" CA ASN S 106 " pdb=" CB ASN S 106 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.75e-02 3.27e+03 6.56e+00 bond pdb=" CA ASN U 106 " pdb=" CB ASN U 106 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.75e-02 3.27e+03 6.49e+00 bond pdb=" CA ASN Q 106 " pdb=" CB ASN Q 106 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.75e-02 3.27e+03 6.48e+00 bond pdb=" CA ASN M 106 " pdb=" CB ASN M 106 " ideal model delta sigma weight residual 1.527 1.482 0.044 1.75e-02 3.27e+03 6.43e+00 bond pdb=" CA ASN C 106 " pdb=" CB ASN C 106 " ideal model delta sigma weight residual 1.527 1.482 0.044 1.75e-02 3.27e+03 6.42e+00 ... (remaining 6309 not shown) Histogram of bond angle deviations from ideal: 102.90 - 108.70: 585 108.70 - 114.50: 3001 114.50 - 120.31: 2140 120.31 - 126.11: 2799 126.11 - 131.91: 33 Bond angle restraints: 8558 Sorted by residual: angle pdb=" CA ASN N 106 " pdb=" CB ASN N 106 " pdb=" CG ASN N 106 " ideal model delta sigma weight residual 112.60 118.08 -5.48 1.00e+00 1.00e+00 3.00e+01 angle pdb=" CA ASN V 106 " pdb=" CB ASN V 106 " pdb=" CG ASN V 106 " ideal model delta sigma weight residual 112.60 118.06 -5.46 1.00e+00 1.00e+00 2.99e+01 angle pdb=" CA ASN P 106 " pdb=" CB ASN P 106 " pdb=" CG ASN P 106 " ideal model delta sigma weight residual 112.60 118.06 -5.46 1.00e+00 1.00e+00 2.98e+01 angle pdb=" CA ASN H 106 " pdb=" CB ASN H 106 " pdb=" CG ASN H 106 " ideal model delta sigma weight residual 112.60 118.06 -5.46 1.00e+00 1.00e+00 2.98e+01 angle pdb=" CA ASN L 106 " pdb=" CB ASN L 106 " pdb=" CG ASN L 106 " ideal model delta sigma weight residual 112.60 118.05 -5.45 1.00e+00 1.00e+00 2.97e+01 ... (remaining 8553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.47: 2641 7.47 - 14.94: 604 14.94 - 22.40: 143 22.40 - 29.87: 66 29.87 - 37.34: 22 Dihedral angle restraints: 3476 sinusoidal: 1122 harmonic: 2354 Sorted by residual: dihedral pdb=" CA THR K 85 " pdb=" C THR K 85 " pdb=" N GLY K 86 " pdb=" CA GLY K 86 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA THR I 85 " pdb=" C THR I 85 " pdb=" N GLY I 86 " pdb=" CA GLY I 86 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA THR G 85 " pdb=" C THR G 85 " pdb=" N GLY G 86 " pdb=" CA GLY G 86 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 3473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 654 0.069 - 0.139: 248 0.139 - 0.208: 22 0.208 - 0.277: 33 0.277 - 0.347: 33 Chirality restraints: 990 Sorted by residual: chirality pdb=" CB THR O 94 " pdb=" CA THR O 94 " pdb=" OG1 THR O 94 " pdb=" CG2 THR O 94 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CB THR E 94 " pdb=" CA THR E 94 " pdb=" OG1 THR E 94 " pdb=" CG2 THR E 94 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB THR S 94 " pdb=" CA THR S 94 " pdb=" OG1 THR S 94 " pdb=" CG2 THR S 94 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 987 not shown) Planarity restraints: 1144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN N 106 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C ASN N 106 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN N 106 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN N 107 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 106 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C ASN F 106 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN F 106 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN F 107 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN L 106 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C ASN L 106 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN L 106 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN L 107 " -0.012 2.00e-02 2.50e+03 ... (remaining 1141 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 576 2.71 - 3.26: 6253 3.26 - 3.80: 12009 3.80 - 4.35: 14019 4.35 - 4.90: 28813 Nonbonded interactions: 61670 Sorted by model distance: nonbonded pdb=" O GLY E 93 " pdb=" OG SER G 96 " model vdw 2.159 2.440 nonbonded pdb=" O GLY O 93 " pdb=" OG SER Q 96 " model vdw 2.159 2.440 nonbonded pdb=" O GLY Q 93 " pdb=" OG SER S 96 " model vdw 2.159 2.440 nonbonded pdb=" O GLY K 93 " pdb=" OG SER M 96 " model vdw 2.159 2.440 nonbonded pdb=" O GLY S 93 " pdb=" OG SER U 96 " model vdw 2.159 2.440 ... (remaining 61665 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 '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' } 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: 0.770 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: 0.000 Extract box with map and model: 3.480 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.330 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 : 0.016 0.073 6314 Z= 1.048 Angle : 1.561 10.109 8558 Z= 0.897 Chirality : 0.097 0.347 990 Planarity : 0.006 0.021 1144 Dihedral : 10.100 37.337 1980 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 8.33 % Allowed : 3.18 % Favored : 88.48 % 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: -5.74 (0.13), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.10), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.005 PHE V 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 217 time to evaluate : 0.690 Fit side-chains REVERT: A 89 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8661 (p0) REVERT: A 113 LYS cc_start: 0.8860 (ptpt) cc_final: 0.8125 (mmpt) REVERT: C 89 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8627 (p0) REVERT: H 124 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.9127 (p) REVERT: L 112 ASN cc_start: 0.8513 (t0) cc_final: 0.8289 (t0) REVERT: L 124 THR cc_start: 0.9267 (OUTLIER) cc_final: 0.9024 (p) REVERT: M 115 THR cc_start: 0.8610 (p) cc_final: 0.8185 (m) REVERT: N 104 SER cc_start: 0.8834 (m) cc_final: 0.8615 (m) REVERT: N 112 ASN cc_start: 0.8251 (t0) cc_final: 0.7984 (t0) REVERT: O 115 THR cc_start: 0.8657 (p) cc_final: 0.8405 (m) REVERT: R 87 THR cc_start: 0.9106 (t) cc_final: 0.8904 (m) REVERT: S 89 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8672 (p0) REVERT: U 89 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8521 (p0) REVERT: U 113 LYS cc_start: 0.8978 (ptpt) cc_final: 0.8593 (ptpp) outliers start: 55 outliers final: 34 residues processed: 254 average time/residue: 0.1417 time to fit residues: 49.7724 Evaluate side-chains 194 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 154 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 89 ASN Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 91 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 106 ASN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6314 Z= 0.189 Angle : 0.634 6.413 8558 Z= 0.335 Chirality : 0.032 0.135 990 Planarity : 0.004 0.024 1144 Dihedral : 8.897 56.921 917 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 10.30 % Allowed : 12.12 % Favored : 77.58 % 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: -5.66 (0.14), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.31 (0.10), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.030 0.001 PHE V 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 197 time to evaluate : 0.663 Fit side-chains REVERT: A 89 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8544 (p0) REVERT: A 113 LYS cc_start: 0.8930 (ptpt) cc_final: 0.7848 (mmmt) REVERT: L 124 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8834 (p) REVERT: M 87 THR cc_start: 0.7894 (OUTLIER) cc_final: 0.7549 (t) REVERT: S 113 LYS cc_start: 0.8724 (ptpp) cc_final: 0.8451 (mttm) REVERT: T 111 GLN cc_start: 0.7819 (pt0) cc_final: 0.7491 (mt0) outliers start: 68 outliers final: 40 residues processed: 227 average time/residue: 0.1311 time to fit residues: 42.0271 Evaluate side-chains 189 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 146 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain N residue 111 GLN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 91 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN C 89 ASN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** L 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN ** M 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 GLN S 89 ASN ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 GLN ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.049 6314 Z= 0.576 Angle : 0.807 8.130 8558 Z= 0.424 Chirality : 0.041 0.183 990 Planarity : 0.004 0.022 1144 Dihedral : 8.202 54.229 896 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 14.39 % Allowed : 11.97 % Favored : 73.64 % 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: -5.56 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.002 PHE V 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 151 time to evaluate : 0.595 Fit side-chains REVERT: A 113 LYS cc_start: 0.9029 (ptpt) cc_final: 0.7990 (mmpt) REVERT: I 91 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8573 (tp) REVERT: M 89 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8576 (p0) REVERT: M 91 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8696 (pp) REVERT: N 112 ASN cc_start: 0.8078 (t0) cc_final: 0.7822 (t0) REVERT: V 124 THR cc_start: 0.9343 (t) cc_final: 0.8989 (m) outliers start: 95 outliers final: 78 residues processed: 207 average time/residue: 0.1226 time to fit residues: 36.4628 Evaluate side-chains 210 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 129 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 111 GLN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 123 SER Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 97 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 97 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 ASN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6314 Z= 0.274 Angle : 0.652 6.972 8558 Z= 0.334 Chirality : 0.033 0.150 990 Planarity : 0.003 0.018 1144 Dihedral : 6.612 59.757 881 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 12.88 % Allowed : 13.33 % Favored : 73.79 % 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: -5.51 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.20 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.001 PHE V 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 160 time to evaluate : 0.687 Fit side-chains REVERT: A 113 LYS cc_start: 0.8983 (ptpt) cc_final: 0.7778 (mmmt) REVERT: K 89 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8233 (p0) REVERT: L 106 ASN cc_start: 0.8869 (OUTLIER) cc_final: 0.8666 (p0) REVERT: M 89 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8059 (p0) REVERT: O 113 LYS cc_start: 0.8840 (ptpp) cc_final: 0.8565 (mttm) REVERT: S 113 LYS cc_start: 0.8865 (ptpp) cc_final: 0.8638 (mttm) REVERT: V 124 THR cc_start: 0.9150 (t) cc_final: 0.8878 (m) outliers start: 85 outliers final: 73 residues processed: 201 average time/residue: 0.1299 time to fit residues: 37.4318 Evaluate side-chains 224 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 148 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain L residue 106 ASN Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 111 GLN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 106 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** L 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 6314 Z= 0.457 Angle : 0.713 7.368 8558 Z= 0.373 Chirality : 0.037 0.131 990 Planarity : 0.003 0.017 1144 Dihedral : 6.870 58.150 879 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 14.09 % Allowed : 12.42 % Favored : 73.48 % 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: -5.31 (0.16), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.12), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.002 PHE V 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 150 time to evaluate : 0.691 Fit side-chains REVERT: A 113 LYS cc_start: 0.9051 (ptpt) cc_final: 0.7839 (mmmt) REVERT: L 106 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8697 (p0) REVERT: S 113 LYS cc_start: 0.8883 (ptpp) cc_final: 0.8625 (mttm) REVERT: V 124 THR cc_start: 0.9227 (t) cc_final: 0.8982 (m) outliers start: 93 outliers final: 81 residues processed: 197 average time/residue: 0.1382 time to fit residues: 38.1413 Evaluate side-chains 224 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 142 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain L residue 106 ASN Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 111 GLN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 123 SER Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain V residue 104 SER Chi-restraints excluded: chain V residue 106 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 ASN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 ASN ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6314 Z= 0.349 Angle : 0.656 6.931 8558 Z= 0.342 Chirality : 0.035 0.124 990 Planarity : 0.003 0.016 1144 Dihedral : 6.348 45.259 879 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 13.94 % Allowed : 14.24 % Favored : 71.82 % 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 (0.16), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.12), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.001 PHE V 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 144 time to evaluate : 0.671 Fit side-chains REVERT: A 113 LYS cc_start: 0.9034 (ptpt) cc_final: 0.7811 (mmmt) REVERT: K 89 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8464 (p0) REVERT: S 113 LYS cc_start: 0.8885 (ptpp) cc_final: 0.8597 (mttm) REVERT: T 104 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8300 (p) REVERT: V 124 THR cc_start: 0.9172 (t) cc_final: 0.8950 (m) outliers start: 92 outliers final: 84 residues processed: 192 average time/residue: 0.1255 time to fit residues: 34.3377 Evaluate side-chains 222 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 136 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 111 GLN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 123 SER Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 104 SER Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 97 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain V residue 104 SER Chi-restraints excluded: chain V residue 106 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 GLN ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN ** V 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6314 Z= 0.404 Angle : 0.673 7.667 8558 Z= 0.353 Chirality : 0.036 0.126 990 Planarity : 0.003 0.017 1144 Dihedral : 6.424 46.025 875 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 13.94 % Allowed : 15.61 % Favored : 70.45 % 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: -5.17 (0.16), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.12), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.001 PHE V 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 144 time to evaluate : 0.712 Fit side-chains REVERT: A 113 LYS cc_start: 0.9061 (ptpt) cc_final: 0.7849 (mmmt) REVERT: S 113 LYS cc_start: 0.8870 (ptpp) cc_final: 0.8625 (mttm) REVERT: T 104 SER cc_start: 0.8464 (p) cc_final: 0.8214 (p) REVERT: V 124 THR cc_start: 0.9179 (t) cc_final: 0.8947 (m) outliers start: 92 outliers final: 84 residues processed: 193 average time/residue: 0.1343 time to fit residues: 37.5371 Evaluate side-chains 218 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 134 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 111 GLN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 123 SER Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 85 THR Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 97 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain V residue 104 SER Chi-restraints excluded: chain V residue 106 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6314 Z= 0.180 Angle : 0.589 7.045 8558 Z= 0.301 Chirality : 0.031 0.114 990 Planarity : 0.002 0.021 1144 Dihedral : 5.644 43.629 875 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 10.00 % Allowed : 19.70 % Favored : 70.30 % 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: -5.23 (0.16), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.12), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.001 PHE V 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 159 time to evaluate : 0.603 Fit side-chains REVERT: A 113 LYS cc_start: 0.8957 (ptpt) cc_final: 0.7763 (mmmt) REVERT: K 113 LYS cc_start: 0.8744 (ptpp) cc_final: 0.8430 (mttp) REVERT: S 113 LYS cc_start: 0.8800 (ptpp) cc_final: 0.8565 (mttp) outliers start: 66 outliers final: 61 residues processed: 191 average time/residue: 0.1279 time to fit residues: 34.8251 Evaluate side-chains 204 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 143 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 111 GLN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 0.0570 chunk 83 optimal weight: 3.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 ASN ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN ** M 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6314 Z= 0.311 Angle : 0.624 7.319 8558 Z= 0.324 Chirality : 0.034 0.119 990 Planarity : 0.003 0.017 1144 Dihedral : 5.803 36.913 873 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 11.21 % Allowed : 19.39 % Favored : 69.39 % 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: -5.15 (0.16), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.12), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.001 PHE V 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 140 time to evaluate : 0.690 Fit side-chains REVERT: A 113 LYS cc_start: 0.9040 (ptpt) cc_final: 0.7805 (mmmt) REVERT: R 87 THR cc_start: 0.8832 (t) cc_final: 0.8526 (m) REVERT: S 113 LYS cc_start: 0.8862 (ptpp) cc_final: 0.8619 (mttm) outliers start: 74 outliers final: 68 residues processed: 181 average time/residue: 0.1208 time to fit residues: 32.0711 Evaluate side-chains 206 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 138 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 111 GLN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 97 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain V residue 106 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 69 optimal weight: 9.9990 chunk 7 optimal weight: 0.3980 chunk 53 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN ** M 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN ** V 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6314 Z= 0.203 Angle : 0.585 7.788 8558 Z= 0.299 Chirality : 0.031 0.114 990 Planarity : 0.002 0.020 1144 Dihedral : 5.491 40.280 873 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 10.45 % Allowed : 20.00 % Favored : 69.55 % 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: -5.20 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.12), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.001 PHE V 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 155 time to evaluate : 0.671 Fit side-chains REVERT: A 113 LYS cc_start: 0.9000 (ptpt) cc_final: 0.7769 (mmmt) REVERT: K 113 LYS cc_start: 0.8748 (ptpp) cc_final: 0.8475 (mttp) REVERT: S 113 LYS cc_start: 0.8788 (ptpp) cc_final: 0.8584 (mttp) outliers start: 69 outliers final: 68 residues processed: 188 average time/residue: 0.1195 time to fit residues: 32.6669 Evaluate side-chains 215 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 147 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 111 GLN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 97 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain V residue 106 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 GLN ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.088768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.072997 restraints weight = 10198.313| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.40 r_work: 0.3142 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6314 Z= 0.296 Angle : 0.611 7.117 8558 Z= 0.317 Chirality : 0.033 0.118 990 Planarity : 0.003 0.020 1144 Dihedral : 5.722 42.528 873 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 10.91 % Allowed : 19.39 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.14 (0.16), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.12), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.001 PHE V 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1712.23 seconds wall clock time: 32 minutes 32.62 seconds (1952.62 seconds total)