Starting phenix.real_space_refine on Fri Dec 8 00:46:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q65_13852/12_2023/7q65_13852.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q65_13852/12_2023/7q65_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_13852/12_2023/7q65_13852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q65_13852/12_2023/7q65_13852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q65_13852/12_2023/7q65_13852.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q65_13852/12_2023/7q65_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-1.21rc1-5172/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: 3.42, per 1000 atoms: 0.55 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: 2.35 Conformation dependent library (CDL) restraints added in 1.4 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: 0.84 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: 1.65 Time building geometry restraints manager: 2.55 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.380 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 21.100 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: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.060 ------------------------------------------------------------------------------- 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 : 0.843 Fit side-chains outliers start: 55 outliers final: 34 residues processed: 254 average time/residue: 0.1427 time to fit residues: 50.1985 Evaluate side-chains 187 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 153 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.0590 time to fit residues: 4.5240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN 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** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6314 Z= 0.194 Angle : 0.649 6.810 8558 Z= 0.343 Chirality : 0.035 0.159 990 Planarity : 0.003 0.024 1144 Dihedral : 5.144 17.627 858 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 6.82 % Allowed : 14.24 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.67 (0.14), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.32 (0.10), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.029 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 248 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 203 time to evaluate : 0.659 Fit side-chains outliers start: 45 outliers final: 28 residues processed: 209 average time/residue: 0.1350 time to fit residues: 39.7635 Evaluate side-chains 174 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 0.661 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.0602 time to fit residues: 3.9199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 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** ** 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 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 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 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2648 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= 0.580 Angle : 0.787 7.415 8558 Z= 0.421 Chirality : 0.043 0.191 990 Planarity : 0.004 0.023 1144 Dihedral : 5.711 21.362 858 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 9.85 % Allowed : 15.00 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.57 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.24 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 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 215 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 150 time to evaluate : 0.616 Fit side-chains outliers start: 65 outliers final: 56 residues processed: 190 average time/residue: 0.1327 time to fit residues: 36.1891 Evaluate side-chains 183 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 127 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.0611 time to fit residues: 7.1225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 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** ** H 107 ASN ** 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** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** P 112 ASN ** 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** U 105 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6314 Z= 0.256 Angle : 0.646 7.525 8558 Z= 0.335 Chirality : 0.036 0.197 990 Planarity : 0.003 0.021 1144 Dihedral : 4.864 18.071 858 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 5.76 % Allowed : 16.97 % Favored : 77.27 % 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 : -4.19 (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 205 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 167 time to evaluate : 0.730 Fit side-chains outliers start: 38 outliers final: 27 residues processed: 183 average time/residue: 0.1337 time to fit residues: 34.8179 Evaluate side-chains 172 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 0.626 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.0589 time to fit residues: 3.7125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 63 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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 105 GLN ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6314 Z= 0.347 Angle : 0.654 7.698 8558 Z= 0.343 Chirality : 0.036 0.168 990 Planarity : 0.003 0.022 1144 Dihedral : 4.933 19.007 858 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 7.88 % Allowed : 15.91 % Favored : 76.21 % 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: -5.40 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.12), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.001 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 205 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 153 time to evaluate : 0.648 Fit side-chains outliers start: 52 outliers final: 41 residues processed: 176 average time/residue: 0.1309 time to fit residues: 33.0977 Evaluate side-chains 182 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 141 time to evaluate : 0.698 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.0636 time to fit residues: 5.6320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** ** H 107 ASN ** 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 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6314 Z= 0.337 Angle : 0.650 8.278 8558 Z= 0.340 Chirality : 0.038 0.214 990 Planarity : 0.003 0.020 1144 Dihedral : 4.889 18.806 858 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 6.52 % Allowed : 16.67 % Favored : 76.82 % 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: -5.28 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (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 195 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 152 time to evaluate : 0.668 Fit side-chains outliers start: 43 outliers final: 28 residues processed: 173 average time/residue: 0.1318 time to fit residues: 32.9550 Evaluate side-chains 167 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 139 time to evaluate : 0.694 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.0596 time to fit residues: 3.8893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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** ** G 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** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN ** V 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6314 Z= 0.233 Angle : 0.598 8.596 8558 Z= 0.310 Chirality : 0.034 0.199 990 Planarity : 0.003 0.020 1144 Dihedral : 4.579 17.591 858 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 4.09 % Allowed : 19.55 % Favored : 76.36 % 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: -5.25 (0.15), 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 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 185 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 158 time to evaluate : 0.670 Fit side-chains outliers start: 27 outliers final: 18 residues processed: 166 average time/residue: 0.1247 time to fit residues: 30.0536 Evaluate side-chains 158 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0653 time to fit residues: 3.0678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 81 optimal weight: 0.0470 chunk 74 optimal weight: 0.7980 overall best weight: 1.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN ** 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** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 105 GLN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 GLN ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN ** V 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6314 Z= 0.249 Angle : 0.604 8.270 8558 Z= 0.314 Chirality : 0.036 0.212 990 Planarity : 0.003 0.021 1144 Dihedral : 4.560 17.852 858 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.33 % Allowed : 20.61 % Favored : 76.06 % 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 : -3.95 (0.12), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 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 168 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 0.650 Fit side-chains outliers start: 22 outliers final: 18 residues processed: 157 average time/residue: 0.1219 time to fit residues: 28.2660 Evaluate side-chains 155 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 0.670 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0606 time to fit residues: 2.8421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 5.9990 chunk 81 optimal weight: 0.4980 chunk 47 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 83 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6314 Z= 0.185 Angle : 0.573 8.321 8558 Z= 0.296 Chirality : 0.033 0.195 990 Planarity : 0.003 0.020 1144 Dihedral : 4.330 16.888 858 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 1.97 % Allowed : 21.97 % Favored : 76.06 % 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: -5.25 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 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 152 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 0.625 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 145 average time/residue: 0.1207 time to fit residues: 25.8198 Evaluate side-chains 143 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 0.689 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0656 time to fit residues: 1.9836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** 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 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 112 ASN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN ** 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: 0.8192 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6314 Z= 0.267 Angle : 0.608 7.901 8558 Z= 0.320 Chirality : 0.037 0.237 990 Planarity : 0.003 0.019 1144 Dihedral : 4.549 17.878 858 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.27 % Allowed : 22.27 % Favored : 75.45 % 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: -5.16 (0.15), 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 0.023 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 152 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 0.683 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 142 average time/residue: 0.1253 time to fit residues: 26.2776 Evaluate side-chains 147 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 0.708 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0638 time to fit residues: 2.2491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 10 optimal weight: 0.0060 chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- 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 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 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** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.094841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.079019 restraints weight = 9883.284| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.30 r_work: 0.3272 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6314 Z= 0.184 Angle : 0.572 7.837 8558 Z= 0.298 Chirality : 0.033 0.207 990 Planarity : 0.003 0.021 1144 Dihedral : 4.336 16.825 858 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.91 % Allowed : 23.94 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1727.26 seconds wall clock time: 32 minutes 35.08 seconds (1955.08 seconds total)