Starting phenix.real_space_refine on Sat Sep 28 03:37:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxp_15013/09_2024/7zxp_15013.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxp_15013/09_2024/7zxp_15013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxp_15013/09_2024/7zxp_15013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxp_15013/09_2024/7zxp_15013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxp_15013/09_2024/7zxp_15013.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxp_15013/09_2024/7zxp_15013.cif" } resolution = 2.39 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 12192 2.51 5 N 3060 2.21 5 O 3000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18420 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1535 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 7.60, per 1000 atoms: 0.41 Number of scatterers: 18420 At special positions: 0 Unit cell: (106.602, 98.754, 164.154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 3000 8.00 N 3060 7.00 C 12192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 168 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 4.80 Conformation dependent library (CDL) restraints added in 2.3 seconds 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 74.9% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 107 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 220 Processing helix chain 'B' and resid 21 through 43 removed outlier: 3.735A pdb=" N GLU B 41 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 107 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 220 Processing helix chain 'C' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU C 41 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 107 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP C 133 " --> pdb=" O GLY C 129 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C 134 " --> pdb=" O THR C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 220 Processing helix chain 'D' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER D 42 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 107 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR D 134 " --> pdb=" O THR D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 220 Processing helix chain 'E' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU E 41 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER E 42 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 107 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP E 133 " --> pdb=" O GLY E 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR E 134 " --> pdb=" O THR E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 220 Processing helix chain 'F' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU F 41 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER F 42 " --> pdb=" O VAL F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 107 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP F 133 " --> pdb=" O GLY F 129 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR F 134 " --> pdb=" O THR F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 220 Processing helix chain 'G' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER G 42 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 72 through 107 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP G 133 " --> pdb=" O GLY G 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR G 134 " --> pdb=" O THR G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 220 Processing helix chain 'H' and resid 21 through 43 removed outlier: 3.735A pdb=" N GLU H 41 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 72 through 107 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP H 133 " --> pdb=" O GLY H 129 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR H 134 " --> pdb=" O THR H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 220 Processing helix chain 'I' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU I 41 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER I 42 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 72 through 107 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP I 133 " --> pdb=" O GLY I 129 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR I 134 " --> pdb=" O THR I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 220 Processing helix chain 'J' and resid 21 through 43 removed outlier: 3.735A pdb=" N GLU J 41 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 69 Processing helix chain 'J' and resid 72 through 107 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 123 through 157 removed outlier: 3.598A pdb=" N TRP J 133 " --> pdb=" O GLY J 129 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR J 134 " --> pdb=" O THR J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 220 Processing helix chain 'K' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU K 41 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER K 42 " --> pdb=" O VAL K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 72 through 107 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP K 133 " --> pdb=" O GLY K 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR K 134 " --> pdb=" O THR K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 220 Processing helix chain 'L' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU L 41 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER L 42 " --> pdb=" O VAL L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 69 Processing helix chain 'L' and resid 72 through 107 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP L 133 " --> pdb=" O GLY L 129 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR L 134 " --> pdb=" O THR L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 220 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE A 52 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE B 52 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE C 52 " --> pdb=" O PHE C 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE D 52 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE E 52 " --> pdb=" O PHE E 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE F 52 " --> pdb=" O PHE F 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE G 52 " --> pdb=" O PHE G 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE H 52 " --> pdb=" O PHE H 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE I 52 " --> pdb=" O PHE I 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE J 52 " --> pdb=" O PHE J 180 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE K 52 " --> pdb=" O PHE K 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE L 52 " --> pdb=" O PHE L 180 " (cutoff:3.500A) 1452 hydrogen bonds defined for protein. 4320 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: 5.54 Time building geometry restraints manager: 5.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5544 1.35 - 1.46: 4666 1.46 - 1.58: 8474 1.58 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 18924 Sorted by residual: bond pdb=" CA THR D 86 " pdb=" C THR D 86 " ideal model delta sigma weight residual 1.522 1.534 -0.013 1.26e-02 6.30e+03 9.91e-01 bond pdb=" CA THR G 86 " pdb=" C THR G 86 " ideal model delta sigma weight residual 1.522 1.534 -0.013 1.26e-02 6.30e+03 9.91e-01 bond pdb=" CA THR E 86 " pdb=" C THR E 86 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.26e-02 6.30e+03 9.82e-01 bond pdb=" CA THR K 86 " pdb=" C THR K 86 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.26e-02 6.30e+03 9.82e-01 bond pdb=" CA THR C 86 " pdb=" C THR C 86 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.26e-02 6.30e+03 9.58e-01 ... (remaining 18919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 25155 1.15 - 2.30: 501 2.30 - 3.46: 108 3.46 - 4.61: 0 4.61 - 5.76: 12 Bond angle restraints: 25776 Sorted by residual: angle pdb=" C THR K 86 " pdb=" N PRO K 87 " pdb=" CD PRO K 87 " ideal model delta sigma weight residual 125.00 130.76 -5.76 4.10e+00 5.95e-02 1.97e+00 angle pdb=" C THR I 86 " pdb=" N PRO I 87 " pdb=" CD PRO I 87 " ideal model delta sigma weight residual 125.00 130.75 -5.75 4.10e+00 5.95e-02 1.96e+00 angle pdb=" C THR L 86 " pdb=" N PRO L 87 " pdb=" CD PRO L 87 " ideal model delta sigma weight residual 125.00 130.75 -5.75 4.10e+00 5.95e-02 1.96e+00 angle pdb=" C THR H 86 " pdb=" N PRO H 87 " pdb=" CD PRO H 87 " ideal model delta sigma weight residual 125.00 130.72 -5.72 4.10e+00 5.95e-02 1.95e+00 angle pdb=" C THR B 86 " pdb=" N PRO B 87 " pdb=" CD PRO B 87 " ideal model delta sigma weight residual 125.00 130.71 -5.71 4.10e+00 5.95e-02 1.94e+00 ... (remaining 25771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.86: 9350 12.86 - 25.72: 988 25.72 - 38.58: 387 38.58 - 51.44: 240 51.44 - 64.30: 36 Dihedral angle restraints: 11001 sinusoidal: 4221 harmonic: 6780 Sorted by residual: dihedral pdb=" CB CYS A 64 " pdb=" SG CYS A 64 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual -86.00 -117.19 31.19 1 1.00e+01 1.00e-02 1.39e+01 dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 173 " pdb=" CB CYS A 173 " ideal model delta sinusoidal sigma weight residual 93.00 122.32 -29.32 1 1.00e+01 1.00e-02 1.23e+01 dihedral pdb=" CB MET E 194 " pdb=" CG MET E 194 " pdb=" SD MET E 194 " pdb=" CE MET E 194 " ideal model delta sinusoidal sigma weight residual -60.00 -114.35 54.35 3 1.50e+01 4.44e-03 9.28e+00 ... (remaining 10998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2182 0.033 - 0.067: 590 0.067 - 0.100: 228 0.100 - 0.134: 12 0.134 - 0.167: 36 Chirality restraints: 3048 Sorted by residual: chirality pdb=" CB VAL C 95 " pdb=" CA VAL C 95 " pdb=" CG1 VAL C 95 " pdb=" CG2 VAL C 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CB VAL F 95 " pdb=" CA VAL F 95 " pdb=" CG1 VAL F 95 " pdb=" CG2 VAL F 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CB VAL L 95 " pdb=" CA VAL L 95 " pdb=" CG1 VAL L 95 " pdb=" CG2 VAL L 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 3045 not shown) Planarity restraints: 3084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 29 " -0.013 2.00e-02 2.50e+03 1.28e-02 2.88e+00 pdb=" CG PHE H 29 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE H 29 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE H 29 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE H 29 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE H 29 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE H 29 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 29 " -0.013 2.00e-02 2.50e+03 1.28e-02 2.87e+00 pdb=" CG PHE K 29 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE K 29 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE K 29 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE K 29 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE K 29 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE K 29 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 29 " -0.013 2.00e-02 2.50e+03 1.28e-02 2.86e+00 pdb=" CG PHE J 29 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE J 29 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE J 29 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE J 29 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE J 29 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE J 29 " 0.000 2.00e-02 2.50e+03 ... (remaining 3081 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 129 2.60 - 3.18: 15565 3.18 - 3.75: 31227 3.75 - 4.33: 37029 4.33 - 4.90: 64306 Nonbonded interactions: 148256 Sorted by model distance: nonbonded pdb=" SG CYS H 64 " pdb=" SG CYS H 168 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 60 " pdb=" SG CYS B 173 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS K 64 " pdb=" SG CYS K 168 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS D 64 " pdb=" SG CYS D 168 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS J 64 " pdb=" SG CYS J 168 " model vdw 2.030 3.760 ... (remaining 148251 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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' } 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: 6.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.150 Process input model: 37.460 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 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:10.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 18924 Z= 0.129 Angle : 0.423 5.761 25776 Z= 0.242 Chirality : 0.039 0.167 3048 Planarity : 0.003 0.017 3084 Dihedral : 14.726 64.301 6576 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.17 % Allowed : 17.35 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.20 (0.17), residues: 2244 helix: 4.00 (0.10), residues: 1632 sheet: -0.27 (0.43), residues: 204 loop : -1.17 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 132 HIS 0.003 0.001 HIS H 73 PHE 0.030 0.002 PHE H 29 TYR 0.008 0.001 TYR G 65 ARG 0.002 0.000 ARG I 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 290 time to evaluate : 2.114 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 314 average time/residue: 0.8693 time to fit residues: 321.2358 Evaluate side-chains 207 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 191 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain L residue 42 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 178 optimal weight: 10.0000 chunk 69 optimal weight: 0.4980 chunk 108 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS D 73 HIS G 73 HIS J 73 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 18924 Z= 0.176 Angle : 0.436 5.613 25776 Z= 0.237 Chirality : 0.040 0.169 3048 Planarity : 0.003 0.015 3084 Dihedral : 3.813 38.207 2504 Min Nonbonded Distance : 2.675 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.27 % Allowed : 17.54 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.35 (0.16), residues: 2244 helix: 4.20 (0.10), residues: 1632 sheet: -0.90 (0.39), residues: 204 loop : -1.13 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 133 HIS 0.005 0.001 HIS I 73 PHE 0.011 0.002 PHE C 68 TYR 0.013 0.001 TYR A 65 ARG 0.002 0.000 ARG L 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 211 time to evaluate : 1.972 Fit side-chains REVERT: A 105 MET cc_start: 0.3061 (OUTLIER) cc_final: 0.2688 (tpp) REVERT: B 105 MET cc_start: 0.3127 (OUTLIER) cc_final: 0.2780 (tpp) REVERT: C 105 MET cc_start: 0.2929 (OUTLIER) cc_final: 0.2626 (tpp) REVERT: D 105 MET cc_start: 0.3057 (OUTLIER) cc_final: 0.2683 (tpp) REVERT: E 105 MET cc_start: 0.3138 (OUTLIER) cc_final: 0.2795 (tpp) REVERT: F 105 MET cc_start: 0.2928 (OUTLIER) cc_final: 0.2630 (tpp) REVERT: G 105 MET cc_start: 0.3064 (OUTLIER) cc_final: 0.2687 (tpp) REVERT: H 105 MET cc_start: 0.3134 (OUTLIER) cc_final: 0.2786 (tpp) REVERT: I 105 MET cc_start: 0.2925 (OUTLIER) cc_final: 0.2637 (tpp) REVERT: J 105 MET cc_start: 0.3063 (OUTLIER) cc_final: 0.2685 (tpp) REVERT: K 105 MET cc_start: 0.3130 (OUTLIER) cc_final: 0.2782 (tpp) REVERT: L 105 MET cc_start: 0.2926 (OUTLIER) cc_final: 0.2628 (tpp) outliers start: 67 outliers final: 12 residues processed: 251 average time/residue: 1.0447 time to fit residues: 300.7119 Evaluate side-chains 203 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 179 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain J residue 105 MET Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain L residue 97 HIS Chi-restraints excluded: chain L residue 105 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 57 optimal weight: 20.0000 chunk 207 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 chunk 184 optimal weight: 0.2980 chunk 205 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 18924 Z= 0.127 Angle : 0.395 5.623 25776 Z= 0.210 Chirality : 0.038 0.162 3048 Planarity : 0.002 0.012 3084 Dihedral : 3.522 37.222 2492 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.29 % Allowed : 17.88 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.53 (0.16), residues: 2244 helix: 4.36 (0.10), residues: 1632 sheet: -0.83 (0.39), residues: 204 loop : -1.22 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 133 HIS 0.003 0.000 HIS C 73 PHE 0.007 0.001 PHE H 29 TYR 0.011 0.001 TYR A 65 ARG 0.001 0.000 ARG L 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 181 time to evaluate : 2.296 Fit side-chains REVERT: A 105 MET cc_start: 0.3009 (OUTLIER) cc_final: 0.2636 (tpp) REVERT: C 105 MET cc_start: 0.2895 (OUTLIER) cc_final: 0.2560 (tpp) REVERT: D 105 MET cc_start: 0.3008 (OUTLIER) cc_final: 0.2633 (tpp) REVERT: F 105 MET cc_start: 0.2916 (OUTLIER) cc_final: 0.2573 (tpp) REVERT: G 105 MET cc_start: 0.3020 (OUTLIER) cc_final: 0.2645 (tpp) REVERT: I 105 MET cc_start: 0.2911 (OUTLIER) cc_final: 0.2507 (tpp) REVERT: J 105 MET cc_start: 0.3013 (OUTLIER) cc_final: 0.2637 (tpp) REVERT: L 105 MET cc_start: 0.2897 (OUTLIER) cc_final: 0.2553 (tpp) outliers start: 88 outliers final: 36 residues processed: 249 average time/residue: 0.9247 time to fit residues: 268.5933 Evaluate side-chains 220 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 176 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 97 HIS Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 105 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 97 HIS Chi-restraints excluded: chain L residue 105 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 197 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 18924 Z= 0.156 Angle : 0.412 5.712 25776 Z= 0.221 Chirality : 0.039 0.168 3048 Planarity : 0.002 0.013 3084 Dihedral : 3.625 38.767 2492 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.12 % Allowed : 19.15 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.57 (0.16), residues: 2244 helix: 4.37 (0.09), residues: 1632 sheet: -0.80 (0.38), residues: 204 loop : -1.13 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 133 HIS 0.004 0.001 HIS I 73 PHE 0.010 0.002 PHE J 180 TYR 0.011 0.001 TYR A 65 ARG 0.002 0.000 ARG G 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 181 time to evaluate : 2.011 Fit side-chains REVERT: A 105 MET cc_start: 0.3079 (OUTLIER) cc_final: 0.2680 (tpp) REVERT: B 105 MET cc_start: 0.3121 (OUTLIER) cc_final: 0.2786 (tpp) REVERT: C 105 MET cc_start: 0.2878 (OUTLIER) cc_final: 0.2436 (tpp) REVERT: D 105 MET cc_start: 0.3080 (OUTLIER) cc_final: 0.2683 (tpp) REVERT: E 105 MET cc_start: 0.3117 (OUTLIER) cc_final: 0.2781 (tpp) REVERT: F 105 MET cc_start: 0.2928 (OUTLIER) cc_final: 0.2482 (tpp) REVERT: G 105 MET cc_start: 0.3091 (OUTLIER) cc_final: 0.2693 (tpp) REVERT: H 105 MET cc_start: 0.3111 (OUTLIER) cc_final: 0.2777 (tpp) REVERT: I 105 MET cc_start: 0.2901 (OUTLIER) cc_final: 0.2448 (tpp) REVERT: J 105 MET cc_start: 0.3092 (OUTLIER) cc_final: 0.2696 (tpp) REVERT: K 105 MET cc_start: 0.3123 (OUTLIER) cc_final: 0.2784 (tpp) REVERT: L 105 MET cc_start: 0.2884 (OUTLIER) cc_final: 0.2443 (tpp) outliers start: 64 outliers final: 34 residues processed: 221 average time/residue: 0.9521 time to fit residues: 244.5448 Evaluate side-chains 217 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 171 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 97 HIS Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 105 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 97 HIS Chi-restraints excluded: chain L residue 105 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 152 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 18924 Z= 0.207 Angle : 0.428 5.779 25776 Z= 0.231 Chirality : 0.039 0.164 3048 Planarity : 0.002 0.016 3084 Dihedral : 3.746 40.125 2492 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 4.19 % Allowed : 17.59 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.57 (0.16), residues: 2244 helix: 4.35 (0.10), residues: 1632 sheet: -0.72 (0.38), residues: 204 loop : -1.08 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 133 HIS 0.004 0.001 HIS C 73 PHE 0.012 0.002 PHE G 180 TYR 0.012 0.001 TYR A 65 ARG 0.002 0.000 ARG J 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 185 time to evaluate : 2.151 Fit side-chains REVERT: A 105 MET cc_start: 0.3086 (OUTLIER) cc_final: 0.2696 (tpp) REVERT: B 105 MET cc_start: 0.3145 (OUTLIER) cc_final: 0.2654 (tpp) REVERT: D 105 MET cc_start: 0.3162 (OUTLIER) cc_final: 0.2771 (tpp) REVERT: E 105 MET cc_start: 0.3183 (OUTLIER) cc_final: 0.2708 (tpp) REVERT: F 105 MET cc_start: 0.3009 (OUTLIER) cc_final: 0.2551 (tpp) REVERT: F 131 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7306 (tp) REVERT: G 105 MET cc_start: 0.3093 (OUTLIER) cc_final: 0.2705 (tpp) REVERT: H 105 MET cc_start: 0.3198 (OUTLIER) cc_final: 0.2722 (tpp) REVERT: I 105 MET cc_start: 0.2984 (OUTLIER) cc_final: 0.2528 (tpp) REVERT: I 131 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7310 (tp) REVERT: J 105 MET cc_start: 0.3170 (OUTLIER) cc_final: 0.2780 (tpp) REVERT: K 105 MET cc_start: 0.3175 (OUTLIER) cc_final: 0.2699 (tpp) REVERT: L 105 MET cc_start: 0.3002 (OUTLIER) cc_final: 0.2547 (tpp) outliers start: 86 outliers final: 40 residues processed: 221 average time/residue: 0.9671 time to fit residues: 249.4750 Evaluate side-chains 233 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 180 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 97 HIS Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 105 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 97 HIS Chi-restraints excluded: chain L residue 105 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.9990 chunk 198 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 18924 Z= 0.183 Angle : 0.411 5.784 25776 Z= 0.221 Chirality : 0.039 0.169 3048 Planarity : 0.002 0.014 3084 Dihedral : 3.656 39.438 2492 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.80 % Allowed : 18.32 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.63 (0.16), residues: 2244 helix: 4.43 (0.09), residues: 1632 sheet: -0.74 (0.38), residues: 204 loop : -1.18 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 24 HIS 0.003 0.001 HIS F 73 PHE 0.010 0.002 PHE A 180 TYR 0.012 0.001 TYR A 65 ARG 0.002 0.000 ARG J 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 183 time to evaluate : 2.308 Fit side-chains REVERT: F 131 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7260 (tp) REVERT: I 131 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7268 (tp) outliers start: 78 outliers final: 44 residues processed: 217 average time/residue: 0.9313 time to fit residues: 236.3770 Evaluate side-chains 229 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 183 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 97 HIS Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 161 optimal weight: 40.0000 chunk 124 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 123 optimal weight: 30.0000 chunk 219 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 101 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 97 HIS E 97 HIS G 97 HIS H 97 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 18924 Z= 0.190 Angle : 0.419 5.803 25776 Z= 0.227 Chirality : 0.039 0.169 3048 Planarity : 0.002 0.015 3084 Dihedral : 3.712 40.262 2492 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.61 % Allowed : 18.52 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.63 (0.16), residues: 2244 helix: 4.43 (0.09), residues: 1632 sheet: -0.71 (0.38), residues: 204 loop : -1.19 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 133 HIS 0.004 0.001 HIS F 73 PHE 0.011 0.002 PHE A 68 TYR 0.012 0.001 TYR A 65 ARG 0.002 0.000 ARG G 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 186 time to evaluate : 2.914 Fit side-chains outliers start: 74 outliers final: 36 residues processed: 216 average time/residue: 0.9730 time to fit residues: 246.7164 Evaluate side-chains 222 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 186 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 66 optimal weight: 40.0000 chunk 43 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 172 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 97 HIS D 97 HIS E 97 HIS G 97 HIS H 97 HIS J 97 HIS K 97 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 18924 Z= 0.127 Angle : 0.384 5.763 25776 Z= 0.208 Chirality : 0.038 0.166 3048 Planarity : 0.002 0.013 3084 Dihedral : 3.496 38.779 2492 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.78 % Allowed : 19.05 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.79 (0.16), residues: 2244 helix: 4.57 (0.09), residues: 1632 sheet: -0.71 (0.38), residues: 204 loop : -1.26 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 132 HIS 0.003 0.000 HIS K 73 PHE 0.007 0.001 PHE F 180 TYR 0.012 0.001 TYR J 65 ARG 0.002 0.000 ARG J 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 215 time to evaluate : 2.156 Fit side-chains REVERT: F 105 MET cc_start: 0.3335 (OUTLIER) cc_final: 0.2703 (tmm) outliers start: 57 outliers final: 28 residues processed: 242 average time/residue: 0.9265 time to fit residues: 261.8339 Evaluate side-chains 235 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 206 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 30.0000 chunk 210 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 123 optimal weight: 40.0000 chunk 89 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 97 HIS C 97 HIS D 97 HIS E 97 HIS F 73 HIS F 97 HIS G 97 HIS H 97 HIS I 97 HIS J 97 HIS K 97 HIS L 73 HIS L 97 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 18924 Z= 0.324 Angle : 0.475 6.100 25776 Z= 0.262 Chirality : 0.042 0.202 3048 Planarity : 0.003 0.022 3084 Dihedral : 3.913 40.978 2492 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.39 % Allowed : 19.64 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.46 (0.16), residues: 2244 helix: 4.26 (0.09), residues: 1632 sheet: -0.64 (0.38), residues: 204 loop : -1.16 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 77 HIS 0.005 0.001 HIS E 73 PHE 0.018 0.002 PHE D 180 TYR 0.017 0.002 TYR K 211 ARG 0.002 0.000 ARG J 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 181 time to evaluate : 2.075 Fit side-chains outliers start: 49 outliers final: 26 residues processed: 213 average time/residue: 1.0787 time to fit residues: 264.6017 Evaluate side-chains 200 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 174 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 18 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 209 optimal weight: 20.0000 chunk 180 optimal weight: 30.0000 chunk 18 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 97 HIS C 97 HIS D 97 HIS E 97 HIS F 97 HIS G 97 HIS H 97 HIS I 97 HIS J 97 HIS K 97 HIS L 97 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 18924 Z= 0.248 Angle : 0.438 6.429 25776 Z= 0.242 Chirality : 0.040 0.188 3048 Planarity : 0.003 0.020 3084 Dihedral : 3.794 39.610 2492 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.10 % Allowed : 19.69 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.48 (0.16), residues: 2244 helix: 4.29 (0.09), residues: 1632 sheet: -0.66 (0.37), residues: 204 loop : -1.18 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 44 HIS 0.004 0.001 HIS K 73 PHE 0.014 0.002 PHE J 180 TYR 0.013 0.001 TYR D 65 ARG 0.002 0.000 ARG G 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 196 time to evaluate : 2.200 Fit side-chains outliers start: 43 outliers final: 24 residues processed: 226 average time/residue: 0.9553 time to fit residues: 251.6616 Evaluate side-chains 216 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 192 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 18 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 166 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 97 HIS C 97 HIS D 97 HIS E 97 HIS F 97 HIS G 97 HIS H 97 HIS I 97 HIS J 97 HIS K 97 HIS L 97 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.128589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.077006 restraints weight = 25863.020| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.88 r_work: 0.2796 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18924 Z= 0.199 Angle : 0.420 6.386 25776 Z= 0.232 Chirality : 0.039 0.177 3048 Planarity : 0.003 0.018 3084 Dihedral : 3.708 39.316 2492 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.90 % Allowed : 20.03 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.59 (0.16), residues: 2244 helix: 4.39 (0.09), residues: 1632 sheet: -0.70 (0.37), residues: 204 loop : -1.19 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 44 HIS 0.004 0.001 HIS I 73 PHE 0.012 0.002 PHE D 180 TYR 0.014 0.001 TYR J 211 ARG 0.002 0.000 ARG J 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6458.76 seconds wall clock time: 115 minutes 40.05 seconds (6940.05 seconds total)