Starting phenix.real_space_refine on Fri Apr 5 13:42:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovk_17218/04_2024/8ovk_17218.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovk_17218/04_2024/8ovk_17218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovk_17218/04_2024/8ovk_17218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovk_17218/04_2024/8ovk_17218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovk_17218/04_2024/8ovk_17218.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovk_17218/04_2024/8ovk_17218.pdb" } resolution = 2.88 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= 0.009 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 10 5.16 5 C 1940 2.51 5 N 530 2.21 5 O 580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3060 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "B" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "C" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "D" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "E" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "F" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "G" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "H" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "I" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "J" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Time building chain proxies: 1.98, per 1000 atoms: 0.65 Number of scatterers: 3060 At special positions: 0 Unit cell: (100.8, 124.95, 39.9, 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 10 16.00 O 580 8.00 N 530 7.00 C 1940 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: 0.93 Conformation dependent library (CDL) restraints added in 551.7 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 680 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 47.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 24 removed outlier: 6.224A pdb=" N LYS A 16 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE C 19 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL A 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA C 21 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE A 20 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP C 23 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU A 22 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS C 16 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE E 19 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL C 18 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA E 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE C 20 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ASP E 23 " --> pdb=" O PHE C 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU C 22 " --> pdb=" O ASP E 23 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS E 16 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE G 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL E 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA G 21 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE E 20 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP G 23 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU E 22 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS G 16 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE I 19 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL G 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA I 21 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE G 20 " --> pdb=" O ALA I 21 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP I 23 " --> pdb=" O PHE G 20 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N GLU G 22 " --> pdb=" O ASP I 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 39 removed outlier: 6.785A pdb=" N ILE C 32 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY A 33 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 39 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE E 32 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY C 33 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL C 39 " --> pdb=" O GLY E 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE G 32 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY E 33 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL E 39 " --> pdb=" O GLY G 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE I 32 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY G 33 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL G 39 " --> pdb=" O GLY I 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 13 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 24 removed outlier: 6.225A pdb=" N LYS B 16 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE D 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL B 18 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA D 21 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE B 20 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP D 23 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU B 22 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS D 16 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE F 19 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL D 18 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA F 21 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE D 20 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ASP F 23 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU D 22 " --> pdb=" O ASP F 23 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS F 16 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE H 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL F 18 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA H 21 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE F 20 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP H 23 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU F 22 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS H 16 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE J 19 " --> pdb=" O LYS H 16 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL H 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA J 21 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE H 20 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP J 23 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU H 22 " --> pdb=" O ASP J 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 39 removed outlier: 6.785A pdb=" N ILE D 32 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY B 33 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 39 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE F 32 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY D 33 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL D 39 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE H 32 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY F 33 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL F 39 " --> pdb=" O GLY H 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE J 32 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY H 33 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL H 39 " --> pdb=" O GLY J 38 " (cutoff:3.500A) 64 hydrogen bonds defined for protein. 192 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: 0.64 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1003 1.33 - 1.45: 538 1.45 - 1.57: 1559 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3120 Sorted by residual: bond pdb=" CA GLN D 15 " pdb=" C GLN D 15 " ideal model delta sigma weight residual 1.523 1.485 0.038 1.28e-02 6.10e+03 8.65e+00 bond pdb=" CA GLN B 15 " pdb=" C GLN B 15 " ideal model delta sigma weight residual 1.523 1.485 0.037 1.28e-02 6.10e+03 8.51e+00 bond pdb=" CA GLN I 15 " pdb=" C GLN I 15 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.28e-02 6.10e+03 8.45e+00 bond pdb=" CA GLN G 15 " pdb=" C GLN G 15 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.28e-02 6.10e+03 8.44e+00 bond pdb=" CA GLN E 15 " pdb=" C GLN E 15 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.28e-02 6.10e+03 8.43e+00 ... (remaining 3115 not shown) Histogram of bond angle deviations from ideal: 100.41 - 106.57: 141 106.57 - 112.74: 1279 112.74 - 118.91: 1005 118.91 - 125.07: 1715 125.07 - 131.24: 50 Bond angle restraints: 4190 Sorted by residual: angle pdb=" O GLY H 29 " pdb=" C GLY H 29 " pdb=" N ALA H 30 " ideal model delta sigma weight residual 123.59 119.55 4.04 8.70e-01 1.32e+00 2.16e+01 angle pdb=" O GLY E 29 " pdb=" C GLY E 29 " pdb=" N ALA E 30 " ideal model delta sigma weight residual 123.59 119.58 4.01 8.70e-01 1.32e+00 2.12e+01 angle pdb=" O GLY C 29 " pdb=" C GLY C 29 " pdb=" N ALA C 30 " ideal model delta sigma weight residual 123.59 119.58 4.01 8.70e-01 1.32e+00 2.12e+01 angle pdb=" N PHE D 4 " pdb=" CA PHE D 4 " pdb=" C PHE D 4 " ideal model delta sigma weight residual 111.52 117.84 -6.32 1.40e+00 5.10e-01 2.04e+01 angle pdb=" N PHE J 4 " pdb=" CA PHE J 4 " pdb=" C PHE J 4 " ideal model delta sigma weight residual 111.52 117.84 -6.32 1.40e+00 5.10e-01 2.04e+01 ... (remaining 4185 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 10.60: 1390 10.60 - 21.18: 193 21.18 - 31.75: 97 31.75 - 42.33: 50 42.33 - 52.90: 20 Dihedral angle restraints: 1750 sinusoidal: 670 harmonic: 1080 Sorted by residual: dihedral pdb=" CA LEU J 34 " pdb=" C LEU J 34 " pdb=" N MET J 35 " pdb=" CA MET J 35 " ideal model delta harmonic sigma weight residual 180.00 157.89 22.11 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA LEU A 34 " pdb=" C LEU A 34 " pdb=" N MET A 35 " pdb=" CA MET A 35 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA LEU G 34 " pdb=" C LEU G 34 " pdb=" N MET G 35 " pdb=" CA MET G 35 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 1747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 90 0.046 - 0.092: 141 0.092 - 0.137: 129 0.137 - 0.183: 50 0.183 - 0.229: 30 Chirality restraints: 440 Sorted by residual: chirality pdb=" CA GLU C 11 " pdb=" N GLU C 11 " pdb=" C GLU C 11 " pdb=" CB GLU C 11 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA GLU B 11 " pdb=" N GLU B 11 " pdb=" C GLU B 11 " pdb=" CB GLU B 11 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA GLU G 11 " pdb=" N GLU G 11 " pdb=" C GLU G 11 " pdb=" CB GLU G 11 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 437 not shown) Planarity restraints: 560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 10 " 0.062 2.00e-02 2.50e+03 3.56e-02 2.54e+01 pdb=" CG TYR H 10 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR H 10 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR H 10 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR H 10 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR H 10 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR H 10 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR H 10 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 10 " 0.062 2.00e-02 2.50e+03 3.56e-02 2.53e+01 pdb=" CG TYR D 10 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR D 10 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR D 10 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR D 10 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR D 10 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR D 10 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 10 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 10 " -0.061 2.00e-02 2.50e+03 3.55e-02 2.52e+01 pdb=" CG TYR A 10 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 10 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR A 10 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 10 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 10 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR A 10 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 10 " -0.058 2.00e-02 2.50e+03 ... (remaining 557 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1120 2.89 - 3.39: 2591 3.39 - 3.89: 5434 3.89 - 4.40: 6090 4.40 - 4.90: 11642 Nonbonded interactions: 26877 Sorted by model distance: nonbonded pdb=" NH2 ARG H 5 " pdb=" OD2 ASP J 7 " model vdw 2.386 2.520 nonbonded pdb=" NH2 ARG A 5 " pdb=" OD2 ASP C 7 " model vdw 2.387 2.520 nonbonded pdb=" NH2 ARG G 5 " pdb=" OD2 ASP I 7 " model vdw 2.387 2.520 nonbonded pdb=" NH2 ARG D 5 " pdb=" OD2 ASP F 7 " model vdw 2.387 2.520 nonbonded pdb=" NH2 ARG B 5 " pdb=" OD2 ASP D 7 " model vdw 2.387 2.520 ... (remaining 26872 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' } 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: 0.640 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: 3.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.740 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.012 0.038 3120 Z= 0.812 Angle : 1.803 7.261 4190 Z= 1.167 Chirality : 0.109 0.229 440 Planarity : 0.011 0.036 560 Dihedral : 14.992 52.904 1070 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 12.90 % Allowed : 9.68 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.027 0.009 PHE B 19 TYR 0.062 0.030 TYR H 10 ARG 0.002 0.001 ARG I 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 156 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6818 (pm20) REVERT: A 5 ARG cc_start: 0.8391 (mtp180) cc_final: 0.6681 (pmt170) REVERT: B 3 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7068 (pm20) REVERT: B 5 ARG cc_start: 0.8356 (mtp180) cc_final: 0.6701 (pmt170) REVERT: C 3 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7026 (mm-30) REVERT: D 3 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6746 (mm-30) REVERT: D 28 LYS cc_start: 0.8549 (mttt) cc_final: 0.8026 (mttm) REVERT: E 3 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6813 (mp0) REVERT: E 15 GLN cc_start: 0.8909 (tt0) cc_final: 0.8641 (tt0) REVERT: F 3 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6865 (mm-30) REVERT: G 3 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6991 (mm-30) REVERT: H 3 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6670 (mm-30) REVERT: H 15 GLN cc_start: 0.8933 (tt0) cc_final: 0.8684 (tt0) REVERT: I 3 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: I 5 ARG cc_start: 0.8259 (mtp180) cc_final: 0.6763 (tpm170) REVERT: I 34 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8935 (mt) REVERT: J 3 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7501 (mm-30) REVERT: J 5 ARG cc_start: 0.8261 (mtp180) cc_final: 0.7012 (tpm170) outliers start: 40 outliers final: 5 residues processed: 166 average time/residue: 1.1728 time to fit residues: 199.2574 Evaluate side-chains 135 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 3 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3120 Z= 0.207 Angle : 0.499 8.222 4190 Z= 0.269 Chirality : 0.051 0.124 440 Planarity : 0.002 0.018 560 Dihedral : 10.571 58.689 462 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.13 % Allowed : 30.00 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.29), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.22), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 13 PHE 0.011 0.001 PHE H 20 TYR 0.010 0.002 TYR G 10 ARG 0.007 0.001 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.360 Fit side-chains REVERT: A 3 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7042 (pm20) REVERT: A 5 ARG cc_start: 0.8247 (mtp180) cc_final: 0.6403 (pmt170) REVERT: A 40 VAL cc_start: 0.8695 (m) cc_final: 0.8406 (p) REVERT: B 3 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: B 5 ARG cc_start: 0.8291 (mtp180) cc_final: 0.6298 (pmt170) REVERT: B 23 ASP cc_start: 0.8879 (m-30) cc_final: 0.8664 (m-30) REVERT: B 28 LYS cc_start: 0.8846 (mttm) cc_final: 0.8295 (mttt) REVERT: C 3 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7320 (mm-30) REVERT: C 5 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7816 (ttt-90) REVERT: D 3 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: D 28 LYS cc_start: 0.8864 (mttt) cc_final: 0.8636 (mttm) REVERT: E 3 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7261 (mm-30) REVERT: E 28 LYS cc_start: 0.8745 (mttt) cc_final: 0.8446 (mttm) REVERT: F 3 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7247 (mm-30) REVERT: F 28 LYS cc_start: 0.8725 (mttt) cc_final: 0.8500 (mtpt) REVERT: G 3 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7231 (mm-30) REVERT: G 5 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7769 (ttt-90) REVERT: H 3 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7109 (mm-30) REVERT: H 5 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7938 (ttt-90) REVERT: H 28 LYS cc_start: 0.8814 (mttt) cc_final: 0.8565 (mttm) REVERT: I 3 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6973 (mm-30) REVERT: I 5 ARG cc_start: 0.8055 (mtp180) cc_final: 0.6876 (tpm170) REVERT: I 28 LYS cc_start: 0.8696 (mttm) cc_final: 0.8473 (mttm) REVERT: J 5 ARG cc_start: 0.8132 (mtp180) cc_final: 0.6936 (tpm170) outliers start: 19 outliers final: 3 residues processed: 119 average time/residue: 1.3225 time to fit residues: 160.8705 Evaluate side-chains 113 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain I residue 3 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 HIS D 14 HIS D 15 GLN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 HIS F 14 HIS ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS G 27 ASN H 14 HIS H 15 GLN ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 ASN J 6 HIS J 14 HIS ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 3120 Z= 0.491 Angle : 0.561 7.688 4190 Z= 0.301 Chirality : 0.052 0.125 440 Planarity : 0.002 0.016 560 Dihedral : 10.194 59.940 447 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 7.74 % Allowed : 28.06 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.30), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 14 PHE 0.010 0.002 PHE H 20 TYR 0.008 0.001 TYR F 10 ARG 0.004 0.001 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 0.342 Fit side-chains REVERT: A 3 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6596 (pm20) REVERT: A 5 ARG cc_start: 0.8268 (mtp180) cc_final: 0.6327 (pmt170) REVERT: B 3 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.6743 (pm20) REVERT: B 5 ARG cc_start: 0.8367 (mtp180) cc_final: 0.6318 (pmt170) REVERT: B 22 GLU cc_start: 0.8056 (tt0) cc_final: 0.7630 (tt0) REVERT: C 3 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7492 (mm-30) REVERT: D 3 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7281 (mm-30) REVERT: D 28 LYS cc_start: 0.8986 (mttt) cc_final: 0.8741 (mttm) REVERT: E 3 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7381 (mm-30) REVERT: E 5 ARG cc_start: 0.8478 (ttp80) cc_final: 0.8187 (tpp80) REVERT: E 28 LYS cc_start: 0.8968 (mttt) cc_final: 0.8691 (mttp) REVERT: F 3 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7425 (mm-30) REVERT: G 3 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7180 (mm-30) REVERT: G 5 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7794 (ttt-90) REVERT: G 40 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8631 (t) REVERT: H 3 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7175 (mm-30) REVERT: H 5 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7970 (ttt-90) REVERT: H 28 LYS cc_start: 0.9018 (mttt) cc_final: 0.8746 (mttm) REVERT: I 3 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7139 (mm-30) REVERT: I 5 ARG cc_start: 0.8058 (mtp180) cc_final: 0.6739 (tpm170) REVERT: I 23 ASP cc_start: 0.8742 (m-30) cc_final: 0.8501 (m-30) REVERT: I 28 LYS cc_start: 0.8931 (mttm) cc_final: 0.8661 (mttm) REVERT: J 5 ARG cc_start: 0.8085 (mtp180) cc_final: 0.6884 (tpm170) outliers start: 24 outliers final: 6 residues processed: 121 average time/residue: 1.3316 time to fit residues: 164.7293 Evaluate side-chains 114 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain I residue 3 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS D 15 GLN D 27 ASN ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 ASN G 15 GLN H 27 ASN J 27 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3120 Z= 0.318 Angle : 0.503 7.681 4190 Z= 0.268 Chirality : 0.051 0.132 440 Planarity : 0.002 0.014 560 Dihedral : 9.962 59.753 447 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 6.77 % Allowed : 28.39 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.30), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 14 PHE 0.008 0.001 PHE F 20 TYR 0.006 0.001 TYR F 10 ARG 0.003 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.343 Fit side-chains REVERT: A 3 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.6590 (pm20) REVERT: A 5 ARG cc_start: 0.8299 (mtp180) cc_final: 0.6215 (pmt170) REVERT: B 3 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.6680 (pm20) REVERT: B 28 LYS cc_start: 0.8939 (mttm) cc_final: 0.8568 (mttt) REVERT: C 3 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7501 (mm-30) REVERT: D 3 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: D 5 ARG cc_start: 0.8288 (tpt-90) cc_final: 0.7740 (tpt-90) REVERT: D 28 LYS cc_start: 0.8977 (mttt) cc_final: 0.8737 (mttm) REVERT: E 3 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7314 (mm-30) REVERT: E 5 ARG cc_start: 0.8430 (ttp80) cc_final: 0.7833 (tpt-90) REVERT: E 28 LYS cc_start: 0.8971 (mttt) cc_final: 0.8680 (mttp) REVERT: F 3 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7476 (mm-30) REVERT: G 3 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7168 (mm-30) REVERT: G 5 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7931 (ttt-90) REVERT: G 7 ASP cc_start: 0.8504 (p0) cc_final: 0.8152 (p0) REVERT: H 3 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7305 (mm-30) REVERT: H 5 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7989 (ttt-90) REVERT: H 28 LYS cc_start: 0.8997 (mttt) cc_final: 0.8736 (mttm) REVERT: I 3 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7162 (mm-30) REVERT: I 5 ARG cc_start: 0.8017 (mtp180) cc_final: 0.6841 (tpm170) REVERT: I 23 ASP cc_start: 0.8763 (m-30) cc_final: 0.8472 (m-30) REVERT: I 28 LYS cc_start: 0.8918 (mttm) cc_final: 0.8623 (mttp) REVERT: J 5 ARG cc_start: 0.8112 (mtp180) cc_final: 0.6881 (tpm170) outliers start: 21 outliers final: 6 residues processed: 106 average time/residue: 1.2493 time to fit residues: 135.5027 Evaluate side-chains 104 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain I residue 3 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3120 Z= 0.334 Angle : 0.503 7.832 4190 Z= 0.262 Chirality : 0.050 0.125 440 Planarity : 0.002 0.011 560 Dihedral : 9.838 59.930 447 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 7.42 % Allowed : 28.39 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.30), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 14 PHE 0.007 0.001 PHE B 20 TYR 0.013 0.001 TYR J 10 ARG 0.002 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 0.303 Fit side-chains REVERT: A 3 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.6606 (pm20) REVERT: A 5 ARG cc_start: 0.8333 (mtp180) cc_final: 0.6124 (pmt170) REVERT: B 3 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.6662 (pm20) REVERT: B 28 LYS cc_start: 0.8908 (mttm) cc_final: 0.8659 (mttt) REVERT: C 3 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7440 (mm-30) REVERT: D 3 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7549 (mm-30) REVERT: D 5 ARG cc_start: 0.8442 (tpt-90) cc_final: 0.7997 (tpt-90) REVERT: D 28 LYS cc_start: 0.8988 (mttt) cc_final: 0.8748 (mttm) REVERT: E 3 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7266 (mm-30) REVERT: E 5 ARG cc_start: 0.8446 (ttp80) cc_final: 0.7981 (tpt-90) REVERT: E 28 LYS cc_start: 0.8905 (mttt) cc_final: 0.8616 (mttp) REVERT: F 3 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7474 (mm-30) REVERT: F 28 LYS cc_start: 0.8941 (mttm) cc_final: 0.8727 (mttp) REVERT: F 40 VAL cc_start: 0.8720 (m) cc_final: 0.8464 (p) REVERT: G 3 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7245 (mm-30) REVERT: G 5 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7983 (ttt-90) REVERT: G 7 ASP cc_start: 0.8498 (p0) cc_final: 0.8201 (p0) REVERT: G 15 GLN cc_start: 0.8791 (tt0) cc_final: 0.8571 (tt0) REVERT: G 40 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8615 (t) REVERT: H 3 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7381 (mm-30) REVERT: H 5 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8116 (ttt-90) REVERT: H 28 LYS cc_start: 0.9045 (mttt) cc_final: 0.8751 (mttm) REVERT: I 5 ARG cc_start: 0.7916 (mtp180) cc_final: 0.6829 (tpm170) REVERT: I 23 ASP cc_start: 0.8762 (m-30) cc_final: 0.8441 (m-30) REVERT: I 28 LYS cc_start: 0.8923 (mttm) cc_final: 0.8607 (mttp) REVERT: J 5 ARG cc_start: 0.8065 (mtp180) cc_final: 0.6820 (tpm170) outliers start: 23 outliers final: 7 residues processed: 107 average time/residue: 1.2717 time to fit residues: 139.1576 Evaluate side-chains 105 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 5 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3120 Z= 0.375 Angle : 0.509 6.324 4190 Z= 0.268 Chirality : 0.050 0.124 440 Planarity : 0.002 0.011 560 Dihedral : 9.429 59.165 444 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 6.45 % Allowed : 30.32 % Favored : 63.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.30), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 14 PHE 0.008 0.001 PHE B 20 TYR 0.013 0.001 TYR J 10 ARG 0.002 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.370 Fit side-chains REVERT: A 3 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.6375 (pm20) REVERT: A 5 ARG cc_start: 0.8368 (mtp180) cc_final: 0.6010 (pmt170) REVERT: B 3 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.6683 (pm20) REVERT: C 3 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7484 (mm-30) REVERT: C 15 GLN cc_start: 0.8874 (tt0) cc_final: 0.8647 (tt0) REVERT: D 3 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7581 (mm-30) REVERT: D 5 ARG cc_start: 0.8455 (tpt-90) cc_final: 0.8112 (tpt-90) REVERT: D 28 LYS cc_start: 0.8985 (mttt) cc_final: 0.8765 (mttm) REVERT: E 3 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7300 (mm-30) REVERT: E 5 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8047 (tpt-90) REVERT: E 28 LYS cc_start: 0.8889 (mttt) cc_final: 0.8586 (mttp) REVERT: F 3 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7560 (mm-30) REVERT: F 28 LYS cc_start: 0.9037 (mttm) cc_final: 0.8777 (mttp) REVERT: F 40 VAL cc_start: 0.8682 (m) cc_final: 0.8458 (p) REVERT: G 3 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7220 (mm-30) REVERT: G 5 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7932 (ttt-90) REVERT: G 7 ASP cc_start: 0.8490 (p0) cc_final: 0.8216 (p0) REVERT: G 40 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8598 (t) REVERT: H 3 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7367 (mm-30) REVERT: H 28 LYS cc_start: 0.9002 (mttt) cc_final: 0.8739 (mttm) REVERT: I 5 ARG cc_start: 0.7974 (mtp180) cc_final: 0.6814 (tpm170) REVERT: I 28 LYS cc_start: 0.8955 (mttm) cc_final: 0.8627 (mttm) outliers start: 20 outliers final: 7 residues processed: 100 average time/residue: 1.2770 time to fit residues: 130.6790 Evaluate side-chains 106 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 3 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 0.0060 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3120 Z= 0.154 Angle : 0.437 5.711 4190 Z= 0.229 Chirality : 0.051 0.122 440 Planarity : 0.001 0.009 560 Dihedral : 9.005 59.574 444 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 6.45 % Allowed : 30.65 % Favored : 62.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.30), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 6 PHE 0.005 0.001 PHE B 4 TYR 0.017 0.001 TYR J 10 ARG 0.002 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 0.349 Fit side-chains REVERT: A 3 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.6309 (pm20) REVERT: B 3 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.6711 (pm20) REVERT: C 3 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7514 (mm-30) REVERT: D 3 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7638 (mm-30) REVERT: D 28 LYS cc_start: 0.9001 (mttt) cc_final: 0.8758 (mttm) REVERT: E 3 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7167 (mm-30) REVERT: E 5 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8106 (tpt-90) REVERT: E 28 LYS cc_start: 0.8823 (mttt) cc_final: 0.8517 (mttp) REVERT: F 3 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7521 (mm-30) REVERT: G 3 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7451 (mm-30) REVERT: G 7 ASP cc_start: 0.8403 (p0) cc_final: 0.8046 (p0) REVERT: G 28 LYS cc_start: 0.9086 (mttt) cc_final: 0.8817 (mttp) REVERT: H 3 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7514 (mm-30) REVERT: H 28 LYS cc_start: 0.8992 (mttt) cc_final: 0.8696 (mttp) REVERT: I 5 ARG cc_start: 0.7892 (mtp180) cc_final: 0.6867 (tpm170) REVERT: I 28 LYS cc_start: 0.8949 (mttm) cc_final: 0.8655 (mttm) outliers start: 20 outliers final: 3 residues processed: 100 average time/residue: 1.1974 time to fit residues: 122.7389 Evaluate side-chains 94 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain H residue 3 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.0040 chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 28 optimal weight: 0.0470 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.5694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3120 Z= 0.145 Angle : 0.466 7.403 4190 Z= 0.235 Chirality : 0.050 0.120 440 Planarity : 0.002 0.031 560 Dihedral : 8.876 59.411 444 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.19 % Allowed : 33.55 % Favored : 62.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.30), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 13 PHE 0.008 0.001 PHE A 4 TYR 0.015 0.001 TYR J 10 ARG 0.006 0.001 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.359 Fit side-chains REVERT: A 3 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.6331 (pm20) REVERT: B 3 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.6671 (pm20) REVERT: B 28 LYS cc_start: 0.8956 (mttt) cc_final: 0.8646 (mttp) REVERT: C 3 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7586 (mm-30) REVERT: D 28 LYS cc_start: 0.9047 (mttt) cc_final: 0.8816 (mttm) REVERT: E 3 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.7060 (mm-30) REVERT: E 5 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8146 (tpt-90) REVERT: E 28 LYS cc_start: 0.8724 (mttt) cc_final: 0.8405 (mttp) REVERT: G 3 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7574 (mm-30) REVERT: G 7 ASP cc_start: 0.8364 (p0) cc_final: 0.8053 (p0) REVERT: G 28 LYS cc_start: 0.9078 (mttt) cc_final: 0.8815 (mttp) REVERT: H 28 LYS cc_start: 0.8995 (mttt) cc_final: 0.8734 (mttm) REVERT: I 5 ARG cc_start: 0.8025 (mtp180) cc_final: 0.6855 (tpm170) REVERT: I 28 LYS cc_start: 0.8924 (mttm) cc_final: 0.8574 (mttp) outliers start: 13 outliers final: 3 residues processed: 92 average time/residue: 1.2228 time to fit residues: 115.3909 Evaluate side-chains 87 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 35 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 36 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3120 Z= 0.274 Angle : 0.507 6.301 4190 Z= 0.260 Chirality : 0.051 0.125 440 Planarity : 0.002 0.025 560 Dihedral : 7.973 59.640 435 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.23 % Allowed : 37.10 % Favored : 59.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 13 PHE 0.008 0.001 PHE B 4 TYR 0.014 0.002 TYR J 10 ARG 0.006 0.001 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.358 Fit side-chains REVERT: A 3 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.6146 (pm20) REVERT: B 3 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.6665 (pm20) REVERT: C 3 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7623 (mm-30) REVERT: D 28 LYS cc_start: 0.9002 (mttt) cc_final: 0.8759 (mttm) REVERT: E 3 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7059 (mm-30) REVERT: E 5 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8134 (tpt-90) REVERT: E 28 LYS cc_start: 0.8730 (mttt) cc_final: 0.8380 (mttm) REVERT: G 3 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7433 (mm-30) REVERT: G 7 ASP cc_start: 0.8411 (p0) cc_final: 0.8087 (p0) REVERT: G 28 LYS cc_start: 0.9063 (mttt) cc_final: 0.8790 (mttp) REVERT: H 28 LYS cc_start: 0.8983 (mttt) cc_final: 0.8706 (mttm) REVERT: I 5 ARG cc_start: 0.8018 (mtp180) cc_final: 0.6844 (tpm170) REVERT: I 28 LYS cc_start: 0.8977 (mttm) cc_final: 0.8667 (mttp) outliers start: 10 outliers final: 4 residues processed: 90 average time/residue: 1.1892 time to fit residues: 109.8266 Evaluate side-chains 94 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.0670 chunk 9 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 0.0980 chunk 32 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3120 Z= 0.123 Angle : 0.482 6.367 4190 Z= 0.245 Chirality : 0.051 0.121 440 Planarity : 0.002 0.029 560 Dihedral : 7.759 58.470 435 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.94 % Allowed : 38.39 % Favored : 59.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS I 6 PHE 0.011 0.001 PHE A 4 TYR 0.016 0.001 TYR J 10 ARG 0.006 0.000 ARG D 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.276 Fit side-chains REVERT: A 3 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.6264 (pm20) REVERT: B 3 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.6560 (pm20) REVERT: C 3 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7773 (mm-30) REVERT: D 28 LYS cc_start: 0.9014 (mttt) cc_final: 0.8811 (mttm) REVERT: E 28 LYS cc_start: 0.8583 (mttt) cc_final: 0.8293 (mttm) REVERT: G 7 ASP cc_start: 0.8352 (p0) cc_final: 0.8111 (p0) REVERT: G 28 LYS cc_start: 0.9072 (mttt) cc_final: 0.8815 (mttp) REVERT: H 28 LYS cc_start: 0.8910 (mttt) cc_final: 0.8670 (mttm) REVERT: I 5 ARG cc_start: 0.8105 (mtp180) cc_final: 0.6936 (tpm170) REVERT: I 28 LYS cc_start: 0.8901 (mttm) cc_final: 0.8561 (mttp) outliers start: 6 outliers final: 1 residues processed: 87 average time/residue: 1.1604 time to fit residues: 103.5219 Evaluate side-chains 87 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 7.9990 chunk 36 optimal weight: 0.0970 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** 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 = 0.3950 r_free = 0.3950 target = 0.113195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.086001 restraints weight = 3879.798| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.25 r_work: 0.3359 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3120 Z= 0.315 Angle : 0.531 6.217 4190 Z= 0.272 Chirality : 0.051 0.124 440 Planarity : 0.002 0.026 560 Dihedral : 7.287 59.345 429 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.61 % Allowed : 38.39 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 13 PHE 0.013 0.001 PHE E 4 TYR 0.014 0.002 TYR J 10 ARG 0.006 0.001 ARG D 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2386.55 seconds wall clock time: 43 minutes 15.84 seconds (2595.84 seconds total)