Starting phenix.real_space_refine on Tue Feb 13 08:42:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aex_15388/02_2024/8aex_15388.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aex_15388/02_2024/8aex_15388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aex_15388/02_2024/8aex_15388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aex_15388/02_2024/8aex_15388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aex_15388/02_2024/8aex_15388.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aex_15388/02_2024/8aex_15388.pdb" } resolution = 2.76 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 2925 2.51 5 N 810 2.21 5 O 930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4665 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 483 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain breaks: 1 Chain: "B" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 450 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "C" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 483 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain breaks: 1 Chain: "D" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 450 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "E" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 483 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain breaks: 1 Chain: "F" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 450 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "G" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 483 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain breaks: 1 Chain: "H" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 450 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "I" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 483 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain breaks: 1 Chain: "J" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 450 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Time building chain proxies: 2.81, per 1000 atoms: 0.60 Number of scatterers: 4665 At special positions: 0 Unit cell: (109.2, 94.5, 49.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 930 8.00 N 810 7.00 C 2925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 934.6 milliseconds 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 47.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 44 removed outlier: 6.694A pdb=" N GLY A 36 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY C 36 " --> pdb=" O GLU E 35 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY E 36 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY G 36 " --> pdb=" O GLU I 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 6.526A pdb=" N VAL A 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL C 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLY A 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N THR C 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL E 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLY C 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N THR E 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N ALA C 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 49 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL G 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLY E 51 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 10.097A pdb=" N THR G 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N ALA E 53 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL G 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL I 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLY G 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 10.097A pdb=" N THR I 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N ALA G 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 66 Processing sheet with id=AA4, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA5, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.319A pdb=" N VAL A 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL C 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL E 77 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL G 77 " --> pdb=" O ALA I 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 88 through 96 Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 43 Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 57 removed outlier: 6.847A pdb=" N GLY B 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL D 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS D 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY B 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY D 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL F 48 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL D 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS F 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY D 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY F 47 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL H 48 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL F 49 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS H 50 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY F 51 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY H 47 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL J 48 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL H 49 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS J 50 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY H 51 " --> pdb=" O HIS J 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 62 through 67 removed outlier: 6.371A pdb=" N VAL B 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL D 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASN B 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL D 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL F 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASN D 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL F 63 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL H 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASN F 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL H 63 " --> pdb=" O THR J 64 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL J 66 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASN H 65 " --> pdb=" O VAL J 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 70 through 72 Processing sheet with id=AB2, first strand: chain 'B' and resid 75 through 79 Processing sheet with id=AB3, first strand: chain 'B' and resid 88 through 94 180 hydrogen bonds defined for protein. 540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.25: 810 1.25 - 1.33: 514 1.33 - 1.41: 366 1.41 - 1.48: 790 1.48 - 1.56: 2200 Bond restraints: 4680 Sorted by residual: bond pdb=" C LYS E 60 " pdb=" O LYS E 60 " ideal model delta sigma weight residual 1.234 1.196 0.039 8.30e-03 1.45e+04 2.17e+01 bond pdb=" C LYS A 60 " pdb=" O LYS A 60 " ideal model delta sigma weight residual 1.234 1.196 0.039 8.30e-03 1.45e+04 2.16e+01 bond pdb=" C LYS I 60 " pdb=" O LYS I 60 " ideal model delta sigma weight residual 1.234 1.196 0.039 8.30e-03 1.45e+04 2.16e+01 bond pdb=" C LYS C 60 " pdb=" O LYS C 60 " ideal model delta sigma weight residual 1.234 1.196 0.038 8.30e-03 1.45e+04 2.15e+01 bond pdb=" C LYS G 60 " pdb=" O LYS G 60 " ideal model delta sigma weight residual 1.234 1.196 0.038 8.30e-03 1.45e+04 2.14e+01 ... (remaining 4675 not shown) Histogram of bond angle deviations from ideal: 102.84 - 108.53: 314 108.53 - 114.23: 2722 114.23 - 119.92: 1175 119.92 - 125.62: 2089 125.62 - 131.32: 15 Bond angle restraints: 6315 Sorted by residual: angle pdb=" N ALA B 90 " pdb=" CA ALA B 90 " pdb=" C ALA B 90 " ideal model delta sigma weight residual 109.52 117.52 -8.00 1.55e+00 4.16e-01 2.66e+01 angle pdb=" N ALA H 90 " pdb=" CA ALA H 90 " pdb=" C ALA H 90 " ideal model delta sigma weight residual 109.52 117.51 -7.99 1.55e+00 4.16e-01 2.66e+01 angle pdb=" N ALA F 90 " pdb=" CA ALA F 90 " pdb=" C ALA F 90 " ideal model delta sigma weight residual 109.52 117.50 -7.98 1.55e+00 4.16e-01 2.65e+01 angle pdb=" N ALA D 90 " pdb=" CA ALA D 90 " pdb=" C ALA D 90 " ideal model delta sigma weight residual 109.52 117.50 -7.98 1.55e+00 4.16e-01 2.65e+01 angle pdb=" N ALA J 90 " pdb=" CA ALA J 90 " pdb=" C ALA J 90 " ideal model delta sigma weight residual 109.52 117.50 -7.98 1.55e+00 4.16e-01 2.65e+01 ... (remaining 6310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.02: 2365 14.02 - 28.03: 210 28.03 - 42.04: 100 42.04 - 56.06: 35 56.06 - 70.07: 25 Dihedral angle restraints: 2735 sinusoidal: 910 harmonic: 1825 Sorted by residual: dihedral pdb=" CA VAL E 82 " pdb=" C VAL E 82 " pdb=" N GLU E 83 " pdb=" CA GLU E 83 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA VAL I 82 " pdb=" C VAL I 82 " pdb=" N GLU I 83 " pdb=" CA GLU I 83 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA VAL C 82 " pdb=" C VAL C 82 " pdb=" N GLU C 83 " pdb=" CA GLU C 83 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 2732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 487 0.051 - 0.101: 253 0.101 - 0.152: 90 0.152 - 0.202: 0 0.202 - 0.253: 5 Chirality restraints: 835 Sorted by residual: chirality pdb=" CA GLU J 35 " pdb=" N GLU J 35 " pdb=" C GLU J 35 " pdb=" CB GLU J 35 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA GLU H 35 " pdb=" N GLU H 35 " pdb=" C GLU H 35 " pdb=" CB GLU H 35 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA GLU F 35 " pdb=" N GLU F 35 " pdb=" C GLU F 35 " pdb=" CB GLU F 35 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 832 not shown) Planarity restraints: 775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 60 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C LYS F 60 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS F 60 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU F 61 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 60 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C LYS D 60 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS D 60 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU D 61 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS J 60 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C LYS J 60 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS J 60 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU J 61 " 0.013 2.00e-02 2.50e+03 ... (remaining 772 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1414 2.83 - 3.35: 3724 3.35 - 3.87: 8513 3.87 - 4.38: 9482 4.38 - 4.90: 17976 Nonbonded interactions: 41109 Sorted by model distance: nonbonded pdb=" O GLU A 83 " pdb=" OE1 GLU A 83 " model vdw 2.313 3.040 nonbonded pdb=" O GLU C 83 " pdb=" OE1 GLU C 83 " model vdw 2.313 3.040 nonbonded pdb=" O GLU I 83 " pdb=" OE1 GLU I 83 " model vdw 2.313 3.040 nonbonded pdb=" O GLU G 83 " pdb=" OE1 GLU G 83 " model vdw 2.313 3.040 nonbonded pdb=" O GLU E 83 " pdb=" OE1 GLU E 83 " model vdw 2.313 3.040 ... (remaining 41104 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' and resid 33 through 97) selection = chain 'B' selection = (chain 'C' and resid 33 through 97) selection = chain 'D' selection = (chain 'E' and resid 33 through 97) selection = chain 'F' selection = (chain 'G' and resid 33 through 97) selection = chain 'H' selection = (chain 'I' and resid 33 through 97) 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.370 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 17.240 Find NCS groups from input model: 0.340 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:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.009 0.059 4680 Z= 0.617 Angle : 1.159 10.601 6315 Z= 0.728 Chirality : 0.064 0.253 835 Planarity : 0.005 0.022 775 Dihedral : 16.568 70.074 1585 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.19 % Allowed : 19.15 % Favored : 77.66 % 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: -3.01 (0.28), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.21), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS G 50 PHE 0.012 0.003 PHE A 94 TYR 0.012 0.004 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 0.556 Fit side-chains REVERT: A 45 LYS cc_start: 0.8522 (tttp) cc_final: 0.8303 (tttp) REVERT: A 58 LYS cc_start: 0.8821 (mtpt) cc_final: 0.8314 (mttp) REVERT: B 58 LYS cc_start: 0.8779 (mttm) cc_final: 0.8391 (mttm) REVERT: C 45 LYS cc_start: 0.8492 (tttp) cc_final: 0.8284 (tttp) REVERT: C 58 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8385 (mttm) REVERT: D 58 LYS cc_start: 0.8589 (mttm) cc_final: 0.8231 (mttp) REVERT: E 45 LYS cc_start: 0.8442 (tttp) cc_final: 0.8239 (tttp) REVERT: H 44 THR cc_start: 0.8967 (t) cc_final: 0.8657 (m) REVERT: H 58 LYS cc_start: 0.8652 (mttm) cc_final: 0.8282 (mttp) REVERT: I 34 LYS cc_start: 0.8387 (mttt) cc_final: 0.8173 (mtmt) REVERT: I 58 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8294 (mttp) REVERT: J 35 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6545 (tm-30) outliers start: 15 outliers final: 5 residues processed: 111 average time/residue: 1.3842 time to fit residues: 158.6295 Evaluate side-chains 105 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 44 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN D 62 GLN D 65 ASN E 62 GLN F 62 GLN H 62 GLN H 65 ASN I 62 GLN J 62 GLN J 65 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4680 Z= 0.214 Angle : 0.598 5.257 6315 Z= 0.340 Chirality : 0.052 0.133 835 Planarity : 0.003 0.011 775 Dihedral : 5.740 21.765 680 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 4.89 % Allowed : 20.21 % Favored : 74.89 % 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: -2.53 (0.30), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 PHE 0.018 0.004 PHE D 94 TYR 0.014 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 0.522 Fit side-chains REVERT: A 45 LYS cc_start: 0.8733 (tttp) cc_final: 0.8464 (tttp) REVERT: A 58 LYS cc_start: 0.8654 (mtpt) cc_final: 0.8150 (mttp) REVERT: B 58 LYS cc_start: 0.8886 (mttm) cc_final: 0.8499 (mttm) REVERT: B 62 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8482 (tm-30) REVERT: C 44 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8638 (t) REVERT: D 58 LYS cc_start: 0.8687 (mttm) cc_final: 0.8467 (mttm) REVERT: H 58 LYS cc_start: 0.8799 (mttm) cc_final: 0.8584 (mttm) REVERT: H 83 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6827 (tp30) REVERT: I 58 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8257 (mttp) REVERT: J 35 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6858 (tm-30) outliers start: 23 outliers final: 10 residues processed: 111 average time/residue: 1.4179 time to fit residues: 162.2800 Evaluate side-chains 102 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 49 optimal weight: 0.0870 chunk 40 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN B 65 ASN G 62 GLN G 65 ASN I 62 GLN J 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 4680 Z= 0.364 Angle : 0.649 5.769 6315 Z= 0.363 Chirality : 0.053 0.132 835 Planarity : 0.003 0.013 775 Dihedral : 5.932 22.563 680 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 5.74 % Allowed : 20.21 % Favored : 74.04 % 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: -2.44 (0.30), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 50 PHE 0.019 0.004 PHE G 94 TYR 0.013 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 0.594 Fit side-chains REVERT: A 58 LYS cc_start: 0.8667 (mtpt) cc_final: 0.8141 (mttp) REVERT: B 58 LYS cc_start: 0.8858 (mttm) cc_final: 0.8514 (mttp) REVERT: C 58 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8290 (mttm) REVERT: D 58 LYS cc_start: 0.8627 (mttm) cc_final: 0.8392 (mttm) REVERT: D 61 GLU cc_start: 0.8411 (pm20) cc_final: 0.8134 (mp0) REVERT: H 46 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7478 (tt0) REVERT: H 58 LYS cc_start: 0.8630 (mttm) cc_final: 0.8371 (mttm) REVERT: I 58 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8167 (mttp) REVERT: J 35 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6843 (tm-30) outliers start: 27 outliers final: 12 residues processed: 110 average time/residue: 1.5178 time to fit residues: 171.9165 Evaluate side-chains 106 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 39 optimal weight: 0.0270 chunk 59 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 2.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN C 62 GLN D 65 ASN I 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4680 Z= 0.237 Angle : 0.587 5.087 6315 Z= 0.330 Chirality : 0.052 0.133 835 Planarity : 0.002 0.014 775 Dihedral : 5.659 22.338 679 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 4.68 % Allowed : 21.49 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.30), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.017 0.004 PHE G 94 TYR 0.012 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.627 Fit side-chains REVERT: A 58 LYS cc_start: 0.8552 (mtpt) cc_final: 0.8076 (mttp) REVERT: B 58 LYS cc_start: 0.8856 (mttm) cc_final: 0.8477 (mttm) REVERT: C 58 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8418 (mttm) REVERT: D 58 LYS cc_start: 0.8494 (mttm) cc_final: 0.8100 (mttp) REVERT: D 83 GLU cc_start: 0.7037 (tm-30) cc_final: 0.6645 (tp30) REVERT: G 44 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8479 (m) REVERT: G 57 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: H 46 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7461 (tt0) REVERT: H 58 LYS cc_start: 0.8641 (mttm) cc_final: 0.8306 (mttp) REVERT: H 83 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6713 (tp30) REVERT: I 58 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8134 (mttp) REVERT: I 62 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8098 (tm130) REVERT: J 35 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6835 (tm-30) outliers start: 22 outliers final: 11 residues processed: 101 average time/residue: 1.4927 time to fit residues: 155.3082 Evaluate side-chains 103 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN H 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.071 4680 Z= 0.659 Angle : 0.780 7.005 6315 Z= 0.436 Chirality : 0.058 0.160 835 Planarity : 0.003 0.011 775 Dihedral : 6.384 26.305 678 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 6.38 % Allowed : 20.85 % Favored : 72.77 % 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: -2.54 (0.29), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 50 PHE 0.024 0.005 PHE G 94 TYR 0.013 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 98 time to evaluate : 0.495 Fit side-chains REVERT: A 58 LYS cc_start: 0.8688 (mtpt) cc_final: 0.8186 (mttp) REVERT: B 45 LYS cc_start: 0.7928 (mmtp) cc_final: 0.7686 (mttp) REVERT: B 58 LYS cc_start: 0.8906 (mttm) cc_final: 0.8561 (mttm) REVERT: B 83 GLU cc_start: 0.7376 (tm-30) cc_final: 0.7131 (tp30) REVERT: C 58 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8370 (mttm) REVERT: D 58 LYS cc_start: 0.8611 (mttm) cc_final: 0.8348 (mttm) REVERT: F 58 LYS cc_start: 0.8947 (mttm) cc_final: 0.8735 (mttm) REVERT: G 57 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7387 (tm-30) REVERT: H 58 LYS cc_start: 0.8625 (mttm) cc_final: 0.8354 (mttm) REVERT: H 83 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6799 (tp30) REVERT: I 58 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8167 (mttp) REVERT: J 35 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6848 (tm-30) REVERT: J 96 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7677 (mtpp) outliers start: 30 outliers final: 22 residues processed: 116 average time/residue: 1.4554 time to fit residues: 174.0200 Evaluate side-chains 115 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN I 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4680 Z= 0.262 Angle : 0.617 5.638 6315 Z= 0.342 Chirality : 0.053 0.135 835 Planarity : 0.002 0.017 775 Dihedral : 5.895 24.836 678 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 5.96 % Allowed : 22.55 % Favored : 71.49 % 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: -2.55 (0.29), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.017 0.004 PHE F 94 TYR 0.012 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 0.485 Fit side-chains REVERT: A 58 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8109 (mttp) REVERT: A 62 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: B 58 LYS cc_start: 0.8904 (mttm) cc_final: 0.8525 (mttm) REVERT: C 58 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8364 (mttm) REVERT: C 62 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7219 (tt0) REVERT: G 44 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8462 (m) REVERT: G 57 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: H 46 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: H 58 LYS cc_start: 0.8627 (mttm) cc_final: 0.8289 (mttp) REVERT: H 60 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8651 (ttmt) REVERT: H 83 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6707 (tp30) REVERT: I 58 LYS cc_start: 0.8665 (mtpt) cc_final: 0.8174 (mttp) REVERT: I 62 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8087 (tm130) REVERT: J 35 GLU cc_start: 0.7311 (tm-30) cc_final: 0.6824 (tm-30) outliers start: 28 outliers final: 19 residues processed: 113 average time/residue: 1.2984 time to fit residues: 151.7440 Evaluate side-chains 118 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN G 65 ASN H 65 ASN I 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 4680 Z= 0.480 Angle : 0.723 8.277 6315 Z= 0.400 Chirality : 0.055 0.164 835 Planarity : 0.003 0.016 775 Dihedral : 6.210 26.667 678 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 7.02 % Allowed : 21.70 % Favored : 71.28 % 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: -2.54 (0.29), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 50 PHE 0.022 0.005 PHE G 94 TYR 0.014 0.003 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 96 time to evaluate : 0.537 Fit side-chains REVERT: A 58 LYS cc_start: 0.8643 (mtpt) cc_final: 0.8144 (mttp) REVERT: A 62 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8116 (tm130) REVERT: B 58 LYS cc_start: 0.8898 (mttm) cc_final: 0.8620 (mttm) REVERT: B 83 GLU cc_start: 0.7281 (tm-30) cc_final: 0.7023 (tp30) REVERT: C 58 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8344 (mttm) REVERT: E 62 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8025 (tt0) REVERT: G 57 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: H 46 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: H 58 LYS cc_start: 0.8628 (mttm) cc_final: 0.8399 (mttm) REVERT: H 60 LYS cc_start: 0.8931 (ttmt) cc_final: 0.8682 (ttmt) REVERT: H 83 GLU cc_start: 0.7310 (tm-30) cc_final: 0.6811 (tp30) REVERT: I 58 LYS cc_start: 0.8673 (mtpt) cc_final: 0.8182 (mttp) REVERT: J 35 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6819 (tm-30) REVERT: J 96 LYS cc_start: 0.8086 (ttmt) cc_final: 0.7613 (mtpp) outliers start: 33 outliers final: 23 residues processed: 120 average time/residue: 1.2962 time to fit residues: 160.7805 Evaluate side-chains 121 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN C 62 GLN D 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4680 Z= 0.390 Angle : 0.702 8.603 6315 Z= 0.388 Chirality : 0.054 0.148 835 Planarity : 0.003 0.021 775 Dihedral : 6.163 26.631 678 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 6.60 % Allowed : 22.55 % Favored : 70.85 % 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: -2.54 (0.29), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 50 PHE 0.019 0.004 PHE G 94 TYR 0.015 0.002 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 0.527 Fit side-chains REVERT: A 58 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8194 (mttp) REVERT: B 58 LYS cc_start: 0.8867 (mttm) cc_final: 0.8590 (mttm) REVERT: B 83 GLU cc_start: 0.7317 (tm-30) cc_final: 0.7012 (tp30) REVERT: C 58 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8395 (mttm) REVERT: E 62 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8103 (tm-30) REVERT: G 57 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: H 46 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7556 (tt0) REVERT: H 58 LYS cc_start: 0.8612 (mttm) cc_final: 0.8391 (mttm) REVERT: H 83 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6713 (tp30) REVERT: I 58 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8148 (mttp) REVERT: J 35 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6805 (tm-30) REVERT: J 96 LYS cc_start: 0.8086 (ttmt) cc_final: 0.7607 (mtpp) outliers start: 31 outliers final: 22 residues processed: 121 average time/residue: 1.3389 time to fit residues: 167.3915 Evaluate side-chains 122 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN C 62 GLN H 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 4680 Z= 0.385 Angle : 0.713 9.267 6315 Z= 0.393 Chirality : 0.054 0.133 835 Planarity : 0.003 0.020 775 Dihedral : 6.212 26.914 678 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 6.81 % Allowed : 23.19 % Favored : 70.00 % 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: -2.53 (0.30), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 PHE 0.020 0.004 PHE G 94 TYR 0.011 0.002 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8594 (mtpt) cc_final: 0.8139 (mttp) REVERT: B 58 LYS cc_start: 0.8872 (mttm) cc_final: 0.8594 (mttm) REVERT: B 83 GLU cc_start: 0.7327 (tm-30) cc_final: 0.7002 (tp30) REVERT: C 58 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8240 (mttm) REVERT: E 62 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: G 57 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7431 (tm-30) REVERT: H 46 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: H 58 LYS cc_start: 0.8606 (mttm) cc_final: 0.8392 (mttm) REVERT: H 83 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6709 (tp30) REVERT: I 58 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8220 (mttp) REVERT: J 35 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6912 (tm-30) REVERT: J 96 LYS cc_start: 0.8102 (ttmt) cc_final: 0.7620 (mtpp) outliers start: 32 outliers final: 24 residues processed: 119 average time/residue: 1.3329 time to fit residues: 163.8636 Evaluate side-chains 123 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 5 optimal weight: 0.0470 chunk 39 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 overall best weight: 1.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN D 65 ASN E 62 GLN G 62 GLN I 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4680 Z= 0.194 Angle : 0.647 9.525 6315 Z= 0.357 Chirality : 0.053 0.138 835 Planarity : 0.002 0.022 775 Dihedral : 5.725 24.789 678 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 5.74 % Allowed : 23.83 % Favored : 70.43 % 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: -2.46 (0.30), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS G 50 PHE 0.018 0.004 PHE D 94 TYR 0.016 0.002 TYR F 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 0.532 Fit side-chains REVERT: B 58 LYS cc_start: 0.8888 (mttm) cc_final: 0.8641 (mttm) REVERT: B 83 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6942 (tp30) REVERT: C 58 LYS cc_start: 0.8460 (mtpt) cc_final: 0.8162 (mttm) REVERT: D 58 LYS cc_start: 0.8716 (mttm) cc_final: 0.8458 (mttp) REVERT: G 57 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7411 (tm-30) REVERT: H 46 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: H 58 LYS cc_start: 0.8612 (mttm) cc_final: 0.8279 (mttp) REVERT: H 60 LYS cc_start: 0.8847 (ttmt) cc_final: 0.8610 (ttmt) REVERT: H 83 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6634 (tp30) REVERT: I 58 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8202 (mttp) REVERT: J 35 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6981 (tp30) outliers start: 27 outliers final: 17 residues processed: 113 average time/residue: 1.3293 time to fit residues: 155.2409 Evaluate side-chains 108 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 0.0870 chunk 34 optimal weight: 6.9990 overall best weight: 5.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN E 62 GLN H 65 ASN I 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.103355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.087206 restraints weight = 6480.694| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.00 r_work: 0.3307 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 4680 Z= 0.519 Angle : 0.792 10.759 6315 Z= 0.436 Chirality : 0.056 0.150 835 Planarity : 0.003 0.019 775 Dihedral : 6.227 25.425 676 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.89 % Allowed : 24.26 % Favored : 70.85 % 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: -2.49 (0.30), residues: 650 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 50 PHE 0.022 0.005 PHE G 94 TYR 0.015 0.003 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2682.39 seconds wall clock time: 48 minutes 15.31 seconds (2895.31 seconds total)