Starting phenix.real_space_refine on Thu Dec 7 16:34:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo1_33333/12_2023/7xo1_33333.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo1_33333/12_2023/7xo1_33333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo1_33333/12_2023/7xo1_33333.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo1_33333/12_2023/7xo1_33333.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo1_33333/12_2023/7xo1_33333.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo1_33333/12_2023/7xo1_33333.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 1602 2.51 5 N 444 2.21 5 O 504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2550 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "A" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "D" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "B" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "E" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "C" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Time building chain proxies: 1.81, per 1000 atoms: 0.71 Number of scatterers: 2550 At special positions: 0 Unit cell: (128.26, 71.02, 33.92, 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 504 8.00 N 444 7.00 C 1602 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: 0.90 Conformation dependent library (CDL) restraints added in 547.1 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 45.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 37 through 42 removed outlier: 6.508A pdb=" N VAL F 37 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL D 40 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR F 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER D 42 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY F 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL D 37 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL E 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR D 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N SER E 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY D 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 48 through 57 removed outlier: 6.547A pdb=" N VAL F 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY D 51 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N HIS F 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA D 53 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N VAL F 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 10.526A pdb=" N VAL D 55 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N THR F 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N GLU D 57 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N ALA F 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL D 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLY E 51 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N HIS D 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA E 53 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N VAL D 52 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 10.566A pdb=" N VAL E 55 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N THR D 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 10.395A pdb=" N GLU E 57 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ALA D 56 " --> pdb=" O GLU E 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 61 through 66 removed outlier: 6.220A pdb=" N GLU F 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR D 64 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL F 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL D 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN F 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU D 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR E 64 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL E 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASN D 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 69 through 72 Processing sheet with id=AA5, first strand: chain 'F' and resid 75 through 79 Processing sheet with id=AA6, first strand: chain 'F' and resid 82 through 83 removed outlier: 6.261A pdb=" N VAL F 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL D 82 " --> pdb=" O GLU E 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 95 through 96 Processing sheet with id=AA8, first strand: chain 'A' and resid 37 through 42 removed outlier: 6.503A pdb=" N VAL A 37 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL B 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TYR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N SER B 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLY A 41 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 37 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL C 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER C 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY B 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 48 through 57 removed outlier: 6.563A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLY B 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N HIS A 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA B 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N VAL A 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 10.558A pdb=" N VAL B 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N GLU B 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ALA A 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLY C 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N HIS B 50 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA C 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N VAL B 52 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N VAL C 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N THR B 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 10.363A pdb=" N GLU C 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N ALA B 56 " --> pdb=" O GLU C 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 61 through 66 removed outlier: 6.231A pdb=" N GLU A 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N THR B 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU B 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N THR C 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL C 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASN B 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 69 through 72 Processing sheet with id=AB3, first strand: chain 'A' and resid 75 through 79 Processing sheet with id=AB4, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.273A pdb=" N VAL A 82 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL B 82 " --> pdb=" O GLU C 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 95 through 96 32 hydrogen bonds defined for protein. 96 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: 0.55 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 438 1.29 - 1.36: 402 1.36 - 1.42: 102 1.42 - 1.48: 420 1.48 - 1.55: 1200 Bond restraints: 2562 Sorted by residual: bond pdb=" CB LYS F 97 " pdb=" CG LYS F 97 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.59e-01 bond pdb=" CB LYS A 97 " pdb=" CG LYS A 97 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.42e-01 bond pdb=" CB LYS D 97 " pdb=" CG LYS D 97 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.21e-01 bond pdb=" CB LYS E 97 " pdb=" CG LYS E 97 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.18e-01 bond pdb=" CB LYS C 97 " pdb=" CG LYS C 97 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.17e-01 ... (remaining 2557 not shown) Histogram of bond angle deviations from ideal: 106.09 - 111.12: 1118 111.12 - 116.16: 743 116.16 - 121.20: 779 121.20 - 126.23: 816 126.23 - 131.27: 6 Bond angle restraints: 3462 Sorted by residual: angle pdb=" CA LYS B 97 " pdb=" CB LYS B 97 " pdb=" CG LYS B 97 " ideal model delta sigma weight residual 114.10 118.87 -4.77 2.00e+00 2.50e-01 5.69e+00 angle pdb=" CA LYS E 97 " pdb=" CB LYS E 97 " pdb=" CG LYS E 97 " ideal model delta sigma weight residual 114.10 118.87 -4.77 2.00e+00 2.50e-01 5.69e+00 angle pdb=" CA LYS C 97 " pdb=" CB LYS C 97 " pdb=" CG LYS C 97 " ideal model delta sigma weight residual 114.10 118.86 -4.76 2.00e+00 2.50e-01 5.67e+00 angle pdb=" CA LYS D 97 " pdb=" CB LYS D 97 " pdb=" CG LYS D 97 " ideal model delta sigma weight residual 114.10 118.85 -4.75 2.00e+00 2.50e-01 5.65e+00 angle pdb=" CA LYS A 97 " pdb=" CB LYS A 97 " pdb=" CG LYS A 97 " ideal model delta sigma weight residual 114.10 118.85 -4.75 2.00e+00 2.50e-01 5.64e+00 ... (remaining 3457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 1314 16.18 - 32.36: 132 32.36 - 48.53: 12 48.53 - 64.71: 18 64.71 - 80.89: 12 Dihedral angle restraints: 1488 sinusoidal: 492 harmonic: 996 Sorted by residual: dihedral pdb=" CA LYS D 43 " pdb=" CB LYS D 43 " pdb=" CG LYS D 43 " pdb=" CD LYS D 43 " ideal model delta sinusoidal sigma weight residual -60.00 -111.69 51.69 3 1.50e+01 4.44e-03 9.04e+00 dihedral pdb=" CA LYS B 43 " pdb=" CB LYS B 43 " pdb=" CG LYS B 43 " pdb=" CD LYS B 43 " ideal model delta sinusoidal sigma weight residual -60.00 -111.69 51.69 3 1.50e+01 4.44e-03 9.04e+00 dihedral pdb=" CA LYS C 43 " pdb=" CB LYS C 43 " pdb=" CG LYS C 43 " pdb=" CD LYS C 43 " ideal model delta sinusoidal sigma weight residual -60.00 -111.66 51.66 3 1.50e+01 4.44e-03 9.04e+00 ... (remaining 1485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 244 0.027 - 0.053: 89 0.053 - 0.080: 33 0.080 - 0.107: 41 0.107 - 0.133: 49 Chirality restraints: 456 Sorted by residual: chirality pdb=" CA ILE F 88 " pdb=" N ILE F 88 " pdb=" C ILE F 88 " pdb=" CB ILE F 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE D 88 " pdb=" N ILE D 88 " pdb=" C ILE D 88 " pdb=" CB ILE D 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 453 not shown) Planarity restraints: 426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 39 " -0.006 2.00e-02 2.50e+03 7.34e-03 1.08e+00 pdb=" CG TYR F 39 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR F 39 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR F 39 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR F 39 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 39 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 39 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR F 39 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 39 " 0.006 2.00e-02 2.50e+03 7.34e-03 1.08e+00 pdb=" CG TYR C 39 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR C 39 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 39 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR C 39 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 39 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 39 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 39 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 39 " 0.006 2.00e-02 2.50e+03 7.33e-03 1.07e+00 pdb=" CG TYR A 39 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 39 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 39 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 39 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 39 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 39 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 39 " 0.000 2.00e-02 2.50e+03 ... (remaining 423 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 383 2.79 - 3.32: 2171 3.32 - 3.85: 3983 3.85 - 4.37: 4040 4.37 - 4.90: 8391 Nonbonded interactions: 18968 Sorted by model distance: nonbonded pdb=" OE1 GLN E 62 " pdb=" OG1 THR E 64 " model vdw 2.269 2.440 nonbonded pdb=" OE1 GLN A 62 " pdb=" OG1 THR A 64 " model vdw 2.269 2.440 nonbonded pdb=" OE1 GLN C 62 " pdb=" OG1 THR C 64 " model vdw 2.269 2.440 nonbonded pdb=" OE1 GLN B 62 " pdb=" OG1 THR B 64 " model vdw 2.270 2.440 nonbonded pdb=" OE1 GLN D 62 " pdb=" OG1 THR D 64 " model vdw 2.270 2.440 ... (remaining 18963 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' } 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: 1.030 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: 4.740 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.580 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2562 Z= 0.141 Angle : 0.528 4.771 3462 Z= 0.288 Chirality : 0.055 0.133 456 Planarity : 0.002 0.008 426 Dihedral : 16.422 80.891 864 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 18.60 % Favored : 81.40 % 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 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.001 0.000 PHE B 94 TYR 0.018 0.005 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.286 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.8819 time to fit residues: 43.7686 Evaluate side-chains 44 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 62 GLN D 65 ASN B 65 ASN E 65 ASN C 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 2562 Z= 0.332 Angle : 0.569 3.578 3462 Z= 0.315 Chirality : 0.053 0.127 456 Planarity : 0.002 0.006 426 Dihedral : 4.902 13.839 372 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 4.65 % Allowed : 16.67 % Favored : 78.68 % 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: -2.49 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS D 50 PHE 0.002 0.001 PHE D 94 TYR 0.015 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.299 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 51 average time/residue: 0.7296 time to fit residues: 38.6470 Evaluate side-chains 45 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.276 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.3869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN E 65 ASN C 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2562 Z= 0.291 Angle : 0.541 3.871 3462 Z= 0.301 Chirality : 0.053 0.133 456 Planarity : 0.002 0.012 426 Dihedral : 4.919 14.065 372 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.71 % Allowed : 19.77 % Favored : 77.52 % 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 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 50 PHE 0.003 0.000 PHE B 94 TYR 0.014 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.284 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.7991 time to fit residues: 38.1197 Evaluate side-chains 44 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.281 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.3714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN E 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.023 2562 Z= 0.401 Angle : 0.597 4.047 3462 Z= 0.335 Chirality : 0.054 0.132 456 Planarity : 0.002 0.012 426 Dihedral : 5.311 15.768 372 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.71 % Allowed : 20.16 % Favored : 77.13 % 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: -2.40 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS D 50 PHE 0.003 0.001 PHE B 94 TYR 0.016 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.257 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 50 average time/residue: 0.8494 time to fit residues: 43.9188 Evaluate side-chains 46 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.255 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.3185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 0.0870 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.0050 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.2178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2562 Z= 0.166 Angle : 0.501 4.347 3462 Z= 0.272 Chirality : 0.053 0.134 456 Planarity : 0.002 0.013 426 Dihedral : 4.572 11.759 372 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.33 % Allowed : 20.54 % Favored : 77.13 % 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: -2.34 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.002 0.000 PHE B 94 TYR 0.016 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.294 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 47 average time/residue: 0.7248 time to fit residues: 35.4420 Evaluate side-chains 45 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.273 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.3640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 2 optimal weight: 0.2980 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN B 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.027 2562 Z= 0.504 Angle : 0.647 4.353 3462 Z= 0.361 Chirality : 0.055 0.129 456 Planarity : 0.002 0.013 426 Dihedral : 5.520 16.158 372 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.33 % Allowed : 22.87 % Favored : 74.81 % 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: -2.35 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 50 PHE 0.004 0.001 PHE B 94 TYR 0.015 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.293 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 49 average time/residue: 0.9115 time to fit residues: 46.0907 Evaluate side-chains 49 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.284 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.3705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN B 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2562 Z= 0.342 Angle : 0.601 4.884 3462 Z= 0.328 Chirality : 0.053 0.136 456 Planarity : 0.002 0.016 426 Dihedral : 5.264 15.089 372 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.33 % Allowed : 23.64 % Favored : 74.03 % 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: -2.31 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 50 PHE 0.003 0.000 PHE B 94 TYR 0.015 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.287 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 48 average time/residue: 0.8532 time to fit residues: 42.3756 Evaluate side-chains 47 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.281 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.3700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 31 optimal weight: 0.0670 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.6724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2562 Z= 0.204 Angle : 0.527 4.742 3462 Z= 0.286 Chirality : 0.053 0.133 456 Planarity : 0.002 0.016 426 Dihedral : 4.729 12.297 372 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.33 % Allowed : 24.03 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.002 0.000 PHE B 94 TYR 0.018 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.298 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 49 average time/residue: 0.8165 time to fit residues: 41.4642 Evaluate side-chains 48 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.267 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.3724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2562 Z= 0.249 Angle : 0.566 5.137 3462 Z= 0.304 Chirality : 0.053 0.130 456 Planarity : 0.002 0.014 426 Dihedral : 4.820 12.376 372 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.33 % Allowed : 24.81 % Favored : 72.87 % 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: -2.18 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 50 PHE 0.002 0.000 PHE B 94 TYR 0.018 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.286 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 48 average time/residue: 0.8076 time to fit residues: 40.1837 Evaluate side-chains 47 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.313 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.4223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.025 2562 Z= 0.440 Angle : 0.644 5.832 3462 Z= 0.357 Chirality : 0.054 0.131 456 Planarity : 0.002 0.012 426 Dihedral : 5.401 14.603 372 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.33 % Allowed : 25.19 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 PHE 0.003 0.001 PHE B 94 TYR 0.018 0.003 TYR A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.285 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 49 average time/residue: 0.8947 time to fit residues: 45.2974 Evaluate side-chains 49 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.280 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.3724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 62 GLN B 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.131556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.107070 restraints weight = 2914.986| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.32 r_work: 0.3313 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 2562 Z= 0.143 Angle : 0.540 6.086 3462 Z= 0.285 Chirality : 0.053 0.136 456 Planarity : 0.002 0.012 426 Dihedral : 4.382 11.260 372 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.33 % Allowed : 23.64 % Favored : 74.03 % 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: -2.11 (0.46), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.001 0.000 PHE D 94 TYR 0.019 0.003 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1382.18 seconds wall clock time: 25 minutes 15.62 seconds (1515.62 seconds total)