Starting phenix.real_space_refine on Sun Mar 10 15:04:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo2_33334/03_2024/7xo2_33334.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo2_33334/03_2024/7xo2_33334.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/7xo2_33334/03_2024/7xo2_33334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo2_33334/03_2024/7xo2_33334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo2_33334/03_2024/7xo2_33334.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo2_33334/03_2024/7xo2_33334.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= 0.001 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 "I TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 61": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2550 Number of models: 1 Model: "" Number of chains: 6 Chain: "I" 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} 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: "A" 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: "B" 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: 1.77, per 1000 atoms: 0.69 Number of scatterers: 2550 At special positions: 0 Unit cell: (96.46, 94.34, 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: 0.94 Conformation dependent library (CDL) restraints added in 535.4 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 16 sheets defined 0.0% alpha, 56.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'I' and resid 37 through 45 removed outlier: 6.598A pdb=" N VAL D 37 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL E 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR D 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N SER E 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY D 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR E 44 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LYS D 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 48 through 57 removed outlier: 6.639A pdb=" N VAL I 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY D 51 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N HIS I 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA D 53 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N VAL I 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 10.566A pdb=" N VAL D 55 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N THR I 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 10.271A pdb=" N GLU D 57 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA I 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL D 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N HIS E 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY D 51 " --> pdb=" O HIS E 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 61 through 66 removed outlier: 6.349A pdb=" N GLU I 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR D 64 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL I 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL D 66 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASN I 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU D 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N THR E 64 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL E 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.074A 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 'I' and resid 69 through 72 Processing sheet with id=AA5, first strand: chain 'I' and resid 75 through 79 Processing sheet with id=AA6, first strand: chain 'I' and resid 82 through 83 removed outlier: 6.488A pdb=" N VAL I 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.567A 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 'I' and resid 87 through 88 Processing sheet with id=AA8, first strand: chain 'I' and resid 92 through 96 Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 45 removed outlier: 6.631A pdb=" N VAL C 37 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL A 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR C 39 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N SER A 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY C 41 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N THR A 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS C 43 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 37 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL B 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N SER B 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY A 41 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR B 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LYS A 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 48 through 57 removed outlier: 6.946A pdb=" N VAL C 49 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N HIS A 50 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY C 51 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLY B 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N HIS A 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA B 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N VAL A 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 10.509A pdb=" N VAL B 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 10.201A pdb=" N GLU B 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ALA A 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 61 through 66 removed outlier: 6.250A pdb=" N GLU C 61 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR A 64 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL C 63 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL A 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN C 65 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLU A 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N THR B 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 69 through 72 Processing sheet with id=AB4, first strand: chain 'C' and resid 75 through 79 Processing sheet with id=AB5, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.573A pdb=" N VAL C 82 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 82 " --> pdb=" O GLU B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AB7, first strand: chain 'C' and resid 92 through 96 68 hydrogen bonds defined for protein. 204 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: 0.71 Time building geometry restraints manager: 1.03 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=" CA LYS A 60 " pdb=" C LYS A 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 3.00e-01 bond pdb=" CA LYS D 60 " pdb=" C LYS D 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 2.97e-01 bond pdb=" CA LYS C 60 " pdb=" C LYS C 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 2.72e-01 bond pdb=" CA LYS B 60 " pdb=" C LYS B 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 2.66e-01 bond pdb=" CA LYS E 60 " pdb=" C LYS E 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 2.53e-01 ... (remaining 2557 not shown) Histogram of bond angle deviations from ideal: 106.07 - 111.11: 1096 111.11 - 116.15: 734 116.15 - 121.19: 833 121.19 - 126.23: 793 126.23 - 131.27: 6 Bond angle restraints: 3462 Sorted by residual: angle pdb=" C THR D 59 " pdb=" N LYS D 60 " pdb=" CA LYS D 60 " ideal model delta sigma weight residual 122.17 120.34 1.83 1.54e+00 4.22e-01 1.42e+00 angle pdb=" C THR C 59 " pdb=" N LYS C 60 " pdb=" CA LYS C 60 " ideal model delta sigma weight residual 122.17 120.35 1.82 1.54e+00 4.22e-01 1.40e+00 angle pdb=" C THR B 59 " pdb=" N LYS B 60 " pdb=" CA LYS B 60 " ideal model delta sigma weight residual 122.17 120.35 1.82 1.54e+00 4.22e-01 1.40e+00 angle pdb=" C THR E 59 " pdb=" N LYS E 60 " pdb=" CA LYS E 60 " ideal model delta sigma weight residual 122.17 120.35 1.82 1.54e+00 4.22e-01 1.39e+00 angle pdb=" C THR A 59 " pdb=" N LYS A 60 " pdb=" CA LYS A 60 " ideal model delta sigma weight residual 122.17 120.37 1.80 1.54e+00 4.22e-01 1.37e+00 ... (remaining 3457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.35: 1296 15.35 - 30.70: 96 30.70 - 46.05: 66 46.05 - 61.40: 24 61.40 - 76.75: 6 Dihedral angle restraints: 1488 sinusoidal: 492 harmonic: 996 Sorted by residual: dihedral pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " pdb=" CG GLU C 83 " pdb=" CD GLU C 83 " ideal model delta sinusoidal sigma weight residual -180.00 -127.38 -52.62 3 1.50e+01 4.44e-03 9.13e+00 dihedral pdb=" CA GLU D 83 " pdb=" CB GLU D 83 " pdb=" CG GLU D 83 " pdb=" CD GLU D 83 " ideal model delta sinusoidal sigma weight residual -180.00 -127.39 -52.61 3 1.50e+01 4.44e-03 9.13e+00 dihedral pdb=" CA GLU E 83 " pdb=" CB GLU E 83 " pdb=" CG GLU E 83 " pdb=" CD GLU E 83 " ideal model delta sinusoidal sigma weight residual -180.00 -127.41 -52.59 3 1.50e+01 4.44e-03 9.13e+00 ... (remaining 1485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 227 0.025 - 0.050: 107 0.050 - 0.075: 38 0.075 - 0.100: 17 0.100 - 0.125: 67 Chirality restraints: 456 Sorted by residual: chirality pdb=" CA ILE E 88 " pdb=" N ILE E 88 " pdb=" C ILE E 88 " pdb=" CB ILE E 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-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 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA ILE B 88 " pdb=" N ILE B 88 " pdb=" C ILE B 88 " pdb=" CB ILE B 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 453 not shown) Planarity restraints: 426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 59 " -0.002 2.00e-02 2.50e+03 4.26e-03 1.81e-01 pdb=" C THR E 59 " 0.007 2.00e-02 2.50e+03 pdb=" O THR E 59 " -0.003 2.00e-02 2.50e+03 pdb=" N LYS E 60 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 59 " 0.002 2.00e-02 2.50e+03 4.13e-03 1.70e-01 pdb=" C THR C 59 " -0.007 2.00e-02 2.50e+03 pdb=" O THR C 59 " 0.003 2.00e-02 2.50e+03 pdb=" N LYS C 60 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 59 " -0.002 2.00e-02 2.50e+03 4.00e-03 1.60e-01 pdb=" C THR D 59 " 0.007 2.00e-02 2.50e+03 pdb=" O THR D 59 " -0.003 2.00e-02 2.50e+03 pdb=" N LYS D 60 " -0.002 2.00e-02 2.50e+03 ... (remaining 423 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 1576 3.05 - 3.51: 2243 3.51 - 3.97: 3534 3.97 - 4.44: 3796 4.44 - 4.90: 7142 Nonbonded interactions: 18291 Sorted by model distance: nonbonded pdb=" NE2 GLN E 62 " pdb=" OG1 THR E 64 " model vdw 2.586 2.520 nonbonded pdb=" NE2 GLN A 62 " pdb=" OG1 THR A 64 " model vdw 2.586 2.520 nonbonded pdb=" NE2 GLN I 62 " pdb=" OG1 THR I 64 " model vdw 2.586 2.520 nonbonded pdb=" NE2 GLN B 62 " pdb=" OG1 THR B 64 " model vdw 2.586 2.520 nonbonded pdb=" NE2 GLN C 62 " pdb=" OG1 THR C 64 " model vdw 2.587 2.520 ... (remaining 18286 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 'I' } 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: 0.970 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: 4.790 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.180 Find NCS groups from input model: 0.180 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:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 : 0.001 0.014 2562 Z= 0.101 Angle : 0.376 2.215 3462 Z= 0.225 Chirality : 0.052 0.125 456 Planarity : 0.001 0.004 426 Dihedral : 18.118 76.747 864 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.10 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: -0.89 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.67 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 50 PHE 0.002 0.000 PHE B 94 TYR 0.006 0.001 TYR D 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 31 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.295 Fit side-chains REVERT: E 58 LYS cc_start: 0.8958 (mmtp) cc_final: 0.6762 (pptt) REVERT: B 39 TYR cc_start: 0.8691 (t80) cc_final: 0.8257 (t80) REVERT: B 58 LYS cc_start: 0.8794 (mmtp) cc_final: 0.6507 (pptt) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 1.3983 time to fit residues: 44.4182 Evaluate side-chains 19 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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: 9.9990 chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 2562 Z= 0.500 Angle : 0.576 3.711 3462 Z= 0.334 Chirality : 0.056 0.143 456 Planarity : 0.003 0.008 426 Dihedral : 5.108 19.742 372 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 5.43 % Allowed : 16.67 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.43), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.93 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 50 PHE 0.013 0.002 PHE I 94 TYR 0.006 0.002 TYR D 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 41 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 27 time to evaluate : 0.287 Fit side-chains REVERT: I 43 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7893 (ttpt) REVERT: E 60 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.6439 (pmtt) REVERT: B 60 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.6296 (pmtt) REVERT: B 80 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.9020 (mtpt) outliers start: 14 outliers final: 6 residues processed: 39 average time/residue: 1.6795 time to fit residues: 66.7155 Evaluate side-chains 34 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 24 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 80 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2562 Z= 0.156 Angle : 0.398 2.571 3462 Z= 0.235 Chirality : 0.053 0.133 456 Planarity : 0.001 0.006 426 Dihedral : 4.247 14.645 372 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.26 % Allowed : 18.99 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.43), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.007 0.002 PHE C 94 TYR 0.009 0.001 TYR E 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 32 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 21 time to evaluate : 0.292 Fit side-chains REVERT: E 60 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6417 (pmtt) REVERT: E 61 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: B 60 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6322 (pmtt) REVERT: B 87 SER cc_start: 0.9096 (p) cc_final: 0.8848 (t) outliers start: 11 outliers final: 0 residues processed: 30 average time/residue: 1.5049 time to fit residues: 46.1448 Evaluate side-chains 24 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 2562 Z= 0.515 Angle : 0.578 3.973 3462 Z= 0.334 Chirality : 0.057 0.151 456 Planarity : 0.002 0.007 426 Dihedral : 5.467 21.518 372 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 4.65 % Allowed : 19.77 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 50 PHE 0.010 0.002 PHE I 94 TYR 0.006 0.002 TYR B 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 37 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 25 time to evaluate : 0.294 Fit side-chains REVERT: D 43 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.7784 (ttpt) REVERT: E 60 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.6397 (pmtt) REVERT: B 60 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.6301 (pmtt) REVERT: B 80 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.9043 (mtpt) outliers start: 12 outliers final: 7 residues processed: 34 average time/residue: 1.8898 time to fit residues: 65.3791 Evaluate side-chains 35 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 24 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 80 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2562 Z= 0.312 Angle : 0.486 2.999 3462 Z= 0.284 Chirality : 0.054 0.134 456 Planarity : 0.002 0.007 426 Dihedral : 5.016 18.850 372 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.65 % Allowed : 20.93 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.008 0.002 PHE C 94 TYR 0.007 0.001 TYR B 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 36 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 24 time to evaluate : 0.291 Fit side-chains REVERT: E 60 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.6375 (pmtt) REVERT: E 61 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: B 60 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.6328 (pmtt) outliers start: 12 outliers final: 7 residues processed: 32 average time/residue: 1.6754 time to fit residues: 54.6889 Evaluate side-chains 31 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 21 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain B residue 60 LYS 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: 0.7980 chunk 28 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2562 Z= 0.362 Angle : 0.506 3.225 3462 Z= 0.294 Chirality : 0.055 0.133 456 Planarity : 0.002 0.007 426 Dihedral : 5.213 19.956 372 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 4.26 % Allowed : 22.09 % 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: -1.57 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.009 0.002 PHE I 94 TYR 0.007 0.001 TYR B 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 35 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 24 time to evaluate : 0.294 Fit side-chains REVERT: E 60 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6288 (pmtt) REVERT: E 61 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: B 60 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.6282 (pmtt) outliers start: 11 outliers final: 8 residues processed: 33 average time/residue: 1.8325 time to fit residues: 61.5851 Evaluate side-chains 34 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 23 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 2562 Z= 0.436 Angle : 0.553 3.513 3462 Z= 0.322 Chirality : 0.056 0.138 456 Planarity : 0.002 0.007 426 Dihedral : 5.404 20.898 372 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.65 % Allowed : 22.48 % 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: -1.63 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.010 0.002 PHE I 94 TYR 0.008 0.001 TYR B 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 35 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 23 time to evaluate : 0.266 Fit side-chains REVERT: E 60 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.6327 (pmtt) REVERT: E 61 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: B 60 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.6347 (pmtt) outliers start: 12 outliers final: 9 residues processed: 33 average time/residue: 1.7235 time to fit residues: 57.9500 Evaluate side-chains 34 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 22 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 2562 Z= 0.468 Angle : 0.566 3.757 3462 Z= 0.329 Chirality : 0.056 0.139 456 Planarity : 0.002 0.008 426 Dihedral : 5.580 22.300 372 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 4.26 % Allowed : 23.64 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.010 0.002 PHE I 94 TYR 0.009 0.002 TYR B 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 34 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 23 time to evaluate : 0.286 Fit side-chains REVERT: E 60 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.6369 (pmtt) REVERT: B 60 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.6223 (pmtt) outliers start: 11 outliers final: 9 residues processed: 32 average time/residue: 1.7030 time to fit residues: 55.5805 Evaluate side-chains 33 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 22 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2562 Z= 0.212 Angle : 0.433 2.665 3462 Z= 0.254 Chirality : 0.053 0.132 456 Planarity : 0.001 0.006 426 Dihedral : 4.759 16.592 372 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.88 % Allowed : 24.03 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.007 0.002 PHE C 94 TYR 0.010 0.001 TYR B 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 31 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 21 time to evaluate : 0.268 Fit side-chains REVERT: I 60 LYS cc_start: 0.6473 (OUTLIER) cc_final: 0.6212 (ptpp) REVERT: E 60 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.6435 (pmtt) REVERT: E 61 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: B 60 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6221 (pmtt) outliers start: 10 outliers final: 6 residues processed: 27 average time/residue: 1.6624 time to fit residues: 45.8726 Evaluate side-chains 30 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 20 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.1980 chunk 22 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.0050 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 overall best weight: 2.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2562 Z= 0.249 Angle : 0.444 2.704 3462 Z= 0.259 Chirality : 0.053 0.130 456 Planarity : 0.001 0.006 426 Dihedral : 4.798 16.432 372 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.88 % Allowed : 24.03 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.007 0.002 PHE I 94 TYR 0.009 0.001 TYR B 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 34 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 24 time to evaluate : 0.254 Fit side-chains REVERT: I 60 LYS cc_start: 0.6708 (OUTLIER) cc_final: 0.6378 (ptpp) REVERT: E 60 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.6405 (pmtt) REVERT: E 61 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: B 60 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.6275 (pmtt) outliers start: 10 outliers final: 6 residues processed: 32 average time/residue: 1.8032 time to fit residues: 58.7830 Evaluate side-chains 34 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 24 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain B residue 60 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.090611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.080212 restraints weight = 4425.817| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.03 r_work: 0.3185 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.049 2562 Z= 0.616 Angle : 0.646 4.372 3462 Z= 0.375 Chirality : 0.059 0.166 456 Planarity : 0.003 0.009 426 Dihedral : 5.909 24.436 372 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 4.65 % Allowed : 23.26 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS C 50 PHE 0.011 0.003 PHE I 94 TYR 0.007 0.002 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1381.07 seconds wall clock time: 25 minutes 13.43 seconds (1513.43 seconds total)