Starting phenix.real_space_refine on Thu Nov 14 00:29:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfb_16019/11_2024/8bfb_16019.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfb_16019/11_2024/8bfb_16019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfb_16019/11_2024/8bfb_16019.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfb_16019/11_2024/8bfb_16019.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfb_16019/11_2024/8bfb_16019.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfb_16019/11_2024/8bfb_16019.cif" } resolution = 3.2 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1810 2.51 5 N 510 2.21 5 O 530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2860 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "B" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "C" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "D" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "E" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "F" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "G" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "H" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "I" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "J" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Time building chain proxies: 2.40, per 1000 atoms: 0.84 Number of scatterers: 2860 At special positions: 0 Unit cell: (91.18, 66.74, 39.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 530 8.00 N 510 7.00 C 1810 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 550.0 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: 620 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 52.6% 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 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 16 removed outlier: 6.372A pdb=" N GLU C 11 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N HIS E 14 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N HIS C 13 " --> pdb=" O HIS E 14 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LYS E 16 " --> pdb=" O HIS C 13 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN C 15 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLU E 11 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N HIS G 14 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N HIS E 13 " --> pdb=" O HIS G 14 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LYS G 16 " --> pdb=" O HIS E 13 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN E 15 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU G 11 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N HIS I 14 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N HIS G 13 " --> pdb=" O HIS I 14 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N LYS I 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN G 15 " --> pdb=" O LYS I 16 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA4, first strand: chain 'A' and resid 24 through 27 removed outlier: 6.823A pdb=" N SER C 26 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN A 27 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER E 26 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASN C 27 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER G 26 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN E 27 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER I 26 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN G 27 " --> pdb=" O SER I 26 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.356A pdb=" N ALA A 30 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLY C 33 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ILE A 32 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N MET C 35 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N LEU A 34 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA C 30 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N GLY E 33 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N ILE C 32 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N MET E 35 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N LEU C 34 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA E 30 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLY G 33 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N ILE E 32 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N MET G 35 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 9.312A pdb=" N LEU E 34 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA G 30 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLY I 33 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N ILE G 32 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N MET I 35 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 9.312A pdb=" N LEU G 34 " --> pdb=" O MET I 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 16 removed outlier: 6.375A pdb=" N GLU B 11 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N HIS D 14 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N HIS B 13 " --> pdb=" O HIS D 14 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LYS D 16 " --> pdb=" O HIS B 13 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN B 15 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU D 11 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N HIS F 14 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N HIS D 13 " --> pdb=" O HIS F 14 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LYS F 16 " --> pdb=" O HIS D 13 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN D 15 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU F 11 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N HIS H 14 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N HIS F 13 " --> pdb=" O HIS H 14 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LYS H 16 " --> pdb=" O HIS F 13 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN F 15 " --> pdb=" O LYS H 16 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AA9, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.821A pdb=" N SER D 26 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN B 27 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER F 26 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN D 27 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER H 26 " --> pdb=" O GLY F 25 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASN F 27 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N SER J 26 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN H 27 " --> pdb=" O SER J 26 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 30 through 36 removed outlier: 6.352A pdb=" N ALA B 30 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY D 33 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N ILE B 32 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N MET D 35 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N LEU B 34 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA D 30 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLY F 33 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N ILE D 32 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N MET F 35 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N LEU D 34 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA F 30 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLY H 33 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N ILE F 32 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N MET H 35 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N LEU F 34 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA H 30 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLY J 33 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ILE H 32 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N MET J 35 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N LEU H 34 " --> pdb=" O MET J 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 60 hydrogen bonds defined for protein. 180 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: 0.67 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 980 1.34 - 1.46: 705 1.46 - 1.58: 1215 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 2920 Sorted by residual: bond pdb=" N ILE D 32 " pdb=" CA ILE D 32 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.17e-02 7.31e+03 9.14e+00 bond pdb=" N ILE C 32 " pdb=" CA ILE C 32 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.17e-02 7.31e+03 9.11e+00 bond pdb=" N ILE E 32 " pdb=" CA ILE E 32 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.94e+00 bond pdb=" N ILE B 32 " pdb=" CA ILE B 32 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.81e+00 bond pdb=" N ILE I 32 " pdb=" CA ILE I 32 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.77e+00 ... (remaining 2915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.61: 3421 0.61 - 1.22: 373 1.22 - 1.83: 77 1.83 - 2.43: 19 2.43 - 3.04: 10 Bond angle restraints: 3900 Sorted by residual: angle pdb=" CA ILE D 32 " pdb=" C ILE D 32 " pdb=" O ILE D 32 " ideal model delta sigma weight residual 120.39 118.16 2.23 1.05e+00 9.07e-01 4.52e+00 angle pdb=" CA ILE F 32 " pdb=" C ILE F 32 " pdb=" O ILE F 32 " ideal model delta sigma weight residual 120.39 118.16 2.23 1.05e+00 9.07e-01 4.49e+00 angle pdb=" CA ILE I 32 " pdb=" C ILE I 32 " pdb=" O ILE I 32 " ideal model delta sigma weight residual 120.39 118.17 2.22 1.05e+00 9.07e-01 4.48e+00 angle pdb=" CA ILE J 32 " pdb=" C ILE J 32 " pdb=" O ILE J 32 " ideal model delta sigma weight residual 120.39 118.17 2.22 1.05e+00 9.07e-01 4.46e+00 angle pdb=" CA ILE E 32 " pdb=" C ILE E 32 " pdb=" O ILE E 32 " ideal model delta sigma weight residual 120.39 118.18 2.21 1.05e+00 9.07e-01 4.44e+00 ... (remaining 3895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.06: 1433 13.06 - 26.12: 98 26.12 - 39.18: 38 39.18 - 52.24: 31 52.24 - 65.30: 10 Dihedral angle restraints: 1610 sinusoidal: 610 harmonic: 1000 Sorted by residual: dihedral pdb=" CA ILE G 32 " pdb=" CB ILE G 32 " pdb=" CG1 ILE G 32 " pdb=" CD1 ILE G 32 " ideal model delta sinusoidal sigma weight residual 60.00 102.06 -42.06 3 1.50e+01 4.44e-03 7.54e+00 dihedral pdb=" CA LEU D 34 " pdb=" CB LEU D 34 " pdb=" CG LEU D 34 " pdb=" CD1 LEU D 34 " ideal model delta sinusoidal sigma weight residual 180.00 140.00 40.00 3 1.50e+01 4.44e-03 7.11e+00 dihedral pdb=" CA LEU C 34 " pdb=" CB LEU C 34 " pdb=" CG LEU C 34 " pdb=" CD1 LEU C 34 " ideal model delta sinusoidal sigma weight residual 180.00 140.02 39.98 3 1.50e+01 4.44e-03 7.11e+00 ... (remaining 1607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 258 0.040 - 0.080: 54 0.080 - 0.121: 46 0.121 - 0.161: 22 0.161 - 0.201: 10 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA ILE H 32 " pdb=" N ILE H 32 " pdb=" C ILE H 32 " pdb=" CB ILE H 32 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE G 32 " pdb=" N ILE G 32 " pdb=" C ILE G 32 " pdb=" CB ILE G 32 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" CA ILE F 32 " pdb=" N ILE F 32 " pdb=" C ILE F 32 " pdb=" CB ILE F 32 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.73e-01 ... (remaining 387 not shown) Planarity restraints: 520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 31 " 0.004 2.00e-02 2.50e+03 8.99e-03 8.09e-01 pdb=" C ILE E 31 " -0.016 2.00e-02 2.50e+03 pdb=" O ILE E 31 " 0.006 2.00e-02 2.50e+03 pdb=" N ILE E 32 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 31 " -0.004 2.00e-02 2.50e+03 8.81e-03 7.75e-01 pdb=" C ILE D 31 " 0.015 2.00e-02 2.50e+03 pdb=" O ILE D 31 " -0.006 2.00e-02 2.50e+03 pdb=" N ILE D 32 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE J 31 " -0.004 2.00e-02 2.50e+03 8.75e-03 7.66e-01 pdb=" C ILE J 31 " 0.015 2.00e-02 2.50e+03 pdb=" O ILE J 31 " -0.006 2.00e-02 2.50e+03 pdb=" N ILE J 32 " -0.005 2.00e-02 2.50e+03 ... (remaining 517 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 1494 3.02 - 3.49: 2516 3.49 - 3.96: 4722 3.96 - 4.43: 4959 4.43 - 4.90: 10576 Nonbonded interactions: 24267 Sorted by model distance: nonbonded pdb=" NZ LYS I 28 " pdb=" OE2 GLU J 11 " model vdw 2.552 3.120 nonbonded pdb=" NZ LYS A 28 " pdb=" OE2 GLU B 11 " model vdw 2.554 3.120 nonbonded pdb=" NZ LYS E 28 " pdb=" OE2 GLU F 11 " model vdw 2.554 3.120 nonbonded pdb=" NZ LYS F 28 " pdb=" OE2 GLU G 11 " model vdw 2.555 3.120 nonbonded pdb=" NZ LYS G 28 " pdb=" OE2 GLU H 11 " model vdw 2.557 3.120 ... (remaining 24262 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.770 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.420 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.003 0.035 2920 Z= 0.230 Angle : 0.443 3.042 3900 Z= 0.300 Chirality : 0.062 0.201 390 Planarity : 0.002 0.009 520 Dihedral : 13.911 65.303 990 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 6 PHE 0.005 0.001 PHE B 20 TYR 0.002 0.001 TYR B 10 ARG 0.001 0.000 ARG A 5 *********************** 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 62 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.307 Fit side-chains REVERT: G 35 MET cc_start: 0.8271 (mtt) cc_final: 0.7971 (mtp) REVERT: H 35 MET cc_start: 0.8393 (mtt) cc_final: 0.8143 (mtm) REVERT: J 35 MET cc_start: 0.8337 (mtt) cc_final: 0.8124 (mtp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1607 time to fit residues: 11.9031 Evaluate side-chains 43 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 27 ASN C 27 ASN D 27 ASN E 27 ASN F 27 ASN G 27 ASN H 27 ASN I 27 ASN J 27 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 2920 Z= 0.564 Angle : 0.637 8.016 3900 Z= 0.323 Chirality : 0.055 0.127 390 Planarity : 0.002 0.007 520 Dihedral : 4.575 14.104 390 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.50 % Allowed : 7.50 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.38), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 6 PHE 0.015 0.003 PHE E 4 TYR 0.010 0.003 TYR C 10 ARG 0.003 0.001 ARG I 5 *********************** 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 43 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.263 Fit side-chains REVERT: F 32 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8170 (mp) REVERT: H 32 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8347 (mt) REVERT: J 35 MET cc_start: 0.8627 (mtt) cc_final: 0.8409 (mtt) outliers start: 7 outliers final: 2 residues processed: 41 average time/residue: 0.1117 time to fit residues: 5.9561 Evaluate side-chains 36 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 32 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 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: 0.8160 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 2920 Z= 0.522 Angle : 0.589 6.938 3900 Z= 0.302 Chirality : 0.054 0.125 390 Planarity : 0.002 0.006 520 Dihedral : 4.522 14.185 390 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.21 % Allowed : 6.43 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 6 PHE 0.013 0.002 PHE I 4 TYR 0.009 0.002 TYR J 10 ARG 0.002 0.001 ARG E 5 *********************** 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 43 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.337 Fit side-chains REVERT: F 32 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8248 (mp) REVERT: H 32 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8318 (mt) REVERT: J 35 MET cc_start: 0.8679 (mtt) cc_final: 0.8357 (mtt) outliers start: 9 outliers final: 3 residues processed: 41 average time/residue: 0.1237 time to fit residues: 6.5175 Evaluate side-chains 38 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.0020 chunk 13 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.9192 ------------------------------------------------------------------------------- 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: 0.8120 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2920 Z= 0.249 Angle : 0.438 5.785 3900 Z= 0.229 Chirality : 0.052 0.127 390 Planarity : 0.001 0.005 520 Dihedral : 3.923 11.269 390 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.79 % Allowed : 8.93 % Favored : 89.29 % 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: -2.64 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 6 PHE 0.007 0.001 PHE I 4 TYR 0.005 0.001 TYR J 10 ARG 0.001 0.000 ARG E 5 *********************** 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 47 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.308 Fit side-chains REVERT: H 32 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8348 (mp) outliers start: 5 outliers final: 2 residues processed: 43 average time/residue: 0.1714 time to fit residues: 8.8246 Evaluate side-chains 42 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 2920 Z= 0.352 Angle : 0.496 7.006 3900 Z= 0.254 Chirality : 0.052 0.127 390 Planarity : 0.002 0.005 520 Dihedral : 4.192 12.451 390 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.79 % Allowed : 8.57 % Favored : 89.64 % 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: -2.65 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 6 PHE 0.009 0.002 PHE J 4 TYR 0.007 0.002 TYR J 10 ARG 0.001 0.000 ARG F 5 *********************** 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 43 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.310 Fit side-chains REVERT: F 32 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8326 (mt) outliers start: 5 outliers final: 2 residues processed: 40 average time/residue: 0.1573 time to fit residues: 7.6874 Evaluate side-chains 41 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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: 0.8189 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.067 2920 Z= 0.699 Angle : 0.667 9.005 3900 Z= 0.339 Chirality : 0.055 0.127 390 Planarity : 0.003 0.007 520 Dihedral : 4.762 15.680 390 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.50 % Allowed : 9.29 % Favored : 88.21 % 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: -2.78 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 6 PHE 0.015 0.003 PHE J 4 TYR 0.011 0.002 TYR J 10 ARG 0.003 0.001 ARG D 5 *********************** 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 43 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.305 Fit side-chains REVERT: F 32 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8258 (mt) REVERT: H 32 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8386 (mt) outliers start: 7 outliers final: 3 residues processed: 39 average time/residue: 0.1360 time to fit residues: 6.6270 Evaluate side-chains 41 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.8113 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2920 Z= 0.164 Angle : 0.412 6.497 3900 Z= 0.217 Chirality : 0.051 0.127 390 Planarity : 0.001 0.003 520 Dihedral : 3.793 11.306 390 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.79 % Allowed : 10.71 % Favored : 87.50 % 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: -2.72 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 14 PHE 0.005 0.001 PHE I 4 TYR 0.003 0.001 TYR A 10 ARG 0.000 0.000 ARG H 5 *********************** 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 43 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.307 Fit side-chains REVERT: H 26 SER cc_start: 0.9336 (OUTLIER) cc_final: 0.8977 (t) REVERT: H 32 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8418 (mt) outliers start: 5 outliers final: 2 residues processed: 40 average time/residue: 0.1590 time to fit residues: 7.7394 Evaluate side-chains 42 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 23 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.0970 chunk 22 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 25 optimal weight: 0.0570 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 overall best weight: 1.6300 ------------------------------------------------------------------------------- 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: 0.8121 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2920 Z= 0.212 Angle : 0.419 6.579 3900 Z= 0.218 Chirality : 0.051 0.127 390 Planarity : 0.001 0.004 520 Dihedral : 3.796 11.746 390 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.79 % Allowed : 11.07 % Favored : 87.14 % 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: -2.70 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 6 PHE 0.006 0.001 PHE I 4 TYR 0.003 0.001 TYR E 10 ARG 0.000 0.000 ARG D 5 *********************** 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 43 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.301 Fit side-chains REVERT: D 26 SER cc_start: 0.9259 (t) cc_final: 0.9047 (t) REVERT: H 26 SER cc_start: 0.9333 (OUTLIER) cc_final: 0.9002 (t) REVERT: H 32 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8404 (mt) outliers start: 5 outliers final: 2 residues processed: 39 average time/residue: 0.1586 time to fit residues: 7.5898 Evaluate side-chains 42 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.8156 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 2920 Z= 0.413 Angle : 0.509 7.293 3900 Z= 0.262 Chirality : 0.052 0.125 390 Planarity : 0.002 0.006 520 Dihedral : 4.251 12.666 390 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.43 % Allowed : 11.79 % Favored : 86.79 % 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: -2.78 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 6 PHE 0.011 0.002 PHE I 4 TYR 0.006 0.001 TYR C 10 ARG 0.001 0.000 ARG I 5 *********************** 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 41 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.312 Fit side-chains REVERT: H 32 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8402 (mt) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.1701 time to fit residues: 7.8469 Evaluate side-chains 41 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 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: 0.8178 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 2920 Z= 0.577 Angle : 0.589 7.752 3900 Z= 0.301 Chirality : 0.054 0.124 390 Planarity : 0.002 0.007 520 Dihedral : 4.538 14.311 390 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.43 % Allowed : 11.07 % Favored : 87.50 % 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: -2.93 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 6 PHE 0.014 0.003 PHE J 4 TYR 0.007 0.002 TYR C 10 ARG 0.002 0.001 ARG D 5 ********************** 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 42 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.316 Fit side-chains REVERT: A 3 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7402 (tt0) REVERT: H 32 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8386 (mt) outliers start: 4 outliers final: 3 residues processed: 39 average time/residue: 0.1709 time to fit residues: 8.0618 Evaluate side-chains 42 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.122309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.101697 restraints weight = 2943.829| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.05 r_work: 0.3390 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2920 Z= 0.268 Angle : 0.449 6.720 3900 Z= 0.232 Chirality : 0.051 0.127 390 Planarity : 0.001 0.005 520 Dihedral : 4.023 12.818 390 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.43 % Allowed : 11.43 % Favored : 87.14 % 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: -2.94 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 6 PHE 0.007 0.001 PHE I 4 TYR 0.003 0.001 TYR C 10 ARG 0.001 0.000 ARG E 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 987.05 seconds wall clock time: 18 minutes 34.83 seconds (1114.83 seconds total)