Starting phenix.real_space_refine on Fri Dec 8 22:35:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnz_32636/12_2023/7wnz_32636.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnz_32636/12_2023/7wnz_32636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnz_32636/12_2023/7wnz_32636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnz_32636/12_2023/7wnz_32636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnz_32636/12_2023/7wnz_32636.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnz_32636/12_2023/7wnz_32636.pdb" } resolution = 3.4 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= 0.001 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 C 2830 2.51 5 N 780 2.21 5 O 910 1.98 5 H 4780 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9300 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 930 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "A" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 930 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "B" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 930 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "C" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 930 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "D" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 930 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "E" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 930 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "F" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 930 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 930 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "I" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 930 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "J" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 930 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Time building chain proxies: 4.31, per 1000 atoms: 0.46 Number of scatterers: 9300 At special positions: 0 Unit cell: (92.13, 95.45, 42.33, 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) O 910 8.00 N 780 7.00 C 2830 6.00 H 4780 1.00 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: 6.82 Conformation dependent library (CDL) restraints added in 993.3 milliseconds 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1100 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.447A pdb=" N LEU F 38 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL G 37 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL H 40 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 45 through 50 removed outlier: 6.832A pdb=" N GLU F 46 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY I 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N LYS H 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL I 48 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY H 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N HIS I 50 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL H 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N LYS G 45 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N VAL H 48 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY G 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N HIS H 50 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL G 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU G 46 " --> pdb=" O LYS J 45 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY J 47 " --> pdb=" O GLU G 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 54 through 57 removed outlier: 6.683A pdb=" N THR H 54 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU I 57 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA H 56 " --> pdb=" O GLU I 57 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR G 54 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N GLU H 57 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA G 56 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 62 through 63 removed outlier: 6.422A pdb=" N GLN F 62 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLN G 62 " --> pdb=" O VAL J 63 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 69 through 71 removed outlier: 6.535A pdb=" N ALA F 69 " --> pdb=" O VAL I 70 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL H 70 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL G 70 " --> pdb=" O VAL H 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 77 through 78 removed outlier: 6.652A pdb=" N VAL F 77 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL G 77 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 81 through 82 removed outlier: 6.528A pdb=" N THR H 81 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR G 81 " --> pdb=" O VAL H 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 87 through 89 removed outlier: 6.185A pdb=" N SER F 87 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER G 87 " --> pdb=" O ILE J 88 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 95 through 98 removed outlier: 6.389A pdb=" N VAL G 95 " --> pdb=" O LYS J 96 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ASP J 98 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS G 97 " --> pdb=" O ASP J 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.452A pdb=" N LEU A 38 " --> pdb=" O TYR B 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 45 through 50 removed outlier: 6.836A pdb=" N GLU A 46 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY B 47 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU B 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY C 47 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU C 46 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY D 47 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU D 46 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY E 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 54 through 57 Processing sheet with id=AB4, first strand: chain 'A' and resid 62 through 63 removed outlier: 6.353A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN B 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLN C 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN D 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AB6, first strand: chain 'A' and resid 77 through 78 removed outlier: 6.630A pdb=" N VAL A 77 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL C 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL D 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AB8, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.228A pdb=" N SER A 87 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER B 87 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER C 87 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER D 87 " --> pdb=" O ILE E 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 95 through 98 removed outlier: 6.481A pdb=" N VAL A 95 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ASP B 98 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS A 97 " --> pdb=" O ASP B 98 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 95 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ASP C 98 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS B 97 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL C 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ASP D 98 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS C 97 " --> pdb=" O ASP D 98 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL D 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ASP E 98 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS D 97 " --> pdb=" O ASP E 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 81 hydrogen bonds defined for protein. 243 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: 3.20 Time building geometry restraints manager: 7.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 0.98: 4780 0.98 - 1.12: 0 1.12 - 1.26: 790 1.26 - 1.40: 860 1.40 - 1.54: 2890 Bond restraints: 9320 Sorted by residual: bond pdb=" CB LYS C 80 " pdb=" CG LYS C 80 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 4.85e-01 bond pdb=" CB LYS F 80 " pdb=" CG LYS F 80 " ideal model delta sigma weight residual 1.520 1.500 0.020 3.00e-02 1.11e+03 4.60e-01 bond pdb=" CB LYS J 80 " pdb=" CG LYS J 80 " ideal model delta sigma weight residual 1.520 1.500 0.020 3.00e-02 1.11e+03 4.58e-01 bond pdb=" CB LYS I 80 " pdb=" CG LYS I 80 " ideal model delta sigma weight residual 1.520 1.500 0.020 3.00e-02 1.11e+03 4.48e-01 bond pdb=" CB LYS D 80 " pdb=" CG LYS D 80 " ideal model delta sigma weight residual 1.520 1.500 0.020 3.00e-02 1.11e+03 4.44e-01 ... (remaining 9315 not shown) Histogram of bond angle deviations from ideal: 105.68 - 110.75: 10840 110.75 - 115.81: 2133 115.81 - 120.87: 1689 120.87 - 125.93: 2274 125.93 - 131.00: 34 Bond angle restraints: 16970 Sorted by residual: angle pdb=" N GLY C 51 " pdb=" CA GLY C 51 " pdb=" C GLY C 51 " ideal model delta sigma weight residual 113.18 118.77 -5.59 2.37e+00 1.78e-01 5.56e+00 angle pdb=" N GLY F 51 " pdb=" CA GLY F 51 " pdb=" C GLY F 51 " ideal model delta sigma weight residual 113.18 118.77 -5.59 2.37e+00 1.78e-01 5.56e+00 angle pdb=" N GLY H 51 " pdb=" CA GLY H 51 " pdb=" C GLY H 51 " ideal model delta sigma weight residual 113.18 118.74 -5.56 2.37e+00 1.78e-01 5.51e+00 angle pdb=" N GLY D 51 " pdb=" CA GLY D 51 " pdb=" C GLY D 51 " ideal model delta sigma weight residual 113.18 118.72 -5.54 2.37e+00 1.78e-01 5.47e+00 angle pdb=" N GLY I 51 " pdb=" CA GLY I 51 " pdb=" C GLY I 51 " ideal model delta sigma weight residual 113.18 118.72 -5.54 2.37e+00 1.78e-01 5.47e+00 ... (remaining 16965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.45: 3329 7.45 - 14.91: 331 14.91 - 22.36: 230 22.36 - 29.81: 70 29.81 - 37.27: 60 Dihedral angle restraints: 4020 sinusoidal: 2150 harmonic: 1870 Sorted by residual: dihedral pdb=" CA HIS E 50 " pdb=" C HIS E 50 " pdb=" N GLY E 51 " pdb=" CA GLY E 51 " ideal model delta harmonic sigma weight residual 180.00 164.67 15.33 0 5.00e+00 4.00e-02 9.39e+00 dihedral pdb=" CA HIS J 50 " pdb=" C HIS J 50 " pdb=" N GLY J 51 " pdb=" CA GLY J 51 " ideal model delta harmonic sigma weight residual 180.00 164.69 15.31 0 5.00e+00 4.00e-02 9.38e+00 dihedral pdb=" CA HIS B 50 " pdb=" C HIS B 50 " pdb=" N GLY B 51 " pdb=" CA GLY B 51 " ideal model delta harmonic sigma weight residual 180.00 164.70 15.30 0 5.00e+00 4.00e-02 9.36e+00 ... (remaining 4017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 430 0.027 - 0.053: 174 0.053 - 0.080: 66 0.080 - 0.106: 67 0.106 - 0.133: 73 Chirality restraints: 810 Sorted by residual: chirality pdb=" CA VAL E 82 " pdb=" N VAL E 82 " pdb=" C VAL E 82 " pdb=" CB VAL E 82 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA VAL J 82 " pdb=" N VAL J 82 " pdb=" C VAL J 82 " pdb=" CB VAL J 82 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA VAL F 82 " pdb=" N VAL F 82 " pdb=" C VAL F 82 " pdb=" CB VAL F 82 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 807 not shown) Planarity restraints: 1400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 51 " -0.004 2.00e-02 2.50e+03 7.54e-03 5.69e-01 pdb=" C GLY D 51 " 0.013 2.00e-02 2.50e+03 pdb=" O GLY D 51 " -0.005 2.00e-02 2.50e+03 pdb=" N VAL D 52 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 51 " -0.004 2.00e-02 2.50e+03 7.47e-03 5.58e-01 pdb=" C GLY A 51 " 0.013 2.00e-02 2.50e+03 pdb=" O GLY A 51 " -0.005 2.00e-02 2.50e+03 pdb=" N VAL A 52 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY I 51 " 0.004 2.00e-02 2.50e+03 7.41e-03 5.49e-01 pdb=" C GLY I 51 " -0.013 2.00e-02 2.50e+03 pdb=" O GLY I 51 " 0.005 2.00e-02 2.50e+03 pdb=" N VAL I 52 " 0.004 2.00e-02 2.50e+03 ... (remaining 1397 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.00: 72 2.00 - 2.63: 11506 2.63 - 3.25: 24647 3.25 - 3.88: 32082 3.88 - 4.50: 46069 Nonbonded interactions: 114376 Sorted by model distance: nonbonded pdb=" HE2 HIS E 50 " pdb=" OE2 GLU J 57 " model vdw 1.376 1.850 nonbonded pdb=" OE2 GLU D 57 " pdb=" HE2 HIS J 50 " model vdw 1.400 1.850 nonbonded pdb=" HE2 HIS A 50 " pdb=" OE2 GLU F 57 " model vdw 1.431 1.850 nonbonded pdb=" OE2 GLU G 57 " pdb=" HE2 HIS D 50 " model vdw 1.445 1.850 nonbonded pdb=" HE2 HIS C 50 " pdb=" OE2 GLU H 57 " model vdw 1.490 1.850 ... (remaining 114371 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.150 Extract box with map and model: 4.960 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 32.180 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 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 0.021 4540 Z= 0.194 Angle : 0.516 5.591 6140 Z= 0.286 Chirality : 0.053 0.133 810 Planarity : 0.002 0.008 760 Dihedral : 10.392 37.268 1550 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.27), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS I 50 PHE 0.007 0.002 PHE H 94 TYR 0.004 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.738 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.2488 time to fit residues: 13.0360 Evaluate side-chains 34 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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: 0.7008 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4540 Z= 0.354 Angle : 0.641 5.661 6140 Z= 0.364 Chirality : 0.051 0.123 810 Planarity : 0.003 0.009 760 Dihedral : 5.944 15.110 650 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: -4.23 (0.24), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.18), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS G 50 PHE 0.007 0.002 PHE J 94 TYR 0.007 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.681 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.2604 time to fit residues: 14.7949 Evaluate side-chains 37 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.740 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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: 0.7040 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4540 Z= 0.276 Angle : 0.558 4.607 6140 Z= 0.322 Chirality : 0.051 0.128 810 Planarity : 0.003 0.008 760 Dihedral : 5.996 14.481 650 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.21 % Allowed : 5.11 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.23), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.17), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS G 50 PHE 0.007 0.002 PHE H 94 TYR 0.006 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.691 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 42 average time/residue: 0.2279 time to fit residues: 14.4763 Evaluate side-chains 40 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1083 time to fit residues: 1.1290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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: 0.7107 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4540 Z= 0.296 Angle : 0.581 4.539 6140 Z= 0.338 Chirality : 0.051 0.136 810 Planarity : 0.003 0.008 760 Dihedral : 6.130 15.052 650 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.49 % Favored : 86.51 % Rotamer: Outliers : 1.49 % Allowed : 4.89 % Favored : 93.62 % 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: -5.02 (0.22), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.17), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS G 50 PHE 0.008 0.002 PHE H 94 TYR 0.005 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.720 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 50 average time/residue: 0.2051 time to fit residues: 15.8671 Evaluate side-chains 40 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.713 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1500 time to fit residues: 1.3787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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: 0.6993 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4540 Z= 0.128 Angle : 0.437 3.338 6140 Z= 0.252 Chirality : 0.053 0.142 810 Planarity : 0.001 0.004 760 Dihedral : 5.211 14.562 650 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.21 % Allowed : 6.60 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.85 (0.23), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.17), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.006 0.002 PHE H 94 TYR 0.008 0.001 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.705 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.2011 time to fit residues: 11.8195 Evaluate side-chains 37 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.758 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1093 time to fit residues: 1.0769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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: 0.7085 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4540 Z= 0.229 Angle : 0.508 4.012 6140 Z= 0.296 Chirality : 0.052 0.144 810 Planarity : 0.002 0.006 760 Dihedral : 5.467 14.607 650 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.49 % Favored : 86.51 % Rotamer: Outliers : 0.21 % Allowed : 7.02 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.23), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.18), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.006 0.002 PHE C 94 TYR 0.014 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.729 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.2076 time to fit residues: 13.1996 Evaluate side-chains 38 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.682 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1093 time to fit residues: 1.0531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7013 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4540 Z= 0.137 Angle : 0.435 3.351 6140 Z= 0.252 Chirality : 0.052 0.145 810 Planarity : 0.001 0.006 760 Dihedral : 5.055 14.012 650 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.23), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.18), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.006 0.002 PHE H 94 TYR 0.009 0.001 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.798 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.2464 time to fit residues: 13.8464 Evaluate side-chains 37 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.690 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 45 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 0.0670 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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: 0.6961 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4540 Z= 0.105 Angle : 0.400 2.891 6140 Z= 0.231 Chirality : 0.053 0.142 810 Planarity : 0.001 0.005 760 Dihedral : 4.569 13.455 650 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.21 % Allowed : 6.81 % Favored : 92.98 % 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: -4.73 (0.24), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.18), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.005 0.001 PHE H 94 TYR 0.006 0.001 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.751 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 0.2111 time to fit residues: 11.2154 Evaluate side-chains 33 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.697 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1078 time to fit residues: 1.0796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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: 0.7064 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4540 Z= 0.221 Angle : 0.485 3.719 6140 Z= 0.283 Chirality : 0.052 0.145 810 Planarity : 0.002 0.007 760 Dihedral : 5.111 13.811 650 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 0.21 % Allowed : 6.81 % Favored : 92.98 % 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: -4.92 (0.24), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.18), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS G 50 PHE 0.004 0.002 PHE D 94 TYR 0.011 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.751 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 42 average time/residue: 0.2100 time to fit residues: 13.6695 Evaluate side-chains 40 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.739 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1102 time to fit residues: 1.0678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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: 0.7151 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 4540 Z= 0.314 Angle : 0.575 4.410 6140 Z= 0.339 Chirality : 0.053 0.154 810 Planarity : 0.003 0.010 760 Dihedral : 5.922 14.285 650 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.92 % Favored : 85.08 % Rotamer: Outliers : 0.21 % Allowed : 7.02 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.31 (0.23), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.18), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS G 50 PHE 0.022 0.003 PHE J 94 TYR 0.016 0.003 TYR E 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 45 average time/residue: 0.2120 time to fit residues: 14.8281 Evaluate side-chains 44 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1112 time to fit residues: 1.0919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.4995 r_free = 0.4995 target = 0.162935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.138430 restraints weight = 18205.298| |-----------------------------------------------------------------------------| r_work (start): 0.4774 rms_B_bonded: 3.24 r_work: 0.4642 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 4540 Z= 0.241 Angle : 0.522 4.046 6140 Z= 0.306 Chirality : 0.053 0.154 810 Planarity : 0.003 0.007 760 Dihedral : 5.718 14.320 650 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 0.21 % Allowed : 7.66 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.45 (0.22), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.15 (0.17), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS G 50 PHE 0.013 0.002 PHE J 94 TYR 0.013 0.002 TYR E 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2704.74 seconds wall clock time: 48 minutes 24.71 seconds (2904.71 seconds total)