Starting phenix.real_space_refine on Thu Mar 14 17:02:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnz_32636/03_2024/7wnz_32636.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnz_32636/03_2024/7wnz_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_32636/03_2024/7wnz_32636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnz_32636/03_2024/7wnz_32636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnz_32636/03_2024/7wnz_32636.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnz_32636/03_2024/7wnz_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-dev-5265/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: 4.33, per 1000 atoms: 0.47 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: 6.15 Conformation dependent library (CDL) restraints added in 872.8 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: 0.84 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: 2.89 Time building geometry restraints manager: 6.52 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 - 11.57: 3590 11.57 - 23.13: 400 23.13 - 34.70: 130 34.70 - 46.26: 50 46.26 - 57.83: 80 Dihedral angle restraints: 4250 sinusoidal: 2380 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 4247 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: 1.020 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: 0.160 Extract box with map and model: 4.800 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 30.670 Find NCS groups from input model: 0.460 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.200 ------------------------------------------------------------------------------- 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 : 0.610 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.2212 time to fit residues: 11.4064 Evaluate side-chains 34 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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: 0.7980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.6984 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4540 Z= 0.322 Angle : 0.614 5.521 6140 Z= 0.346 Chirality : 0.051 0.125 810 Planarity : 0.003 0.009 760 Dihedral : 5.854 14.930 650 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % 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: -4.11 (0.25), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.19), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS J 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 37 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.716 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.2080 time to fit residues: 11.8316 Evaluate side-chains 37 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.9980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2087 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= 0.302 Angle : 0.584 4.665 6140 Z= 0.337 Chirality : 0.052 0.129 810 Planarity : 0.003 0.009 760 Dihedral : 6.188 14.903 650 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.06 % Allowed : 4.68 % Favored : 94.26 % 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: -4.80 (0.22), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.17), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS G 50 PHE 0.008 0.002 PHE H 94 TYR 0.007 0.002 TYR B 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 47 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: B 39 TYR cc_start: 0.7005 (OUTLIER) cc_final: 0.6523 (m-80) REVERT: E 39 TYR cc_start: 0.6241 (OUTLIER) cc_final: 0.5732 (m-80) outliers start: 5 outliers final: 2 residues processed: 47 average time/residue: 0.2336 time to fit residues: 16.1327 Evaluate side-chains 43 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 TYR Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain E residue 39 TYR 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: 2.9990 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.7124 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 4540 Z= 0.302 Angle : 0.588 4.582 6140 Z= 0.342 Chirality : 0.052 0.139 810 Planarity : 0.003 0.009 760 Dihedral : 6.244 15.440 650 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 1.70 % Allowed : 4.89 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.15 (0.22), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.17), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS G 50 PHE 0.007 0.003 PHE H 94 TYR 0.016 0.002 TYR J 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 51 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.701 Fit side-chains REVERT: A 80 LYS cc_start: 0.7163 (mtpt) cc_final: 0.6904 (mttt) REVERT: E 39 TYR cc_start: 0.6210 (OUTLIER) cc_final: 0.5744 (m-80) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.1985 time to fit residues: 15.5708 Evaluate side-chains 44 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 TYR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 39 TYR 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: 4.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 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: 0.7056 moved from start: 0.2595 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= 0.178 Angle : 0.483 3.781 6140 Z= 0.280 Chirality : 0.052 0.146 810 Planarity : 0.002 0.007 760 Dihedral : 5.535 15.069 650 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.85 % Allowed : 7.02 % 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: -5.17 (0.22), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.17), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.015 0.002 PHE G 94 TYR 0.007 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 48 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.609 Fit side-chains REVERT: A 80 LYS cc_start: 0.7004 (mtpt) cc_final: 0.6801 (mttt) outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.1867 time to fit residues: 13.8246 Evaluate side-chains 46 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 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: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.7090 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4540 Z= 0.211 Angle : 0.503 3.973 6140 Z= 0.293 Chirality : 0.052 0.148 810 Planarity : 0.002 0.007 760 Dihedral : 5.525 14.722 650 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.02 % Favored : 86.98 % Rotamer: Outliers : 1.28 % Allowed : 6.81 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.20 (0.22), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.17), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS D 50 PHE 0.016 0.003 PHE G 94 TYR 0.009 0.001 TYR J 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 45 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.731 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 45 average time/residue: 0.1887 time to fit residues: 13.2689 Evaluate side-chains 45 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.7086 moved from start: 0.2895 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= 0.199 Angle : 0.491 3.849 6140 Z= 0.286 Chirality : 0.052 0.149 810 Planarity : 0.002 0.006 760 Dihedral : 5.459 14.381 650 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 1.28 % Allowed : 7.02 % Favored : 91.70 % 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 (0.22), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.17), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS C 50 PHE 0.014 0.002 PHE G 94 TYR 0.008 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 44 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.646 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 44 average time/residue: 0.1880 time to fit residues: 12.9252 Evaluate side-chains 44 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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: 0.7142 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 : 0.004 0.021 4540 Z= 0.255 Angle : 0.543 4.151 6140 Z= 0.318 Chirality : 0.053 0.156 810 Planarity : 0.003 0.007 760 Dihedral : 5.760 14.578 650 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.03 % Favored : 83.97 % Rotamer: Outliers : 1.70 % Allowed : 7.02 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.42 (0.23), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.13 (0.17), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS G 50 PHE 0.016 0.003 PHE J 94 TYR 0.010 0.002 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 52 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.678 Fit side-chains REVERT: B 39 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6428 (m-80) REVERT: E 39 TYR cc_start: 0.6210 (OUTLIER) cc_final: 0.5628 (m-80) outliers start: 8 outliers final: 6 residues processed: 52 average time/residue: 0.1948 time to fit residues: 15.5298 Evaluate side-chains 52 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 39 TYR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 87 SER 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: 3.9990 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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: 0.7167 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4540 Z= 0.283 Angle : 0.571 4.351 6140 Z= 0.335 Chirality : 0.053 0.157 810 Planarity : 0.003 0.008 760 Dihedral : 6.074 15.179 650 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.71 % Favored : 84.29 % Rotamer: Outliers : 1.91 % Allowed : 7.45 % Favored : 90.64 % 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: -5.65 (0.22), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.30 (0.17), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS G 50 PHE 0.015 0.003 PHE J 94 TYR 0.010 0.002 TYR J 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 55 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.617 Fit side-chains REVERT: B 39 TYR cc_start: 0.7009 (OUTLIER) cc_final: 0.6474 (m-80) REVERT: E 39 TYR cc_start: 0.6288 (OUTLIER) cc_final: 0.5701 (m-80) REVERT: F 99 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6516 (mp10) outliers start: 9 outliers final: 6 residues processed: 54 average time/residue: 0.1888 time to fit residues: 15.5575 Evaluate side-chains 55 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 39 TYR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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: 0.7142 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4540 Z= 0.225 Angle : 0.525 4.013 6140 Z= 0.307 Chirality : 0.053 0.155 810 Planarity : 0.002 0.006 760 Dihedral : 5.741 15.068 650 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % Rotamer: Outliers : 1.28 % Allowed : 8.09 % Favored : 90.64 % 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: -5.70 (0.22), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.34 (0.17), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS G 50 PHE 0.013 0.002 PHE J 94 TYR 0.009 0.001 TYR J 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 53 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.716 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 53 average time/residue: 0.1947 time to fit residues: 15.9542 Evaluate side-chains 53 residues out of total 470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 87 SER 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: 1.9990 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.4996 r_free = 0.4996 target = 0.162617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.137784 restraints weight = 18347.547| |-----------------------------------------------------------------------------| r_work (start): 0.4758 rms_B_bonded: 3.28 r_work: 0.4628 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.3314 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= 0.196 Angle : 0.502 3.783 6140 Z= 0.293 Chirality : 0.053 0.154 810 Planarity : 0.002 0.007 760 Dihedral : 5.532 14.449 650 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 1.49 % Allowed : 7.87 % Favored : 90.64 % 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: -5.72 (0.22), residues: 630 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.35 (0.17), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS G 50 PHE 0.015 0.003 PHE J 94 TYR 0.008 0.001 TYR J 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2558.08 seconds wall clock time: 45 minutes 27.65 seconds (2727.65 seconds total)