Starting phenix.real_space_refine (version: dev) on Tue Feb 21 02:57:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbp_30161/02_2023/7dbp_30161.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbp_30161/02_2023/7dbp_30161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbp_30161/02_2023/7dbp_30161.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbp_30161/02_2023/7dbp_30161.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbp_30161/02_2023/7dbp_30161.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbp_30161/02_2023/7dbp_30161.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 22": "NH1" <-> "NH2" Residue "K ARG 27": "NH1" <-> "NH2" Residue "K TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 74": "NH1" <-> "NH2" Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13801 Number of models: 1 Model: "" Number of chains: 11 Chain: "K" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 590 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 3569 Classifications: {'DNA': 175} Link IDs: {'rna3p': 174} Chain: "J" Number of atoms: 3606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 3606 Classifications: {'DNA': 175} Link IDs: {'rna3p': 174} Time building chain proxies: 7.89, per 1000 atoms: 0.57 Number of scatterers: 13801 At special positions: 0 Unit cell: (123.2, 88, 160.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 350 15.00 O 3275 8.00 N 2590 7.00 C 7571 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.87 Conformation dependent library (CDL) restraints added in 1.0 seconds 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1558 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 8 sheets defined 68.8% alpha, 2.4% beta 36 base pairs and 212 stacking pairs defined. Time for finding SS restraints: 4.44 Creating SS restraints... Processing helix chain 'K' and resid 7 through 19 Processing helix chain 'K' and resid 27 through 38 Processing helix chain 'K' and resid 41 through 46 Processing helix chain 'K' and resid 46 through 59 removed outlier: 4.586A pdb=" N LEU K 50 " --> pdb=" O SER K 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.824A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.682A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.517A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.528A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.841A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.566A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.897A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.557A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.517A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.570A pdb=" N MET D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.835A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.824A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.680A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.517A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.528A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.841A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.567A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.898A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.557A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.518A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.570A pdb=" N MET H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.835A pdb=" N ALA H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 25 through 26 removed outlier: 3.501A pdb=" N SER K 25 " --> pdb=" O PHE K 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.432A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.535A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.081A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.727A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.519A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 404 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 212 stacking parallelities Total time for adding SS restraints: 4.33 Time building geometry restraints manager: 7.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2627 1.33 - 1.45: 4905 1.45 - 1.57: 6504 1.57 - 1.69: 698 1.69 - 1.81: 26 Bond restraints: 14760 Sorted by residual: bond pdb=" C3' DC I 20 " pdb=" O3' DC I 20 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.75e+00 bond pdb=" C3' DT J -81 " pdb=" O3' DT J -81 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.40e+00 bond pdb=" C3' DT I -38 " pdb=" O3' DT I -38 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" C3' DT I 54 " pdb=" O3' DT I 54 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.18e+00 bond pdb=" C3' DC J 54 " pdb=" O3' DC J 54 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.08e+00 ... (remaining 14755 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.14: 2165 106.14 - 112.72: 7818 112.72 - 119.31: 3856 119.31 - 125.89: 6430 125.89 - 132.48: 1160 Bond angle restraints: 21429 Sorted by residual: angle pdb=" C TYR B 98 " pdb=" CA TYR B 98 " pdb=" CB TYR B 98 " ideal model delta sigma weight residual 114.16 108.43 5.73 2.31e+00 1.87e-01 6.16e+00 angle pdb=" C TYR F 98 " pdb=" CA TYR F 98 " pdb=" CB TYR F 98 " ideal model delta sigma weight residual 114.16 108.48 5.68 2.31e+00 1.87e-01 6.04e+00 angle pdb=" C3' DC I 20 " pdb=" O3' DC I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 120.20 123.38 -3.18 1.50e+00 4.44e-01 4.50e+00 angle pdb=" N TYR F 98 " pdb=" CA TYR F 98 " pdb=" C TYR F 98 " ideal model delta sigma weight residual 109.31 112.16 -2.85 1.42e+00 4.96e-01 4.04e+00 angle pdb=" N TYR B 98 " pdb=" CA TYR B 98 " pdb=" C TYR B 98 " ideal model delta sigma weight residual 109.31 112.15 -2.84 1.42e+00 4.96e-01 4.01e+00 ... (remaining 21424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 6212 35.47 - 70.94: 1412 70.94 - 106.42: 32 106.42 - 141.89: 6 141.89 - 177.36: 3 Dihedral angle restraints: 7665 sinusoidal: 5246 harmonic: 2419 Sorted by residual: dihedral pdb=" C4' DT J -81 " pdb=" C3' DT J -81 " pdb=" O3' DT J -81 " pdb=" P DA J -80 " ideal model delta sinusoidal sigma weight residual -140.00 37.36 -177.36 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT I 54 " pdb=" C3' DT I 54 " pdb=" O3' DT I 54 " pdb=" P DG I 55 " ideal model delta sinusoidal sigma weight residual -140.00 36.20 -176.20 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I 20 " pdb=" C3' DC I 20 " pdb=" O3' DC I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 51.88 168.12 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 7662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1672 0.024 - 0.048: 553 0.048 - 0.072: 147 0.072 - 0.096: 28 0.096 - 0.120: 34 Chirality restraints: 2434 Sorted by residual: chirality pdb=" CA ILE D 86 " pdb=" N ILE D 86 " pdb=" C ILE D 86 " pdb=" CB ILE D 86 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE H 86 " pdb=" N ILE H 86 " pdb=" C ILE H 86 " pdb=" CB ILE H 86 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 2431 not shown) Planarity restraints: 1497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I -74 " 0.018 2.00e-02 2.50e+03 9.01e-03 1.83e+00 pdb=" N1 DC I -74 " -0.016 2.00e-02 2.50e+03 pdb=" C2 DC I -74 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DC I -74 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DC I -74 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC I -74 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC I -74 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC I -74 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC I -74 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 81 " -0.018 2.00e-02 2.50e+03 7.95e-03 1.74e+00 pdb=" N9 DA I 81 " 0.017 2.00e-02 2.50e+03 pdb=" C8 DA I 81 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 81 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 81 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 81 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 81 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA I 81 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 81 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 81 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 81 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 60 " -0.017 2.00e-02 2.50e+03 7.71e-03 1.63e+00 pdb=" N9 DA I 60 " 0.017 2.00e-02 2.50e+03 pdb=" C8 DA I 60 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 60 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 60 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 60 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 60 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DA I 60 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 60 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 60 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 60 " 0.003 2.00e-02 2.50e+03 ... (remaining 1494 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1767 2.76 - 3.30: 12189 3.30 - 3.83: 24588 3.83 - 4.37: 27978 4.37 - 4.90: 41372 Nonbonded interactions: 107894 Sorted by model distance: nonbonded pdb=" OG1 THR E 45 " pdb=" OP1 DC J 70 " model vdw 2.226 2.440 nonbonded pdb=" N2 DG I 26 " pdb=" O2 DT J -25 " model vdw 2.294 2.520 nonbonded pdb=" N2 DG J 76 " pdb=" O6 DG J 77 " model vdw 2.306 2.520 nonbonded pdb=" O LEU D 77 " pdb=" ND2 ASN D 81 " model vdw 2.320 2.520 nonbonded pdb=" O LEU H 77 " pdb=" ND2 ASN H 81 " model vdw 2.320 2.520 ... (remaining 107889 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' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 16 through 118) selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 27 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 350 5.49 5 S 15 5.16 5 C 7571 2.51 5 N 2590 2.21 5 O 3275 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.010 Extract box with map and model: 4.300 Check model and map are aligned: 0.170 Process input model: 39.790 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:2.540 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 0.040 14760 Z= 0.137 Angle : 0.451 5.734 21429 Z= 0.291 Chirality : 0.028 0.120 2434 Planarity : 0.003 0.026 1497 Dihedral : 27.357 177.360 6107 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.40 % Favored : 94.87 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.27), residues: 819 helix: 0.21 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -2.58 (0.30), residues: 245 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 206 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 210 average time/residue: 0.3790 time to fit residues: 102.8834 Evaluate side-chains 65 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1408 time to fit residues: 2.0167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 29 optimal weight: 30.0000 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 5 HIS K 17 GLN K 31 GLN K 37 HIS A 68 GLN A 76 GLN B 64 ASN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 75 HIS F 93 GLN G 31 HIS ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.061 14760 Z= 0.405 Angle : 0.788 10.690 21429 Z= 0.456 Chirality : 0.042 0.234 2434 Planarity : 0.007 0.066 1497 Dihedral : 32.691 173.194 4449 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 27.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.81 % Favored : 97.07 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.28), residues: 819 helix: 0.92 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -2.33 (0.31), residues: 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 84 average time/residue: 0.3573 time to fit residues: 40.4072 Evaluate side-chains 43 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 30.0000 chunk 28 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.7513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.049 14760 Z= 0.361 Angle : 0.692 6.941 21429 Z= 0.408 Chirality : 0.038 0.153 2434 Planarity : 0.005 0.059 1497 Dihedral : 33.874 169.115 4449 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 29.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.76 % Favored : 95.12 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.28), residues: 819 helix: 1.24 (0.21), residues: 575 sheet: None (None), residues: 0 loop : -2.22 (0.33), residues: 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 75 average time/residue: 0.3521 time to fit residues: 35.7121 Evaluate side-chains 51 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1126 time to fit residues: 1.3916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.8335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 14760 Z= 0.333 Angle : 0.666 7.759 21429 Z= 0.392 Chirality : 0.036 0.144 2434 Planarity : 0.005 0.058 1497 Dihedral : 34.223 169.170 4449 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 28.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.29), residues: 819 helix: 1.38 (0.21), residues: 574 sheet: -0.54 (1.92), residues: 10 loop : -2.07 (0.35), residues: 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.2994 time to fit residues: 26.2823 Evaluate side-chains 45 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 20.0000 chunk 1 optimal weight: 50.0000 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 55 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 overall best weight: 5.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.8574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 14760 Z= 0.247 Angle : 0.592 5.964 21429 Z= 0.351 Chirality : 0.033 0.124 2434 Planarity : 0.004 0.050 1497 Dihedral : 34.168 174.193 4449 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 0.00 % 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: 0.93 (0.29), residues: 819 helix: 1.64 (0.22), residues: 572 sheet: -0.94 (1.87), residues: 10 loop : -1.94 (0.36), residues: 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.3477 time to fit residues: 30.1712 Evaluate side-chains 42 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 0.0010 chunk 57 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 overall best weight: 6.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN F 75 HIS ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.9196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 14760 Z= 0.293 Angle : 0.622 7.297 21429 Z= 0.368 Chirality : 0.035 0.127 2434 Planarity : 0.004 0.041 1497 Dihedral : 34.379 174.685 4449 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 28.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.29), residues: 819 helix: 1.63 (0.22), residues: 572 sheet: -1.59 (1.76), residues: 10 loop : -1.87 (0.37), residues: 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 0.3427 time to fit residues: 29.4168 Evaluate side-chains 39 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.9196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 14760 Z= 0.220 Angle : 0.577 5.718 21429 Z= 0.343 Chirality : 0.033 0.126 2434 Planarity : 0.003 0.037 1497 Dihedral : 34.238 173.548 4449 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 22.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.00 % 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: 1.17 (0.29), residues: 819 helix: 1.89 (0.22), residues: 559 sheet: -1.52 (1.77), residues: 10 loop : -1.79 (0.36), residues: 250 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2936 time to fit residues: 25.6256 Evaluate side-chains 37 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN B 93 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.9564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.037 14760 Z= 0.300 Angle : 0.628 7.638 21429 Z= 0.371 Chirality : 0.035 0.157 2434 Planarity : 0.004 0.044 1497 Dihedral : 34.338 174.366 4449 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 28.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 0.00 % 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: 0.91 (0.29), residues: 819 helix: 1.61 (0.22), residues: 560 sheet: -1.48 (1.81), residues: 10 loop : -1.69 (0.37), residues: 249 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2923 time to fit residues: 23.3476 Evaluate side-chains 33 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.124 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.9495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 14760 Z= 0.209 Angle : 0.573 6.950 21429 Z= 0.340 Chirality : 0.033 0.171 2434 Planarity : 0.003 0.043 1497 Dihedral : 34.214 173.061 4449 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 22.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 0.00 % 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: 1.27 (0.29), residues: 819 helix: 1.93 (0.22), residues: 559 sheet: -1.29 (1.80), residues: 10 loop : -1.69 (0.36), residues: 250 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2801 time to fit residues: 21.6496 Evaluate side-chains 32 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 54 optimal weight: 30.0000 chunk 71 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 1.0117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 14760 Z= 0.325 Angle : 0.650 6.146 21429 Z= 0.382 Chirality : 0.036 0.151 2434 Planarity : 0.004 0.043 1497 Dihedral : 34.611 174.981 4449 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 30.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.00 % 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: 0.89 (0.29), residues: 819 helix: 1.63 (0.21), residues: 560 sheet: -1.84 (1.63), residues: 10 loop : -1.77 (0.36), residues: 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.2629 time to fit residues: 19.5870 Evaluate side-chains 33 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.380 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 30.0000 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.029537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.021258 restraints weight = 289634.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.021797 restraints weight = 176605.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.022164 restraints weight = 128958.780| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 1.0240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 14760 Z= 0.274 Angle : 0.622 6.971 21429 Z= 0.368 Chirality : 0.035 0.147 2434 Planarity : 0.004 0.040 1497 Dihedral : 34.635 172.227 4449 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 27.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.00 % 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: 0.77 (0.29), residues: 819 helix: 1.57 (0.22), residues: 559 sheet: -2.18 (1.51), residues: 10 loop : -1.88 (0.36), residues: 250 =============================================================================== Job complete usr+sys time: 1778.63 seconds wall clock time: 33 minutes 42.02 seconds (2022.02 seconds total)