Starting phenix.real_space_refine on Sat Mar 16 05:14:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbp_30161/03_2024/7dbp_30161.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbp_30161/03_2024/7dbp_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_30161/03_2024/7dbp_30161.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbp_30161/03_2024/7dbp_30161.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbp_30161/03_2024/7dbp_30161.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbp_30161/03_2024/7dbp_30161.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.15, per 1000 atoms: 0.52 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: 7.06 Conformation dependent library (CDL) restraints added in 1.1 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: 4.98 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: 4.14 Time building geometry restraints manager: 7.48 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: 6501 35.47 - 70.94: 1431 70.94 - 106.42: 32 106.42 - 141.89: 6 141.89 - 177.36: 3 Dihedral angle restraints: 7973 sinusoidal: 5554 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 7970 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 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: 0.890 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.770 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 39.960 Find NCS groups from input model: 0.520 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 27.262 177.360 6415 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 % Allowed : 2.15 % Favored : 97.28 % 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: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 113 PHE 0.007 0.001 PHE D 62 TYR 0.010 0.001 TYR C 50 ARG 0.002 0.000 ARG K 54 *********************** 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 : 1.067 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 REVERT: K 65 LYS cc_start: 0.6470 (OUTLIER) cc_final: 0.5878 (pttt) REVERT: B 98 TYR cc_start: 0.7815 (m-10) cc_final: 0.7502 (m-10) REVERT: C 38 ASN cc_start: 0.9559 (m110) cc_final: 0.9130 (t0) REVERT: C 56 GLU cc_start: 0.9307 (tt0) cc_final: 0.9105 (pp20) REVERT: D 34 TYR cc_start: 0.8684 (m-80) cc_final: 0.8456 (m-80) REVERT: D 54 LYS cc_start: 0.9185 (mttt) cc_final: 0.8979 (mppt) REVERT: D 68 GLU cc_start: 0.9595 (mt-10) cc_final: 0.9386 (tm-30) REVERT: E 94 GLU cc_start: 0.9447 (mm-30) cc_final: 0.9124 (tp30) REVERT: E 107 THR cc_start: 0.9627 (m) cc_final: 0.9258 (p) REVERT: F 97 LEU cc_start: 0.8431 (tp) cc_final: 0.8206 (tp) REVERT: G 38 ASN cc_start: 0.9646 (m110) cc_final: 0.9305 (t0) REVERT: H 68 GLU cc_start: 0.9382 (mt-10) cc_final: 0.8992 (pp20) outliers start: 4 outliers final: 2 residues processed: 210 average time/residue: 0.3756 time to fit residues: 101.9310 Evaluate side-chains 75 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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: 4.9990 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 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 5 HIS K 17 GLN K 31 GLN K 37 HIS A 68 GLN A 76 GLN C 38 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 38 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 14760 Z= 0.361 Angle : 0.723 8.945 21429 Z= 0.425 Chirality : 0.040 0.194 2434 Planarity : 0.006 0.059 1497 Dihedral : 31.857 171.564 4757 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.32 % Favored : 97.56 % Rotamer: Outliers : 0.57 % Allowed : 2.15 % Favored : 97.28 % 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: 0.38 (0.28), residues: 819 helix: 1.25 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -2.28 (0.30), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 75 PHE 0.015 0.002 PHE E 104 TYR 0.021 0.002 TYR H 37 ARG 0.012 0.001 ARG H 89 *********************** 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 100 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 1.014 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: B 98 TYR cc_start: 0.8416 (m-10) cc_final: 0.7806 (m-10) REVERT: H 68 GLU cc_start: 0.9494 (mt-10) cc_final: 0.9284 (mm-30) REVERT: H 73 GLU cc_start: 0.9826 (tp30) cc_final: 0.9603 (tp30) outliers start: 4 outliers final: 0 residues processed: 98 average time/residue: 0.3360 time to fit residues: 44.5834 Evaluate side-chains 47 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 0.0070 chunk 28 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 overall best weight: 5.8008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14760 Z= 0.268 Angle : 0.603 6.344 21429 Z= 0.356 Chirality : 0.034 0.128 2434 Planarity : 0.004 0.062 1497 Dihedral : 32.318 169.436 4757 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.14 % Allowed : 2.58 % Favored : 97.28 % 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: 0.82 (0.28), residues: 819 helix: 1.61 (0.21), residues: 575 sheet: None (None), residues: 0 loop : -2.13 (0.32), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 75 PHE 0.015 0.002 PHE B 61 TYR 0.016 0.002 TYR K 8 ARG 0.006 0.001 ARG D 89 *********************** 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 73 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.995 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: A 59 GLU cc_start: 0.9290 (mp0) cc_final: 0.8978 (pm20) REVERT: A 97 GLU cc_start: 0.9324 (pp20) cc_final: 0.8957 (pp20) REVERT: B 98 TYR cc_start: 0.8231 (m-10) cc_final: 0.7712 (m-10) REVERT: D 68 GLU cc_start: 0.9734 (pt0) cc_final: 0.9489 (pt0) REVERT: G 73 ASN cc_start: 0.8939 (t0) cc_final: 0.8542 (t0) REVERT: H 30 ARG cc_start: 0.8974 (mpp-170) cc_final: 0.8159 (ttt180) REVERT: H 68 GLU cc_start: 0.9528 (mt-10) cc_final: 0.9267 (mm-30) REVERT: H 73 GLU cc_start: 0.9772 (tp30) cc_final: 0.9562 (tp30) outliers start: 1 outliers final: 0 residues processed: 73 average time/residue: 0.3302 time to fit residues: 33.2591 Evaluate side-chains 51 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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: 0.9990 chunk 11 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 69 optimal weight: 0.0020 chunk 103 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 overall best weight: 5.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.7247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14760 Z= 0.255 Angle : 0.590 6.034 21429 Z= 0.351 Chirality : 0.033 0.129 2434 Planarity : 0.004 0.058 1497 Dihedral : 32.577 168.391 4757 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 21.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: 1.21 (0.29), residues: 819 helix: 1.87 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -1.91 (0.33), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.021 0.002 PHE D 62 TYR 0.016 0.002 TYR G 50 ARG 0.022 0.001 ARG E 134 *********************** 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 69 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9273 (mp0) cc_final: 0.9047 (mp0) REVERT: A 97 GLU cc_start: 0.9338 (pp20) cc_final: 0.9057 (pp20) REVERT: B 98 TYR cc_start: 0.8440 (m-10) cc_final: 0.7476 (m-10) REVERT: G 73 ASN cc_start: 0.8970 (t0) cc_final: 0.8515 (t0) REVERT: H 68 GLU cc_start: 0.9535 (mt-10) cc_final: 0.9263 (mm-30) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3072 time to fit residues: 29.9414 Evaluate side-chains 52 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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: 8.9990 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 75 optimal weight: 0.1980 chunk 0 optimal weight: 40.0000 chunk 55 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 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: 0.8318 moved from start: 0.7772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14760 Z= 0.236 Angle : 0.571 7.079 21429 Z= 0.340 Chirality : 0.033 0.184 2434 Planarity : 0.004 0.038 1497 Dihedral : 32.719 172.658 4757 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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: 1.39 (0.29), residues: 819 helix: 1.98 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -1.74 (0.34), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 75 PHE 0.017 0.002 PHE D 67 TYR 0.012 0.001 TYR F 88 ARG 0.007 0.000 ARG F 39 *********************** 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 69 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.061 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: A 59 GLU cc_start: 0.9255 (mp0) cc_final: 0.9006 (mp0) REVERT: A 97 GLU cc_start: 0.9329 (pp20) cc_final: 0.9009 (pp20) REVERT: B 98 TYR cc_start: 0.8370 (m-10) cc_final: 0.7425 (m-10) REVERT: D 68 GLU cc_start: 0.9727 (mt-10) cc_final: 0.9512 (pt0) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3150 time to fit residues: 29.9943 Evaluate side-chains 49 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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: 7.9990 chunk 26 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 20.0000 chunk 105 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: C 104 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.8804 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= 0.314 Angle : 0.642 6.462 21429 Z= 0.376 Chirality : 0.035 0.127 2434 Planarity : 0.004 0.038 1497 Dihedral : 33.340 174.210 4757 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 28.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.43 % Allowed : 2.29 % Favored : 97.28 % 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: 1.10 (0.28), residues: 819 helix: 1.79 (0.21), residues: 563 sheet: None (None), residues: 0 loop : -1.76 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.015 0.002 PHE D 62 TYR 0.022 0.002 TYR G 50 ARG 0.005 0.001 ARG B 92 *********************** 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 63 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9276 (mp0) cc_final: 0.9014 (mp0) REVERT: A 90 MET cc_start: 0.9665 (tpt) cc_final: 0.9435 (tpp) REVERT: A 97 GLU cc_start: 0.9374 (pp20) cc_final: 0.9117 (pp20) REVERT: B 98 TYR cc_start: 0.8432 (m-10) cc_final: 0.8001 (m-10) REVERT: D 68 GLU cc_start: 0.9770 (mt-10) cc_final: 0.9565 (pt0) REVERT: H 69 ARG cc_start: 0.9737 (mmp80) cc_final: 0.9514 (mmp80) outliers start: 3 outliers final: 1 residues processed: 63 average time/residue: 0.3236 time to fit residues: 28.5761 Evaluate side-chains 47 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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: 3.9990 chunk 62 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 0.0770 chunk 67 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS ** 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: 0.8318 moved from start: 0.8712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14760 Z= 0.200 Angle : 0.560 6.567 21429 Z= 0.333 Chirality : 0.032 0.139 2434 Planarity : 0.003 0.027 1497 Dihedral : 33.082 172.127 4757 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: 1.47 (0.29), residues: 819 helix: 2.07 (0.21), residues: 562 sheet: None (None), residues: 0 loop : -1.62 (0.35), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.020 0.002 PHE H 67 TYR 0.012 0.001 TYR D 37 ARG 0.003 0.000 ARG E 131 *********************** 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 58 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9225 (mp0) cc_final: 0.8941 (mp0) REVERT: A 94 GLU cc_start: 0.9445 (mm-30) cc_final: 0.9196 (mm-30) REVERT: A 97 GLU cc_start: 0.9326 (pp20) cc_final: 0.9067 (pp20) REVERT: B 98 TYR cc_start: 0.8390 (m-10) cc_final: 0.7954 (m-10) REVERT: D 68 GLU cc_start: 0.9713 (mt-10) cc_final: 0.9478 (pt0) REVERT: H 69 ARG cc_start: 0.9719 (mmp80) cc_final: 0.9430 (mmp80) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2985 time to fit residues: 24.8351 Evaluate side-chains 47 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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: 20.0000 chunk 32 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 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: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN ** 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: 0.8410 moved from start: 0.9605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 14760 Z= 0.351 Angle : 0.661 6.100 21429 Z= 0.389 Chirality : 0.037 0.132 2434 Planarity : 0.004 0.043 1497 Dihedral : 33.716 174.286 4757 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 31.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: 0.94 (0.29), residues: 819 helix: 1.61 (0.21), residues: 563 sheet: None (None), residues: 0 loop : -1.66 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 75 PHE 0.015 0.002 PHE D 62 TYR 0.016 0.002 TYR F 98 ARG 0.008 0.001 ARG F 95 *********************** 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 52 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9256 (mp0) cc_final: 0.8985 (mp0) REVERT: A 97 GLU cc_start: 0.9416 (pp20) cc_final: 0.9105 (pp20) REVERT: B 98 TYR cc_start: 0.8476 (m-10) cc_final: 0.8033 (m-10) REVERT: D 68 GLU cc_start: 0.9758 (mt-10) cc_final: 0.9495 (pt0) REVERT: H 30 ARG cc_start: 0.9071 (mpp-170) cc_final: 0.8508 (ttt180) REVERT: H 69 ARG cc_start: 0.9754 (mmp80) cc_final: 0.9523 (mmp80) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.3455 time to fit residues: 24.9966 Evaluate side-chains 45 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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: 5.9990 chunk 44 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 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: 4.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8382 moved from start: 0.9769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14760 Z= 0.276 Angle : 0.609 6.113 21429 Z= 0.361 Chirality : 0.034 0.148 2434 Planarity : 0.004 0.034 1497 Dihedral : 33.635 170.447 4757 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 27.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: 0.99 (0.29), residues: 819 helix: 1.63 (0.21), residues: 562 sheet: None (None), residues: 0 loop : -1.59 (0.35), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.021 0.002 PHE H 67 TYR 0.015 0.002 TYR D 39 ARG 0.004 0.000 ARG E 131 *********************** 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 55 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9238 (mp0) cc_final: 0.8999 (mp0) REVERT: A 97 GLU cc_start: 0.9379 (pp20) cc_final: 0.9089 (pp20) REVERT: B 98 TYR cc_start: 0.8522 (m-10) cc_final: 0.8135 (m-10) REVERT: D 65 ASP cc_start: 0.9646 (m-30) cc_final: 0.9438 (m-30) REVERT: H 30 ARG cc_start: 0.9078 (mpp-170) cc_final: 0.8491 (ttt180) REVERT: H 69 ARG cc_start: 0.9763 (mmp80) cc_final: 0.9517 (mmp80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.3314 time to fit residues: 25.5240 Evaluate side-chains 41 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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: 20.0000 chunk 74 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 54 optimal weight: 20.0000 chunk 71 optimal weight: 0.0570 chunk 95 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 overall best weight: 3.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8319 moved from start: 0.9635 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= 0.196 Angle : 0.562 5.905 21429 Z= 0.336 Chirality : 0.033 0.188 2434 Planarity : 0.003 0.027 1497 Dihedral : 33.329 171.695 4757 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.29), residues: 819 helix: 1.76 (0.21), residues: 561 sheet: -1.05 (1.69), residues: 10 loop : -1.46 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.013 0.001 PHE D 62 TYR 0.020 0.001 TYR G 50 ARG 0.003 0.000 ARG H 89 ********************** 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 58 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9208 (mp0) cc_final: 0.8943 (mp0) REVERT: A 90 MET cc_start: 0.9614 (tpt) cc_final: 0.9347 (tpp) REVERT: A 94 GLU cc_start: 0.9439 (mm-30) cc_final: 0.9194 (mm-30) REVERT: A 97 GLU cc_start: 0.9346 (pp20) cc_final: 0.9143 (pp20) REVERT: B 98 TYR cc_start: 0.8465 (m-10) cc_final: 0.8085 (m-10) REVERT: D 65 ASP cc_start: 0.9579 (m-30) cc_final: 0.9254 (p0) REVERT: H 30 ARG cc_start: 0.9053 (mpp-170) cc_final: 0.8562 (mtt180) REVERT: H 69 ARG cc_start: 0.9751 (mmp80) cc_final: 0.9479 (mmp80) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.3409 time to fit residues: 27.6276 Evaluate side-chains 43 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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: 10.0000 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: 1.9990 chunk 16 optimal weight: 0.0050 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 overall best weight: 4.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.030228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.021631 restraints weight = 265843.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.022362 restraints weight = 144004.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.022855 restraints weight = 98411.082| |-----------------------------------------------------------------------------| r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.9812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14760 Z= 0.221 Angle : 0.570 5.296 21429 Z= 0.340 Chirality : 0.033 0.146 2434 Planarity : 0.003 0.027 1497 Dihedral : 33.293 172.493 4757 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 1.22 (0.29), residues: 819 helix: 1.76 (0.21), residues: 565 sheet: None (None), residues: 0 loop : -1.43 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.027 0.002 PHE H 67 TYR 0.009 0.001 TYR K 8 ARG 0.002 0.000 ARG C 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1922.49 seconds wall clock time: 36 minutes 9.89 seconds (2169.89 seconds total)