Starting phenix.real_space_refine on Fri Mar 15 11:58:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5r_14334/03_2024/7r5r_14334.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5r_14334/03_2024/7r5r_14334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5r_14334/03_2024/7r5r_14334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5r_14334/03_2024/7r5r_14334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5r_14334/03_2024/7r5r_14334.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5r_14334/03_2024/7r5r_14334.pdb" } resolution = 2.44 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= -0.001 sd= 0.049 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 266 5.49 5 S 8 5.16 5 C 6528 2.51 5 N 2145 2.21 5 O 2678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "L ARG 526": "NH1" <-> "NH2" 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: 11625 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 799 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 96} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 755 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 770 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 784 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2729 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain: "J" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2724 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain breaks: 1 Chain: "K" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 178 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "L" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 185 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Time building chain proxies: 6.46, per 1000 atoms: 0.56 Number of scatterers: 11625 At special positions: 0 Unit cell: (81.888, 116.861, 119.42, 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 8 16.00 P 266 15.00 O 2678 8.00 N 2145 7.00 C 6528 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: 5.36 Conformation dependent library (CDL) restraints added in 1.3 seconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 11 sheets defined 68.5% alpha, 2.8% beta 124 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 5.13 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 removed outlier: 4.293A pdb=" N LYS A 49 " --> pdb=" O GLN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.751A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.703A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.666A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.063A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.515A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.640A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.687A pdb=" N MET D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 47 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.851A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR E 79 " --> pdb=" O CYS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 117 Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.656A pdb=" N VAL E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.646A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.944A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.853A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.437A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.319A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.925A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.306A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'L' and resid 516 through 517 389 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 286 hydrogen bonds 572 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 4.41 Time building geometry restraints manager: 5.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2058 1.33 - 1.45: 4086 1.45 - 1.57: 5694 1.57 - 1.69: 527 1.69 - 1.81: 14 Bond restraints: 12379 Sorted by residual: bond pdb=" O3' DA I 20 " pdb=" P DC I 21 " ideal model delta sigma weight residual 1.607 1.683 -0.076 1.50e-02 4.44e+03 2.54e+01 bond pdb=" O3' DA I 17 " pdb=" P DT I 18 " ideal model delta sigma weight residual 1.607 1.548 0.059 1.50e-02 4.44e+03 1.57e+01 bond pdb=" C1' DG J 34 " pdb=" N9 DG J 34 " ideal model delta sigma weight residual 1.460 1.388 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C1' DG I -20 " pdb=" N9 DG I -20 " ideal model delta sigma weight residual 1.460 1.394 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" O3' DG J -16 " pdb=" P DT J -15 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.50e-02 4.44e+03 9.87e+00 ... (remaining 12374 not shown) Histogram of bond angle deviations from ideal: 94.07 - 102.24: 285 102.24 - 110.41: 4901 110.41 - 118.58: 5794 118.58 - 126.75: 5998 126.75 - 134.92: 882 Bond angle restraints: 17860 Sorted by residual: angle pdb=" C4' DA J -18 " pdb=" C3' DA J -18 " pdb=" O3' DA J -18 " ideal model delta sigma weight residual 110.00 94.07 15.93 1.50e+00 4.44e-01 1.13e+02 angle pdb=" C3' DA I 17 " pdb=" O3' DA I 17 " pdb=" P DT I 18 " ideal model delta sigma weight residual 120.20 134.92 -14.72 1.50e+00 4.44e-01 9.64e+01 angle pdb=" O3' DT I 18 " pdb=" C3' DT I 18 " pdb=" C2' DT I 18 " ideal model delta sigma weight residual 111.50 98.04 13.46 1.50e+00 4.44e-01 8.05e+01 angle pdb=" O3' DA J -18 " pdb=" C3' DA J -18 " pdb=" C2' DA J -18 " ideal model delta sigma weight residual 111.50 100.12 11.38 1.50e+00 4.44e-01 5.76e+01 angle pdb=" C4' DT I 18 " pdb=" C3' DT I 18 " pdb=" O3' DT I 18 " ideal model delta sigma weight residual 110.00 99.69 10.31 1.50e+00 4.44e-01 4.73e+01 ... (remaining 17855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 5618 35.80 - 71.60: 1193 71.60 - 107.40: 19 107.40 - 143.19: 0 143.19 - 178.99: 2 Dihedral angle restraints: 6832 sinusoidal: 4587 harmonic: 2245 Sorted by residual: dihedral pdb=" C4' DA J -49 " pdb=" C3' DA J -49 " pdb=" O3' DA J -49 " pdb=" P DG J -48 " ideal model delta sinusoidal sigma weight residual 220.00 41.01 178.99 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J -16 " pdb=" C3' DG J -16 " pdb=" O3' DG J -16 " pdb=" P DT J -15 " ideal model delta sinusoidal sigma weight residual -140.00 30.40 -170.40 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA GLY E 134 " pdb=" C GLY E 134 " pdb=" N LEU E 135 " pdb=" CA LEU E 135 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 6829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1975 0.098 - 0.196: 47 0.196 - 0.295: 8 0.295 - 0.393: 2 0.393 - 0.491: 1 Chirality restraints: 2033 Sorted by residual: chirality pdb=" C3' DA J -18 " pdb=" C4' DA J -18 " pdb=" O3' DA J -18 " pdb=" C2' DA J -18 " both_signs ideal model delta sigma weight residual False -2.66 -3.15 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" C3' DT I 18 " pdb=" C4' DT I 18 " pdb=" O3' DT I 18 " pdb=" C2' DT I 18 " both_signs ideal model delta sigma weight residual False -2.66 -3.04 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C3' DT J -15 " pdb=" C4' DT J -15 " pdb=" O3' DT J -15 " pdb=" C2' DT J -15 " both_signs ideal model delta sigma weight residual False -2.66 -2.96 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 2030 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J -16 " -0.019 2.00e-02 2.50e+03 2.08e-02 1.29e+01 pdb=" N9 DG J -16 " 0.045 2.00e-02 2.50e+03 pdb=" C8 DG J -16 " -0.025 2.00e-02 2.50e+03 pdb=" N7 DG J -16 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DG J -16 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG J -16 " -0.000 2.00e-02 2.50e+03 pdb=" O6 DG J -16 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DG J -16 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG J -16 " -0.041 2.00e-02 2.50e+03 pdb=" N2 DG J -16 " 0.015 2.00e-02 2.50e+03 pdb=" N3 DG J -16 " 0.014 2.00e-02 2.50e+03 pdb=" C4 DG J -16 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J -19 " 0.015 2.00e-02 2.50e+03 1.93e-02 1.11e+01 pdb=" N9 DG J -19 " 0.002 2.00e-02 2.50e+03 pdb=" C8 DG J -19 " -0.027 2.00e-02 2.50e+03 pdb=" N7 DG J -19 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG J -19 " 0.030 2.00e-02 2.50e+03 pdb=" C6 DG J -19 " 0.042 2.00e-02 2.50e+03 pdb=" O6 DG J -19 " -0.019 2.00e-02 2.50e+03 pdb=" N1 DG J -19 " -0.014 2.00e-02 2.50e+03 pdb=" C2 DG J -19 " -0.009 2.00e-02 2.50e+03 pdb=" N2 DG J -19 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG J -19 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DG J -19 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " 0.013 2.00e-02 2.50e+03 1.94e-02 1.03e+01 pdb=" N9 DA I 20 " -0.031 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.024 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " -0.044 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " 0.015 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " 0.015 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1514 2.76 - 3.30: 9716 3.30 - 3.83: 21549 3.83 - 4.37: 25862 4.37 - 4.90: 37546 Nonbonded interactions: 96187 Sorted by model distance: nonbonded pdb=" OH TYR C 39 " pdb=" OE2 GLU D 71 " model vdw 2.226 2.440 nonbonded pdb=" OG1 THR A 113 " pdb=" OD2 ASP A 125 " model vdw 2.259 2.440 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.273 2.440 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 78 " model vdw 2.283 2.440 nonbonded pdb=" OG1 THR E 113 " pdb=" OD2 ASP E 125 " model vdw 2.334 2.440 ... (remaining 96182 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 46 through 139) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 111) selection = (chain 'G' and resid 15 through 111) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = (chain 'L' and resid 515 through 535) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.020 Extract box with map and model: 9.910 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 37.840 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 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:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3787 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 : 0.004 0.076 12379 Z= 0.187 Angle : 0.656 15.927 17860 Z= 0.422 Chirality : 0.040 0.491 2033 Planarity : 0.004 0.041 1328 Dihedral : 26.939 178.993 5382 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.31 % Allowed : 12.13 % Favored : 87.56 % 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: -0.10 (0.27), residues: 759 helix: 1.05 (0.20), residues: 533 sheet: None (None), residues: 0 loop : -2.86 (0.29), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 86 HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE H 70 TYR 0.006 0.001 TYR B 51 ARG 0.005 0.000 ARG F 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 0.971 Fit side-chains REVERT: B 31 LYS cc_start: 0.5334 (ttmm) cc_final: 0.4862 (tttp) REVERT: B 84 MET cc_start: 0.5751 (mmm) cc_final: 0.5455 (mmm) REVERT: B 91 LYS cc_start: 0.7261 (ttmm) cc_final: 0.6527 (ttpt) REVERT: C 99 ARG cc_start: 0.7074 (mtp180) cc_final: 0.6787 (mtp85) REVERT: D 68 ASP cc_start: 0.5710 (t0) cc_final: 0.5390 (t0) REVERT: D 86 ARG cc_start: 0.6545 (mmt-90) cc_final: 0.6246 (mmt90) REVERT: F 44 LYS cc_start: 0.5833 (tttt) cc_final: 0.5629 (tttm) REVERT: G 41 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6423 (mp0) REVERT: G 77 ARG cc_start: 0.7094 (mtm-85) cc_final: 0.6762 (mmm-85) REVERT: H 86 ARG cc_start: 0.6084 (mmt90) cc_final: 0.5810 (mpt-90) outliers start: 2 outliers final: 1 residues processed: 134 average time/residue: 2.1851 time to fit residues: 306.0396 Evaluate side-chains 115 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 83 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 51 optimal weight: 0.0170 chunk 40 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN B 93 GLN C 94 ASN E 87 GLN F 75 HIS F 93 GLN G 73 ASN G 94 ASN H 84 ASN H 95 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3839 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12379 Z= 0.247 Angle : 0.604 8.160 17860 Z= 0.359 Chirality : 0.036 0.133 2033 Planarity : 0.004 0.038 1328 Dihedral : 30.386 179.209 3885 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.87 % Allowed : 16.80 % Favored : 81.34 % 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: 759 helix: 2.04 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -2.37 (0.31), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 86 HIS 0.003 0.001 HIS E 115 PHE 0.011 0.002 PHE A 78 TYR 0.011 0.002 TYR B 51 ARG 0.003 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 0.913 Fit side-chains REVERT: B 31 LYS cc_start: 0.5293 (ttmm) cc_final: 0.4904 (tttp) REVERT: B 84 MET cc_start: 0.5757 (mmm) cc_final: 0.5495 (mmm) REVERT: D 86 ARG cc_start: 0.6577 (mmt-90) cc_final: 0.5909 (mmt90) REVERT: G 41 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6404 (mp0) REVERT: G 77 ARG cc_start: 0.6934 (mtm-85) cc_final: 0.6610 (mtm-85) REVERT: H 86 ARG cc_start: 0.6014 (mmt90) cc_final: 0.5713 (mpt-90) REVERT: H 108 LYS cc_start: 0.6293 (mtpp) cc_final: 0.5987 (mttt) REVERT: H 122 THR cc_start: 0.7525 (t) cc_final: 0.7180 (p) outliers start: 12 outliers final: 8 residues processed: 128 average time/residue: 2.1260 time to fit residues: 284.7648 Evaluate side-chains 124 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain K residue 535 SER Chi-restraints excluded: chain L residue 515 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 90 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3860 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12379 Z= 0.279 Angle : 0.628 8.654 17860 Z= 0.372 Chirality : 0.037 0.133 2033 Planarity : 0.005 0.044 1328 Dihedral : 30.477 178.281 3883 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.80 % Allowed : 16.33 % Favored : 80.87 % 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: 1.53 (0.29), residues: 759 helix: 2.22 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -2.13 (0.32), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 47 HIS 0.004 0.001 HIS B 75 PHE 0.009 0.002 PHE H 70 TYR 0.013 0.002 TYR B 51 ARG 0.004 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 0.943 Fit side-chains REVERT: B 31 LYS cc_start: 0.5262 (ttmm) cc_final: 0.4897 (tttp) REVERT: B 84 MET cc_start: 0.5660 (mmm) cc_final: 0.5456 (mmm) REVERT: C 73 ASN cc_start: 0.6886 (t0) cc_final: 0.6654 (t0) REVERT: D 68 ASP cc_start: 0.5768 (t0) cc_final: 0.5523 (t0) REVERT: D 86 ARG cc_start: 0.6569 (mmt-90) cc_final: 0.5852 (mmt90) REVERT: G 41 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6379 (mp0) REVERT: G 77 ARG cc_start: 0.6949 (mtm-85) cc_final: 0.6601 (mtm-85) REVERT: H 86 ARG cc_start: 0.5978 (mmt90) cc_final: 0.5703 (mpt-90) outliers start: 18 outliers final: 10 residues processed: 132 average time/residue: 2.0614 time to fit residues: 285.0022 Evaluate side-chains 126 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain K residue 535 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 26 optimal weight: 0.0000 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3845 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12379 Z= 0.197 Angle : 0.599 8.305 17860 Z= 0.357 Chirality : 0.035 0.129 2033 Planarity : 0.004 0.039 1328 Dihedral : 30.444 178.252 3883 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.49 % Allowed : 17.42 % Favored : 80.09 % 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: 1.91 (0.30), residues: 759 helix: 2.50 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.98 (0.33), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 47 HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE F 61 TYR 0.011 0.001 TYR B 51 ARG 0.004 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.893 Fit side-chains REVERT: B 31 LYS cc_start: 0.5195 (ttmm) cc_final: 0.4835 (tttp) REVERT: B 84 MET cc_start: 0.5681 (mmm) cc_final: 0.5442 (mmm) REVERT: C 73 ASN cc_start: 0.6870 (t0) cc_final: 0.6627 (t0) REVERT: D 68 ASP cc_start: 0.5817 (t0) cc_final: 0.5539 (t0) REVERT: D 86 ARG cc_start: 0.6560 (mmt-90) cc_final: 0.5838 (mmt90) REVERT: G 41 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6341 (mp0) REVERT: G 77 ARG cc_start: 0.6901 (mtm-85) cc_final: 0.6506 (mtm-85) REVERT: H 86 ARG cc_start: 0.5960 (mmt90) cc_final: 0.5663 (mmt90) REVERT: H 122 THR cc_start: 0.7546 (t) cc_final: 0.7206 (p) outliers start: 16 outliers final: 11 residues processed: 127 average time/residue: 2.0162 time to fit residues: 268.6545 Evaluate side-chains 127 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain K residue 535 SER Chi-restraints excluded: chain L residue 515 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3889 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 12379 Z= 0.468 Angle : 0.734 9.386 17860 Z= 0.430 Chirality : 0.045 0.163 2033 Planarity : 0.006 0.047 1328 Dihedral : 30.793 177.706 3883 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.42 % Allowed : 17.42 % Favored : 79.16 % 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: 1.36 (0.29), residues: 759 helix: 2.04 (0.21), residues: 532 sheet: None (None), residues: 0 loop : -2.02 (0.34), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 47 HIS 0.005 0.001 HIS F 75 PHE 0.015 0.003 PHE A 78 TYR 0.014 0.003 TYR H 42 ARG 0.004 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 0.921 Fit side-chains REVERT: B 31 LYS cc_start: 0.5435 (ttmm) cc_final: 0.5065 (tttp) REVERT: B 84 MET cc_start: 0.5743 (mmm) cc_final: 0.5478 (mmm) REVERT: D 86 ARG cc_start: 0.6566 (mmt-90) cc_final: 0.6137 (mmt90) REVERT: G 41 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6340 (mp0) REVERT: G 77 ARG cc_start: 0.6827 (mtm-85) cc_final: 0.6488 (mtm-85) outliers start: 22 outliers final: 15 residues processed: 131 average time/residue: 2.0275 time to fit residues: 278.4072 Evaluate side-chains 130 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 535 SER Chi-restraints excluded: chain L residue 515 SER Chi-restraints excluded: chain L residue 535 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3838 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12379 Z= 0.197 Angle : 0.604 8.042 17860 Z= 0.359 Chirality : 0.035 0.125 2033 Planarity : 0.004 0.040 1328 Dihedral : 30.490 178.071 3883 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.33 % Allowed : 18.35 % Favored : 79.32 % 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: 1.99 (0.30), residues: 759 helix: 2.54 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.86 (0.34), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 47 HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE F 61 TYR 0.009 0.001 TYR G 50 ARG 0.005 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 0.841 Fit side-chains REVERT: B 31 LYS cc_start: 0.5179 (ttmm) cc_final: 0.4815 (tttp) REVERT: B 84 MET cc_start: 0.5732 (mmm) cc_final: 0.5451 (mmm) REVERT: D 68 ASP cc_start: 0.5743 (t0) cc_final: 0.5474 (t0) REVERT: D 86 ARG cc_start: 0.6547 (mmt-90) cc_final: 0.5849 (mmt90) REVERT: G 41 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6387 (mp0) REVERT: G 77 ARG cc_start: 0.6915 (mtm-85) cc_final: 0.6588 (mtm-85) outliers start: 15 outliers final: 10 residues processed: 128 average time/residue: 2.0422 time to fit residues: 274.1739 Evaluate side-chains 127 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain K residue 535 SER Chi-restraints excluded: chain L residue 515 SER Chi-restraints excluded: chain L residue 535 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3846 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12379 Z= 0.208 Angle : 0.595 8.253 17860 Z= 0.356 Chirality : 0.035 0.128 2033 Planarity : 0.004 0.038 1328 Dihedral : 30.413 177.302 3883 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.02 % Allowed : 18.82 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.30), residues: 759 helix: 2.70 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.78 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 47 HIS 0.003 0.001 HIS E 115 PHE 0.009 0.001 PHE A 78 TYR 0.008 0.001 TYR B 51 ARG 0.006 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.965 Fit side-chains REVERT: B 31 LYS cc_start: 0.5277 (ttmm) cc_final: 0.4888 (tttp) REVERT: B 84 MET cc_start: 0.5707 (mmm) cc_final: 0.5460 (mmm) REVERT: D 68 ASP cc_start: 0.5804 (t0) cc_final: 0.5531 (t0) REVERT: D 86 ARG cc_start: 0.6442 (mmt-90) cc_final: 0.5781 (mmt90) REVERT: G 41 GLU cc_start: 0.6851 (mm-30) cc_final: 0.6348 (mp0) REVERT: G 77 ARG cc_start: 0.6906 (mtm-85) cc_final: 0.6547 (mtm-85) outliers start: 13 outliers final: 10 residues processed: 126 average time/residue: 2.1081 time to fit residues: 278.2740 Evaluate side-chains 127 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain K residue 535 SER Chi-restraints excluded: chain L residue 535 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3880 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12379 Z= 0.379 Angle : 0.684 9.057 17860 Z= 0.401 Chirality : 0.041 0.145 2033 Planarity : 0.005 0.047 1328 Dihedral : 30.608 177.190 3883 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.80 % Allowed : 18.04 % Favored : 79.16 % 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: 1.75 (0.29), residues: 759 helix: 2.32 (0.21), residues: 532 sheet: None (None), residues: 0 loop : -1.83 (0.34), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 47 HIS 0.005 0.001 HIS F 75 PHE 0.021 0.002 PHE A 78 TYR 0.012 0.002 TYR H 42 ARG 0.009 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 0.938 Fit side-chains REVERT: B 31 LYS cc_start: 0.5298 (ttmm) cc_final: 0.4929 (tttp) REVERT: B 84 MET cc_start: 0.5718 (mmm) cc_final: 0.5450 (mmm) REVERT: D 86 ARG cc_start: 0.6541 (mmt-90) cc_final: 0.5875 (mmt90) REVERT: G 41 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6368 (mp0) REVERT: G 77 ARG cc_start: 0.6892 (mtm-85) cc_final: 0.6495 (mtm-85) outliers start: 18 outliers final: 15 residues processed: 131 average time/residue: 2.2003 time to fit residues: 301.3501 Evaluate side-chains 134 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 535 SER Chi-restraints excluded: chain L residue 515 SER Chi-restraints excluded: chain L residue 535 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3869 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12379 Z= 0.242 Angle : 0.635 8.792 17860 Z= 0.379 Chirality : 0.037 0.132 2033 Planarity : 0.005 0.042 1328 Dihedral : 30.590 177.270 3883 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.33 % Allowed : 18.20 % Favored : 79.47 % 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: 1.89 (0.30), residues: 759 helix: 2.42 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.78 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 47 HIS 0.004 0.001 HIS F 75 PHE 0.012 0.002 PHE A 78 TYR 0.012 0.002 TYR B 51 ARG 0.003 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 0.783 Fit side-chains REVERT: B 31 LYS cc_start: 0.5255 (ttmm) cc_final: 0.4904 (tttp) REVERT: B 84 MET cc_start: 0.5677 (mmm) cc_final: 0.5422 (mmm) REVERT: D 86 ARG cc_start: 0.6514 (mmt-90) cc_final: 0.5826 (mmt90) REVERT: G 41 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6367 (mp0) REVERT: G 77 ARG cc_start: 0.6874 (mtm-85) cc_final: 0.6476 (mtm-85) outliers start: 15 outliers final: 13 residues processed: 127 average time/residue: 2.1004 time to fit residues: 279.3914 Evaluate side-chains 130 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 535 SER Chi-restraints excluded: chain L residue 515 SER Chi-restraints excluded: chain L residue 535 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3867 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12379 Z= 0.269 Angle : 0.642 8.566 17860 Z= 0.379 Chirality : 0.037 0.132 2033 Planarity : 0.005 0.050 1328 Dihedral : 30.544 177.299 3883 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.87 % Allowed : 18.82 % Favored : 79.32 % 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: 1.92 (0.30), residues: 759 helix: 2.45 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.79 (0.34), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 47 HIS 0.004 0.001 HIS F 75 PHE 0.013 0.002 PHE A 78 TYR 0.010 0.002 TYR B 51 ARG 0.008 0.000 ARG A 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 0.923 Fit side-chains REVERT: B 31 LYS cc_start: 0.5263 (ttmm) cc_final: 0.4895 (tttp) REVERT: B 84 MET cc_start: 0.5695 (mmm) cc_final: 0.5401 (mmm) REVERT: D 86 ARG cc_start: 0.6517 (mmt-90) cc_final: 0.5842 (mmt90) REVERT: G 41 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6367 (mp0) REVERT: G 77 ARG cc_start: 0.6888 (mtm-85) cc_final: 0.6509 (mtm-85) outliers start: 12 outliers final: 12 residues processed: 126 average time/residue: 2.2534 time to fit residues: 297.3035 Evaluate side-chains 130 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 535 SER Chi-restraints excluded: chain L residue 515 SER Chi-restraints excluded: chain L residue 535 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.147992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.098736 restraints weight = 15960.012| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.39 r_work: 0.3131 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12379 Z= 0.191 Angle : 0.615 8.507 17860 Z= 0.366 Chirality : 0.035 0.128 2033 Planarity : 0.004 0.040 1328 Dihedral : 30.518 177.307 3883 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.87 % Allowed : 18.66 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.30), residues: 759 helix: 2.60 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.75 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 47 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE F 61 TYR 0.012 0.001 TYR B 51 ARG 0.003 0.000 ARG A 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5043.94 seconds wall clock time: 88 minutes 57.36 seconds (5337.36 seconds total)