Starting phenix.real_space_refine on Fri Mar 15 06:06:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d69_30591/03_2024/7d69_30591.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d69_30591/03_2024/7d69_30591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d69_30591/03_2024/7d69_30591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d69_30591/03_2024/7d69_30591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d69_30591/03_2024/7d69_30591.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d69_30591/03_2024/7d69_30591.pdb" } resolution = 3.57 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= 1.000 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 250 5.49 5 S 13 5.16 5 C 6015 2.51 5 N 2012 2.21 5 O 2567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 60": "OD1" <-> "OD2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E GLU 100": "OE1" <-> "OE2" Residue "E ARG 132": "NH1" <-> "NH2" Residue "F TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 63": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H GLU 75": "OE1" <-> "OE2" Residue "H ARG 107": "NH1" <-> "NH2" Residue "H GLU 112": "OE1" <-> "OE2" Residue "H PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 43": "OD1" <-> "OD2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "G PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G ASP 43": "OD1" <-> "OD2" Residue "G TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G ASP 68": "OD1" <-> "OD2" Residue "G ASP 87": "OD1" <-> "OD2" Residue "G PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 101": "OE1" <-> "OE2" 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: 10857 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 716 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} 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: "D" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 779 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 621 Classifications: {'peptide': 78} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "C" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 754 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "G" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 754 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "I" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2561 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Chain: "J" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2564 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Time building chain proxies: 5.90, per 1000 atoms: 0.54 Number of scatterers: 10857 At special positions: 0 Unit cell: (84, 121.8, 114.45, 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 13 16.00 P 250 15.00 O 2567 8.00 N 2012 7.00 C 6015 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.33 Conformation dependent library (CDL) restraints added in 1.3 seconds 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 74.0% alpha, 1.9% beta 121 base pairs and 227 stacking pairs defined. Time for finding SS restraints: 4.99 Creating SS restraints... Processing helix chain 'A' and resid 51 through 58 removed outlier: 3.897A pdb=" N TYR A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 78 Processing helix chain 'A' and resid 88 through 117 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 26 through 37 Processing helix chain 'B' and resid 45 through 72 removed outlier: 3.698A pdb=" N GLY B 72 " --> pdb=" O TYR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 90 Processing helix chain 'D' and resid 30 through 45 removed outlier: 3.607A pdb=" N ILE D 43 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 84 Processing helix chain 'D' and resid 89 through 101 Processing helix chain 'D' and resid 103 through 122 Processing helix chain 'E' and resid 45 through 58 removed outlier: 4.096A pdb=" N VAL E 49 " --> pdb=" O GLY E 45 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS E 50 " --> pdb=" O MET E 46 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER E 58 " --> pdb=" O LYS E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 79 Processing helix chain 'E' and resid 88 through 117 Processing helix chain 'E' and resid 123 through 133 Processing helix chain 'F' and resid 21 through 25 Processing helix chain 'F' and resid 26 through 38 Processing helix chain 'F' and resid 44 through 72 removed outlier: 4.273A pdb=" N GLN F 48 " --> pdb=" O SER F 44 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY F 72 " --> pdb=" O TYR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 88 Processing helix chain 'H' and resid 30 through 43 Processing helix chain 'H' and resid 54 through 84 Processing helix chain 'H' and resid 89 through 101 Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'C' and resid 13 through 18 Processing helix chain 'C' and resid 23 through 34 Processing helix chain 'C' and resid 42 through 68 removed outlier: 4.162A pdb=" N VAL C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.604A pdb=" N ASP C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'G' and resid 23 through 34 Processing helix chain 'G' and resid 43 through 68 removed outlier: 3.618A pdb=" N TYR G 47 " --> pdb=" O ASP G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 87 removed outlier: 4.103A pdb=" N ASP G 87 " --> pdb=" O ALA G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 removed outlier: 7.028A pdb=" N ARG A 86 " --> pdb=" O VAL B 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA3, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.681A pdb=" N TYR B 94 " --> pdb=" O THR G 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 86 through 87 removed outlier: 7.127A pdb=" N ARG E 86 " --> pdb=" O VAL F 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 121 through 122 Processing sheet with id=AA6, first strand: chain 'F' and resid 92 through 94 removed outlier: 6.189A pdb=" N THR F 92 " --> pdb=" O THR C 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 392 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 315 hydrogen bonds 630 hydrogen bond angles 0 basepair planarities 121 basepair parallelities 227 stacking parallelities Total time for adding SS restraints: 3.75 Time building geometry restraints manager: 6.60 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: 1840 1.33 - 1.45: 3827 1.45 - 1.57: 5355 1.57 - 1.68: 498 1.68 - 1.80: 22 Bond restraints: 11542 Sorted by residual: bond pdb=" CG1 ILE G 24 " pdb=" CD1 ILE G 24 " ideal model delta sigma weight residual 1.513 1.430 0.083 3.90e-02 6.57e+02 4.50e+00 bond pdb=" CG GLN B 89 " pdb=" CD GLN B 89 " ideal model delta sigma weight residual 1.516 1.473 0.043 2.50e-02 1.60e+03 2.89e+00 bond pdb=" CB VAL A 76 " pdb=" CG1 VAL A 76 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.86e+00 bond pdb=" CG LEU F 86 " pdb=" CD1 LEU F 86 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.49e+00 bond pdb=" CB VAL D 37 " pdb=" CG1 VAL D 37 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.49e+00 ... (remaining 11537 not shown) Histogram of bond angle deviations from ideal: 97.69 - 104.66: 950 104.66 - 111.62: 6003 111.62 - 118.58: 3291 118.58 - 125.55: 5575 125.55 - 132.51: 818 Bond angle restraints: 16637 Sorted by residual: angle pdb=" C3' DT J 114 " pdb=" O3' DT J 114 " pdb=" P DC J 115 " ideal model delta sigma weight residual 120.20 125.46 -5.26 1.50e+00 4.44e-01 1.23e+01 angle pdb=" C3' DT I 120 " pdb=" O3' DT I 120 " pdb=" P DC I 121 " ideal model delta sigma weight residual 120.20 124.81 -4.61 1.50e+00 4.44e-01 9.45e+00 angle pdb=" O4' DA I 113 " pdb=" C1' DA I 113 " pdb=" N9 DA I 113 " ideal model delta sigma weight residual 108.40 104.02 4.38 1.50e+00 4.44e-01 8.51e+00 angle pdb=" C4' DA I 72 " pdb=" C3' DA I 72 " pdb=" O3' DA I 72 " ideal model delta sigma weight residual 110.00 105.80 4.20 1.50e+00 4.44e-01 7.83e+00 angle pdb=" O4' DG J 11 " pdb=" C1' DG J 11 " pdb=" C2' DG J 11 " ideal model delta sigma weight residual 106.40 102.23 4.17 1.50e+00 4.44e-01 7.72e+00 ... (remaining 16632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.69: 4776 30.69 - 61.37: 1489 61.37 - 92.05: 46 92.05 - 122.74: 8 122.74 - 153.42: 4 Dihedral angle restraints: 6323 sinusoidal: 4214 harmonic: 2109 Sorted by residual: dihedral pdb=" C4' DT I 120 " pdb=" C3' DT I 120 " pdb=" O3' DT I 120 " pdb=" P DC I 121 " ideal model delta sinusoidal sigma weight residual 220.00 66.58 153.42 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" C4' DT J 114 " pdb=" C3' DT J 114 " pdb=" O3' DT J 114 " pdb=" P DC J 115 " ideal model delta sinusoidal sigma weight residual 220.00 76.89 143.11 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" C4' DC I 100 " pdb=" C3' DC I 100 " pdb=" O3' DC I 100 " pdb=" P DT I 101 " ideal model delta sinusoidal sigma weight residual 220.00 94.95 125.05 1 3.50e+01 8.16e-04 1.23e+01 ... (remaining 6320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1230 0.048 - 0.095: 510 0.095 - 0.143: 142 0.143 - 0.190: 19 0.190 - 0.237: 1 Chirality restraints: 1902 Sorted by residual: chirality pdb=" C3' DT J 114 " pdb=" C4' DT J 114 " pdb=" O3' DT J 114 " pdb=" C2' DT J 114 " both_signs ideal model delta sigma weight residual False -2.66 -2.42 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB THR G 98 " pdb=" CA THR G 98 " pdb=" OG1 THR G 98 " pdb=" CG2 THR G 98 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" C4' DA I 83 " pdb=" C5' DA I 83 " pdb=" O4' DA I 83 " pdb=" C3' DA I 83 " both_signs ideal model delta sigma weight residual False -2.53 -2.34 -0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 1899 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 9 " -0.036 2.00e-02 2.50e+03 1.88e-02 7.92e+00 pdb=" N1 DC I 9 " 0.039 2.00e-02 2.50e+03 pdb=" C2 DC I 9 " -0.005 2.00e-02 2.50e+03 pdb=" O2 DC I 9 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC I 9 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I 9 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 9 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DC I 9 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DC I 9 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 9 " -0.024 2.00e-02 2.50e+03 1.78e-02 7.11e+00 pdb=" N1 DC J 9 " 0.044 2.00e-02 2.50e+03 pdb=" C2 DC J 9 " -0.017 2.00e-02 2.50e+03 pdb=" O2 DC J 9 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DC J 9 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC J 9 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC J 9 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DC J 9 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC J 9 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 31 " -0.038 2.00e-02 2.50e+03 1.60e-02 7.00e+00 pdb=" N9 DA I 31 " 0.029 2.00e-02 2.50e+03 pdb=" C8 DA I 31 " 0.014 2.00e-02 2.50e+03 pdb=" N7 DA I 31 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 31 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 31 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 31 " -0.013 2.00e-02 2.50e+03 pdb=" N1 DA I 31 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 31 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DA I 31 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DA I 31 " 0.004 2.00e-02 2.50e+03 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 186 2.63 - 3.20: 9662 3.20 - 3.76: 21647 3.76 - 4.33: 27367 4.33 - 4.90: 38963 Nonbonded interactions: 97825 Sorted by model distance: nonbonded pdb=" OG SER E 69 " pdb=" NH1 ARG E 73 " model vdw 2.062 2.520 nonbonded pdb=" N ASN D 55 " pdb=" OP1 DA I 12 " model vdw 2.134 2.520 nonbonded pdb=" OG SER C 41 " pdb=" OP1 DG J 98 " model vdw 2.178 2.440 nonbonded pdb=" OH TYR F 68 " pdb=" OE2 GLU H 75 " model vdw 2.203 2.440 nonbonded pdb=" N2 DG I 114 " pdb=" O2 DT J 13 " model vdw 2.210 2.520 ... (remaining 97820 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 51 through 140) } ncs_group { reference = (chain 'B' and (resid 20 through 96 or (resid 97 and (name N or name CA or name \ C )))) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 7 through 65 or resid 67 through 125)) selection = (chain 'J' and (resid 1 through 59 or resid 61 through 119)) } 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: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.500 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 36.110 Find NCS groups from input model: 0.500 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 : 0.009 0.083 11542 Z= 0.528 Angle : 0.883 7.680 16637 Z= 0.522 Chirality : 0.054 0.237 1902 Planarity : 0.005 0.042 1240 Dihedral : 28.860 153.423 4955 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.29), residues: 711 helix: -0.22 (0.21), residues: 513 sheet: None (None), residues: 0 loop : -2.04 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.002 HIS G 79 PHE 0.025 0.004 PHE C 94 TYR 0.020 0.003 TYR C 47 ARG 0.013 0.001 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 138 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7769 (mp0) REVERT: B 35 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7724 (mtt90) REVERT: D 78 ASN cc_start: 0.8833 (t0) cc_final: 0.8304 (t0) REVERT: D 82 ILE cc_start: 0.9136 (mt) cc_final: 0.8678 (mt) REVERT: F 31 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.8033 (mmm160) REVERT: F 87 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8581 (ttmt) REVERT: H 51 LEU cc_start: 0.7360 (pp) cc_final: 0.7109 (pp) REVERT: C 96 ASN cc_start: 0.8080 (p0) cc_final: 0.7802 (p0) REVERT: C 101 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7940 (mt-10) REVERT: G 85 ARG cc_start: 0.7539 (mtt180) cc_final: 0.7337 (mtt180) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.3505 time to fit residues: 55.3555 Evaluate side-chains 100 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN E 44 GLN ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11542 Z= 0.226 Angle : 0.631 6.744 16637 Z= 0.371 Chirality : 0.037 0.180 1902 Planarity : 0.004 0.038 1240 Dihedral : 31.830 178.545 3513 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.94 % Allowed : 14.40 % Favored : 83.66 % 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: 0.35 (0.29), residues: 711 helix: 0.83 (0.21), residues: 524 sheet: None (None), residues: 0 loop : -1.34 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS G 79 PHE 0.022 0.002 PHE G 60 TYR 0.013 0.001 TYR E 55 ARG 0.003 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.7904 (mtt-85) cc_final: 0.7666 (mtt90) REVERT: F 31 ARG cc_start: 0.8326 (mmm-85) cc_final: 0.8044 (mmm160) REVERT: F 51 ARG cc_start: 0.8207 (mtt180) cc_final: 0.7939 (mtt-85) REVERT: F 87 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8525 (ttmt) REVERT: H 84 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7699 (mmtt) REVERT: C 96 ASN cc_start: 0.8018 (p0) cc_final: 0.7747 (p0) REVERT: C 101 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7893 (mt-10) outliers start: 12 outliers final: 5 residues processed: 126 average time/residue: 0.2871 time to fit residues: 48.2539 Evaluate side-chains 101 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11542 Z= 0.275 Angle : 0.620 6.902 16637 Z= 0.362 Chirality : 0.037 0.181 1902 Planarity : 0.004 0.041 1240 Dihedral : 31.647 177.918 3513 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.91 % Allowed : 19.42 % Favored : 77.67 % 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: 0.85 (0.29), residues: 711 helix: 1.24 (0.21), residues: 521 sheet: None (None), residues: 0 loop : -1.27 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS G 79 PHE 0.022 0.002 PHE G 60 TYR 0.014 0.002 TYR E 55 ARG 0.007 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: D 119 LYS cc_start: 0.8678 (ttmt) cc_final: 0.8177 (tmmt) REVERT: F 31 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.8077 (mmm160) REVERT: F 87 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8540 (ttmt) REVERT: H 55 ASN cc_start: 0.8298 (t0) cc_final: 0.8091 (t0) REVERT: H 84 LYS cc_start: 0.8036 (mmtt) cc_final: 0.7581 (mmtt) REVERT: H 104 GLU cc_start: 0.7542 (tp30) cc_final: 0.7260 (tp30) REVERT: H 107 ARG cc_start: 0.7767 (ttp80) cc_final: 0.7538 (ttp80) REVERT: C 62 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7477 (mm-30) REVERT: C 96 ASN cc_start: 0.8041 (p0) cc_final: 0.7800 (p0) REVERT: C 101 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7879 (mt-10) outliers start: 18 outliers final: 12 residues processed: 112 average time/residue: 0.2797 time to fit residues: 42.1706 Evaluate side-chains 105 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN E 44 GLN C 30 HIS C 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 11542 Z= 0.433 Angle : 0.691 11.825 16637 Z= 0.391 Chirality : 0.041 0.218 1902 Planarity : 0.005 0.044 1240 Dihedral : 31.977 175.746 3513 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.72 % Allowed : 19.58 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.29), residues: 711 helix: 0.85 (0.20), residues: 522 sheet: None (None), residues: 0 loop : -1.36 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS G 79 PHE 0.017 0.002 PHE G 60 TYR 0.017 0.002 TYR E 102 ARG 0.004 0.001 ARG F 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: D 78 ASN cc_start: 0.8783 (t0) cc_final: 0.8174 (t0) REVERT: D 82 ILE cc_start: 0.9119 (mt) cc_final: 0.8668 (mt) REVERT: D 119 LYS cc_start: 0.8683 (ttmt) cc_final: 0.8171 (ttmt) REVERT: F 31 ARG cc_start: 0.8203 (mmm-85) cc_final: 0.7962 (mmm160) REVERT: F 87 LYS cc_start: 0.8962 (ttpt) cc_final: 0.8591 (ttmt) REVERT: H 84 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7596 (mmtt) REVERT: C 101 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7831 (mt-10) outliers start: 23 outliers final: 14 residues processed: 125 average time/residue: 0.2653 time to fit residues: 44.5241 Evaluate side-chains 115 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11542 Z= 0.206 Angle : 0.587 8.988 16637 Z= 0.344 Chirality : 0.035 0.151 1902 Planarity : 0.004 0.044 1240 Dihedral : 31.367 177.499 3513 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.78 % Allowed : 22.82 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.30), residues: 711 helix: 1.58 (0.21), residues: 521 sheet: None (None), residues: 0 loop : -1.16 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS G 79 PHE 0.016 0.002 PHE G 60 TYR 0.010 0.001 TYR A 102 ARG 0.006 0.000 ARG E 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 119 LYS cc_start: 0.8643 (ttmt) cc_final: 0.8126 (tmmt) REVERT: F 87 LYS cc_start: 0.8865 (ttpt) cc_final: 0.8503 (ttmt) REVERT: H 84 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7483 (mmtt) REVERT: C 101 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7732 (mt-10) outliers start: 11 outliers final: 8 residues processed: 106 average time/residue: 0.3132 time to fit residues: 43.6440 Evaluate side-chains 97 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 20.0000 chunk 17 optimal weight: 0.2980 chunk 52 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN E 44 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 96 ASN G 54 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 11542 Z= 0.438 Angle : 0.679 13.335 16637 Z= 0.385 Chirality : 0.040 0.198 1902 Planarity : 0.005 0.043 1240 Dihedral : 31.746 176.350 3513 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.72 % Allowed : 23.46 % Favored : 72.82 % 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: 0.62 (0.29), residues: 711 helix: 1.02 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -1.21 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS G 79 PHE 0.015 0.002 PHE B 96 TYR 0.017 0.002 TYR E 102 ARG 0.005 0.001 ARG E 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ASP cc_start: 0.7458 (t0) cc_final: 0.7205 (t0) REVERT: D 78 ASN cc_start: 0.8786 (t0) cc_final: 0.8176 (t0) REVERT: D 82 ILE cc_start: 0.9133 (mt) cc_final: 0.8699 (mt) REVERT: D 119 LYS cc_start: 0.8645 (ttmt) cc_final: 0.8149 (ttmt) REVERT: F 31 ARG cc_start: 0.8315 (mmm-85) cc_final: 0.8019 (mmm160) REVERT: F 87 LYS cc_start: 0.8953 (ttpt) cc_final: 0.8557 (ttmt) REVERT: H 82 ILE cc_start: 0.9017 (mp) cc_final: 0.8775 (mp) REVERT: H 84 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7577 (mmtt) REVERT: C 85 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.8027 (mpt180) REVERT: C 101 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7852 (mt-10) outliers start: 23 outliers final: 17 residues processed: 110 average time/residue: 0.3160 time to fit residues: 45.3870 Evaluate side-chains 111 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.0270 chunk 65 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN D 42 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11542 Z= 0.182 Angle : 0.576 11.082 16637 Z= 0.337 Chirality : 0.034 0.138 1902 Planarity : 0.004 0.044 1240 Dihedral : 31.072 179.041 3513 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.07 % Allowed : 23.30 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.30), residues: 711 helix: 1.71 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.17 (0.39), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS G 79 PHE 0.014 0.002 PHE G 60 TYR 0.010 0.001 TYR A 102 ARG 0.007 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8003 (tp30) cc_final: 0.7694 (tp30) REVERT: D 119 LYS cc_start: 0.8614 (ttmt) cc_final: 0.8110 (tmmt) REVERT: F 51 ARG cc_start: 0.8422 (mtt-85) cc_final: 0.8075 (mtt-85) REVERT: F 87 LYS cc_start: 0.8863 (ttpt) cc_final: 0.8481 (ttmt) REVERT: H 84 LYS cc_start: 0.7983 (mmtt) cc_final: 0.7438 (mmtt) outliers start: 19 outliers final: 11 residues processed: 103 average time/residue: 0.3154 time to fit residues: 42.7132 Evaluate side-chains 99 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 69 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN D 42 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11542 Z= 0.191 Angle : 0.564 10.571 16637 Z= 0.333 Chirality : 0.034 0.131 1902 Planarity : 0.004 0.043 1240 Dihedral : 31.047 178.072 3513 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.91 % Allowed : 23.95 % Favored : 73.14 % 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: 1.77 (0.30), residues: 711 helix: 1.96 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -1.08 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 79 PHE 0.010 0.001 PHE E 68 TYR 0.010 0.001 TYR E 102 ARG 0.004 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8003 (tp30) cc_final: 0.7643 (tp30) REVERT: A 112 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8554 (mp) REVERT: F 31 ARG cc_start: 0.8257 (mmm-85) cc_final: 0.8007 (mmm160) REVERT: F 51 ARG cc_start: 0.8452 (mtt-85) cc_final: 0.8102 (mtt-85) REVERT: F 87 LYS cc_start: 0.8852 (ttpt) cc_final: 0.8469 (ttmt) REVERT: H 41 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7838 (tm-30) REVERT: H 84 LYS cc_start: 0.7928 (mmtt) cc_final: 0.7380 (mmtt) outliers start: 18 outliers final: 11 residues processed: 102 average time/residue: 0.3074 time to fit residues: 41.5175 Evaluate side-chains 101 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN D 42 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 11542 Z= 0.427 Angle : 0.665 10.347 16637 Z= 0.379 Chirality : 0.040 0.161 1902 Planarity : 0.004 0.041 1240 Dihedral : 31.427 176.344 3513 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.40 % Allowed : 23.30 % Favored : 73.30 % 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: 0.87 (0.29), residues: 711 helix: 1.23 (0.21), residues: 525 sheet: None (None), residues: 0 loop : -1.24 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 71 PHE 0.020 0.002 PHE G 60 TYR 0.018 0.002 TYR E 102 ARG 0.005 0.001 ARG B 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.833 Fit side-chains REVERT: D 78 ASN cc_start: 0.8757 (t0) cc_final: 0.8129 (t0) REVERT: D 82 ILE cc_start: 0.9090 (mt) cc_final: 0.8649 (mt) REVERT: D 119 LYS cc_start: 0.8643 (ttmt) cc_final: 0.8382 (ttmt) REVERT: F 31 ARG cc_start: 0.8432 (mmm-85) cc_final: 0.8080 (mmm160) REVERT: F 51 ARG cc_start: 0.8475 (mtt-85) cc_final: 0.8052 (mtt-85) REVERT: F 87 LYS cc_start: 0.8928 (ttpt) cc_final: 0.8578 (ttmt) REVERT: H 84 LYS cc_start: 0.8062 (mmtt) cc_final: 0.7541 (mmtt) REVERT: G 62 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7716 (mm-30) outliers start: 21 outliers final: 16 residues processed: 112 average time/residue: 0.3133 time to fit residues: 45.8187 Evaluate side-chains 110 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11542 Z= 0.224 Angle : 0.582 9.998 16637 Z= 0.342 Chirality : 0.035 0.140 1902 Planarity : 0.004 0.042 1240 Dihedral : 31.112 177.736 3513 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.94 % Allowed : 25.24 % Favored : 72.82 % 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: 1.38 (0.30), residues: 711 helix: 1.62 (0.21), residues: 523 sheet: None (None), residues: 0 loop : -1.10 (0.39), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 79 PHE 0.010 0.002 PHE E 68 TYR 0.024 0.002 TYR D 33 ARG 0.005 0.000 ARG E 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: D 119 LYS cc_start: 0.8606 (ttmt) cc_final: 0.8327 (ttmt) REVERT: F 51 ARG cc_start: 0.8446 (mtt-85) cc_final: 0.8085 (mtt-85) REVERT: F 87 LYS cc_start: 0.8880 (ttpt) cc_final: 0.8505 (ttmt) REVERT: H 56 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.6948 (mppt) REVERT: H 84 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7487 (mmtt) outliers start: 12 outliers final: 10 residues processed: 103 average time/residue: 0.3076 time to fit residues: 41.3165 Evaluate side-chains 103 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN D 42 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.176366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119959 restraints weight = 14649.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120579 restraints weight = 10114.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.121271 restraints weight = 9385.464| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11542 Z= 0.224 Angle : 0.578 9.565 16637 Z= 0.339 Chirality : 0.035 0.172 1902 Planarity : 0.004 0.050 1240 Dihedral : 31.061 177.699 3513 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.75 % Allowed : 24.11 % Favored : 73.14 % 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: 1.48 (0.30), residues: 711 helix: 1.71 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -1.11 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 79 PHE 0.022 0.002 PHE G 60 TYR 0.027 0.002 TYR D 33 ARG 0.010 0.000 ARG F 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1694.72 seconds wall clock time: 31 minutes 39.80 seconds (1899.80 seconds total)