Starting phenix.real_space_refine on Sat Feb 17 15:23:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xd0_33131/02_2024/7xd0_33131.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xd0_33131/02_2024/7xd0_33131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xd0_33131/02_2024/7xd0_33131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xd0_33131/02_2024/7xd0_33131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xd0_33131/02_2024/7xd0_33131.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xd0_33131/02_2024/7xd0_33131.pdb" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5986 atoms to isotropic. 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 292 5.49 5 S 14 5.16 5 C 7398 2.51 5 N 2466 2.21 5 O 3052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L ARG 74": "NH1" <-> "NH2" Residue "K ARG 74": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13222 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 657 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 805 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 811 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 657 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "L" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 residue: pdb=" N ARG L 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG L 74 " occ=0.45 residue: pdb=" N GLY L 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY L 75 " occ=0.25 residue: pdb=" N GLY L 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY L 76 " occ=0.25 residue: pdb=" N LEU K 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU K 73 " occ=0.45 residue: pdb=" N ARG K 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG K 74 " occ=0.45 residue: pdb=" N GLY K 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY K 75 " occ=0.25 residue: pdb=" N GLY K 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY K 76 " occ=0.25 Time building chain proxies: 7.30, per 1000 atoms: 0.55 Number of scatterers: 13222 At special positions: 0 Unit cell: (139.62, 136.398, 93.438, 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 14 16.00 P 292 15.00 O 3052 8.00 N 2466 7.00 C 7398 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: 6.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 9 sheets defined 60.0% alpha, 6.1% beta 141 base pairs and 244 stacking pairs defined. Time for finding SS restraints: 6.07 Creating SS restraints... Processing helix chain 'F' and resid 30 through 35 Processing helix chain 'F' and resid 37 through 42 Processing helix chain 'F' and resid 49 through 57 removed outlier: 3.753A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 87 removed outlier: 3.533A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.467A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.660A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 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 104 through 124 removed outlier: 3.834A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.863A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.565A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.384A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.525A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.933A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.651A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 35 removed outlier: 3.506A pdb=" N LYS L 27 " --> pdb=" O ILE L 23 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN L 31 " --> pdb=" O LYS L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'K' and resid 22 through 35 removed outlier: 3.507A pdb=" N LYS K 27 " --> pdb=" O ILE K 23 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN K 31 " --> pdb=" O LYS K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing sheet with id=AA1, first strand: chain 'F' and resid 45 through 46 removed outlier: 7.530A pdb=" N ARG F 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 96 through 98 removed outlier: 5.985A pdb=" N THR F 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.489A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'G' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.731A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA8, first strand: chain 'L' and resid 12 through 16 removed outlier: 3.598A pdb=" N PHE L 45 " --> pdb=" O LYS L 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 12 through 16 removed outlier: 3.598A pdb=" N PHE K 45 " --> pdb=" O LYS K 48 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 244 stacking parallelities Total time for adding SS restraints: 4.34 Time building geometry restraints manager: 7.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2876 1.33 - 1.45: 4188 1.45 - 1.57: 6370 1.57 - 1.69: 582 1.69 - 1.81: 26 Bond restraints: 14042 Sorted by residual: bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.18e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.06e+00 bond pdb=" N THR F 71 " pdb=" CA THR F 71 " ideal model delta sigma weight residual 1.456 1.471 -0.015 1.23e-02 6.61e+03 1.47e+00 bond pdb=" N ILE F 29 " pdb=" CA ILE F 29 " ideal model delta sigma weight residual 1.474 1.457 0.018 1.57e-02 4.06e+03 1.27e+00 bond pdb=" CA ASP H 51 " pdb=" C ASP H 51 " ideal model delta sigma weight residual 1.526 1.538 -0.011 1.03e-02 9.43e+03 1.17e+00 ... (remaining 14037 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.19: 1264 105.19 - 112.06: 7748 112.06 - 118.94: 3609 118.94 - 125.81: 6611 125.81 - 132.68: 981 Bond angle restraints: 20213 Sorted by residual: angle pdb=" N ASP F 68 " pdb=" CA ASP F 68 " pdb=" C ASP F 68 " ideal model delta sigma weight residual 112.93 108.08 4.85 1.33e+00 5.65e-01 1.33e+01 angle pdb=" C VAL F 70 " pdb=" N THR F 71 " pdb=" CA THR F 71 " ideal model delta sigma weight residual 126.45 132.68 -6.23 1.77e+00 3.19e-01 1.24e+01 angle pdb=" OG1 THR F 71 " pdb=" CB THR F 71 " pdb=" CG2 THR F 71 " ideal model delta sigma weight residual 109.30 102.73 6.57 2.00e+00 2.50e-01 1.08e+01 angle pdb=" C PHE F 100 " pdb=" N GLY F 101 " pdb=" CA GLY F 101 " ideal model delta sigma weight residual 121.70 127.18 -5.48 1.80e+00 3.09e-01 9.27e+00 angle pdb=" CA ARG F 67 " pdb=" C ARG F 67 " pdb=" N ASP F 68 " ideal model delta sigma weight residual 118.87 115.37 3.50 1.18e+00 7.18e-01 8.82e+00 ... (remaining 20208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.47: 6275 34.47 - 68.93: 1416 68.93 - 103.40: 30 103.40 - 137.87: 0 137.87 - 172.33: 3 Dihedral angle restraints: 7724 sinusoidal: 5081 harmonic: 2643 Sorted by residual: dihedral pdb=" CA THR F 71 " pdb=" C THR F 71 " pdb=" N TYR F 72 " pdb=" CA TYR F 72 " ideal model delta harmonic sigma weight residual 180.00 152.64 27.36 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ALA F 89 " pdb=" C ALA F 89 " pdb=" N LEU F 90 " pdb=" CA LEU F 90 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ALA F 69 " pdb=" C ALA F 69 " pdb=" N VAL F 70 " pdb=" CA VAL F 70 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 7721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1759 0.036 - 0.072: 422 0.072 - 0.109: 96 0.109 - 0.145: 32 0.145 - 0.181: 2 Chirality restraints: 2311 Sorted by residual: chirality pdb=" CB THR F 71 " pdb=" CA THR F 71 " pdb=" OG1 THR F 71 " pdb=" CG2 THR F 71 " both_signs ideal model delta sigma weight residual False 2.55 2.73 -0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CA PHE F 100 " pdb=" N PHE F 100 " pdb=" C PHE F 100 " pdb=" CB PHE F 100 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ARG L 42 " pdb=" N ARG L 42 " pdb=" C ARG L 42 " pdb=" CB ARG L 42 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 2308 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 62 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C LEU F 62 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU F 62 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU F 63 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO C 80 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 91 " -0.018 2.00e-02 2.50e+03 8.14e-03 1.82e+00 pdb=" N9 DA I 91 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DA I 91 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 91 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA I 91 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 91 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 91 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 91 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 91 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 91 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 91 " 0.001 2.00e-02 2.50e+03 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 154 2.63 - 3.20: 10839 3.20 - 3.76: 23949 3.76 - 4.33: 31828 4.33 - 4.90: 45569 Nonbonded interactions: 112339 Sorted by model distance: nonbonded pdb=" CG ARG K 42 " pdb=" NH2 ARG K 72 " model vdw 2.062 3.520 nonbonded pdb=" O GLN K 62 " pdb=" OG SER K 65 " model vdw 2.132 2.440 nonbonded pdb=" O GLN L 62 " pdb=" OG SER L 65 " model vdw 2.132 2.440 nonbonded pdb=" O2 DC I 74 " pdb=" N2 DG J 74 " model vdw 2.183 2.496 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.223 2.440 ... (remaining 112334 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 37 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 11 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } 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=0.25 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 4.180 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 41.180 Find NCS groups from input model: 0.480 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14042 Z= 0.178 Angle : 0.573 6.573 20213 Z= 0.346 Chirality : 0.036 0.181 2311 Planarity : 0.003 0.046 1552 Dihedral : 27.036 172.333 6018 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.26 % Allowed : 0.39 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 1.30 (0.29), residues: 895 helix: 1.51 (0.23), residues: 562 sheet: -0.46 (0.79), residues: 50 loop : -0.06 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 31 PHE 0.009 0.001 PHE A 67 TYR 0.018 0.002 TYR F 88 ARG 0.003 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 1.064 Fit side-chains REVERT: G 61 GLU cc_start: 0.7469 (tp30) cc_final: 0.7258 (tp30) REVERT: G 84 GLN cc_start: 0.8809 (tp40) cc_final: 0.8576 (tp40) REVERT: H 59 MET cc_start: 0.8586 (tpp) cc_final: 0.8379 (tpp) REVERT: H 116 LYS cc_start: 0.7879 (ttpp) cc_final: 0.7611 (ttpp) REVERT: E 58 THR cc_start: 0.8782 (p) cc_final: 0.8523 (p) REVERT: D 68 ASP cc_start: 0.8486 (t0) cc_final: 0.8251 (t0) REVERT: L 74 ARG cc_start: -0.0092 (OUTLIER) cc_final: -0.0744 (mmm160) REVERT: K 1 MET cc_start: 0.0618 (tpt) cc_final: 0.0259 (tpt) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.2734 time to fit residues: 54.2989 Evaluate side-chains 124 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 47 optimal weight: 0.4980 chunk 29 optimal weight: 0.0470 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 0.0670 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN C 38 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14042 Z= 0.156 Angle : 0.539 5.739 20213 Z= 0.326 Chirality : 0.035 0.146 2311 Planarity : 0.003 0.045 1552 Dihedral : 29.961 172.237 4206 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.78 % Allowed : 6.80 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 895 helix: 2.00 (0.23), residues: 570 sheet: -0.77 (0.76), residues: 50 loop : 0.15 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 113 PHE 0.008 0.001 PHE F 100 TYR 0.018 0.001 TYR H 40 ARG 0.005 0.000 ARG K 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 0.978 Fit side-chains REVERT: G 61 GLU cc_start: 0.7457 (tp30) cc_final: 0.7226 (tp30) REVERT: H 54 ILE cc_start: 0.8344 (mm) cc_final: 0.8120 (tt) REVERT: E 58 THR cc_start: 0.8834 (p) cc_final: 0.8578 (p) REVERT: B 25 ASN cc_start: 0.8754 (m110) cc_final: 0.8293 (m-40) REVERT: K 1 MET cc_start: 0.0628 (tpt) cc_final: 0.0361 (tpt) outliers start: 6 outliers final: 4 residues processed: 148 average time/residue: 0.2799 time to fit residues: 58.9932 Evaluate side-chains 127 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 38 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 84 ASN A 125 GLN D 63 ASN C 38 ASN C 73 ASN B 25 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14042 Z= 0.376 Angle : 0.667 6.850 20213 Z= 0.384 Chirality : 0.041 0.205 2311 Planarity : 0.005 0.043 1552 Dihedral : 30.821 172.941 4202 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.75 % Allowed : 8.76 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.32 (0.29), residues: 895 helix: 1.58 (0.22), residues: 571 sheet: -0.58 (0.75), residues: 50 loop : -0.23 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 75 PHE 0.017 0.002 PHE F 61 TYR 0.017 0.002 TYR H 40 ARG 0.005 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.139 Fit side-chains REVERT: F 84 MET cc_start: 0.7814 (mmm) cc_final: 0.7608 (mmt) REVERT: D 105 GLU cc_start: 0.7012 (tp30) cc_final: 0.6702 (tp30) REVERT: B 68 ASP cc_start: 0.8187 (m-30) cc_final: 0.7939 (m-30) REVERT: K 1 MET cc_start: 0.0771 (tpt) cc_final: 0.0526 (tpt) outliers start: 21 outliers final: 11 residues processed: 127 average time/residue: 0.2788 time to fit residues: 49.8300 Evaluate side-chains 119 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain B residue 60 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 73 ASN D 63 ASN C 38 ASN C 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14042 Z= 0.286 Angle : 0.611 7.959 20213 Z= 0.359 Chirality : 0.038 0.185 2311 Planarity : 0.004 0.039 1552 Dihedral : 30.610 172.151 4202 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.88 % Allowed : 10.98 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.37 (0.29), residues: 895 helix: 1.66 (0.22), residues: 569 sheet: -0.52 (0.73), residues: 52 loop : -0.30 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.012 0.002 PHE A 67 TYR 0.017 0.002 TYR H 40 ARG 0.003 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 1.125 Fit side-chains REVERT: E 73 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8180 (pp20) REVERT: B 25 ASN cc_start: 0.8759 (m-40) cc_final: 0.8279 (m-40) REVERT: K 1 MET cc_start: 0.0840 (tpt) cc_final: 0.0575 (tpt) outliers start: 22 outliers final: 18 residues processed: 122 average time/residue: 0.2861 time to fit residues: 49.2658 Evaluate side-chains 128 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 71 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 84 ASN D 63 ASN C 38 ASN C 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14042 Z= 0.261 Angle : 0.597 6.456 20213 Z= 0.352 Chirality : 0.038 0.173 2311 Planarity : 0.004 0.037 1552 Dihedral : 30.578 172.150 4202 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.88 % Allowed : 11.90 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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 (0.29), residues: 895 helix: 1.72 (0.23), residues: 571 sheet: -0.35 (0.75), residues: 52 loop : -0.30 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 49 PHE 0.012 0.002 PHE A 67 TYR 0.016 0.002 TYR H 40 ARG 0.003 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 1.125 Fit side-chains REVERT: E 73 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8230 (pp20) REVERT: D 59 MET cc_start: 0.8754 (tpp) cc_final: 0.8298 (tpp) REVERT: B 25 ASN cc_start: 0.8693 (m-40) cc_final: 0.8199 (m-40) REVERT: K 1 MET cc_start: 0.0802 (tpt) cc_final: 0.0528 (tpt) outliers start: 22 outliers final: 16 residues processed: 125 average time/residue: 0.2741 time to fit residues: 48.4272 Evaluate side-chains 127 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 71 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 110 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.0570 chunk 57 optimal weight: 2.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN H 84 ASN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 84 ASN C 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14042 Z= 0.164 Angle : 0.542 6.297 20213 Z= 0.325 Chirality : 0.035 0.146 2311 Planarity : 0.003 0.039 1552 Dihedral : 30.228 171.603 4202 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.22 % Allowed : 12.81 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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 (0.29), residues: 895 helix: 2.05 (0.23), residues: 570 sheet: -0.17 (0.74), residues: 52 loop : -0.10 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 31 PHE 0.010 0.001 PHE E 67 TYR 0.017 0.001 TYR H 40 ARG 0.002 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.058 Fit side-chains REVERT: F 25 ASN cc_start: 0.8363 (m-40) cc_final: 0.8057 (m-40) REVERT: H 42 TYR cc_start: 0.7696 (t80) cc_final: 0.7375 (t80) REVERT: H 86 ARG cc_start: 0.7173 (mtt180) cc_final: 0.6801 (mtt-85) REVERT: E 58 THR cc_start: 0.8858 (p) cc_final: 0.8601 (p) REVERT: E 73 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8128 (pp20) REVERT: D 59 MET cc_start: 0.8749 (tpp) cc_final: 0.8186 (tpp) REVERT: C 101 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8936 (p) REVERT: B 25 ASN cc_start: 0.8631 (m-40) cc_final: 0.8127 (m-40) REVERT: K 1 MET cc_start: 0.0676 (tpt) cc_final: 0.0393 (tpt) outliers start: 17 outliers final: 11 residues processed: 135 average time/residue: 0.2652 time to fit residues: 50.9334 Evaluate side-chains 136 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 63 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN H 84 ASN A 108 ASN A 125 GLN D 84 ASN C 38 ASN C 73 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14042 Z= 0.309 Angle : 0.620 6.460 20213 Z= 0.361 Chirality : 0.039 0.185 2311 Planarity : 0.004 0.036 1552 Dihedral : 30.616 172.342 4202 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.48 % Allowed : 14.12 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.59 (0.29), residues: 895 helix: 1.82 (0.23), residues: 567 sheet: -0.10 (0.77), residues: 52 loop : -0.25 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 75 PHE 0.013 0.002 PHE F 61 TYR 0.018 0.002 TYR H 40 ARG 0.004 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 1.060 Fit side-chains REVERT: F 25 ASN cc_start: 0.8391 (m-40) cc_final: 0.8100 (m-40) REVERT: H 80 LEU cc_start: 0.9107 (tp) cc_final: 0.8880 (tp) REVERT: H 86 ARG cc_start: 0.7309 (mtt180) cc_final: 0.7087 (mtt180) REVERT: E 73 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8182 (pp20) REVERT: C 101 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8918 (p) REVERT: B 25 ASN cc_start: 0.8723 (m-40) cc_final: 0.8296 (m-40) REVERT: K 1 MET cc_start: 0.0670 (tpt) cc_final: 0.0377 (tpt) outliers start: 19 outliers final: 13 residues processed: 127 average time/residue: 0.2857 time to fit residues: 50.8753 Evaluate side-chains 130 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 71 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 0.0770 chunk 86 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN G 84 GLN H 84 ASN D 84 ASN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14042 Z= 0.169 Angle : 0.552 7.990 20213 Z= 0.327 Chirality : 0.035 0.146 2311 Planarity : 0.003 0.038 1552 Dihedral : 30.251 171.496 4202 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.09 % Allowed : 14.38 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 1.93 (0.29), residues: 895 helix: 2.07 (0.23), residues: 570 sheet: 0.12 (0.77), residues: 52 loop : -0.14 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.011 0.001 PHE E 67 TYR 0.019 0.001 TYR H 40 ARG 0.004 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.101 Fit side-chains REVERT: H 80 LEU cc_start: 0.9111 (tp) cc_final: 0.8865 (tp) REVERT: E 58 THR cc_start: 0.8892 (p) cc_final: 0.8648 (p) REVERT: E 73 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8167 (pp20) REVERT: D 59 MET cc_start: 0.8760 (tpp) cc_final: 0.8198 (tpp) REVERT: D 68 ASP cc_start: 0.8467 (t0) cc_final: 0.8229 (t0) REVERT: B 25 ASN cc_start: 0.8649 (m-40) cc_final: 0.8174 (m-40) REVERT: K 1 MET cc_start: 0.0573 (tpt) cc_final: 0.0313 (tpt) outliers start: 16 outliers final: 10 residues processed: 136 average time/residue: 0.2735 time to fit residues: 52.8804 Evaluate side-chains 136 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 71 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 73 ASN H 84 ASN A 108 ASN A 125 GLN D 84 ASN D 109 HIS C 38 ASN C 73 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14042 Z= 0.296 Angle : 0.629 9.145 20213 Z= 0.365 Chirality : 0.039 0.184 2311 Planarity : 0.004 0.035 1552 Dihedral : 30.606 172.224 4202 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.48 % Allowed : 14.77 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 1.59 (0.29), residues: 895 helix: 1.85 (0.23), residues: 567 sheet: 0.13 (0.78), residues: 52 loop : -0.38 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 75 PHE 0.013 0.002 PHE F 61 TYR 0.017 0.002 TYR H 40 ARG 0.003 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.126 Fit side-chains REVERT: H 80 LEU cc_start: 0.9118 (tp) cc_final: 0.8885 (tp) REVERT: H 86 ARG cc_start: 0.7033 (mtt-85) cc_final: 0.6699 (mtt-85) REVERT: E 73 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8266 (pp20) REVERT: D 59 MET cc_start: 0.8715 (tpp) cc_final: 0.8113 (tpp) REVERT: B 25 ASN cc_start: 0.8696 (m-40) cc_final: 0.8347 (m-40) outliers start: 19 outliers final: 13 residues processed: 121 average time/residue: 0.2754 time to fit residues: 46.9606 Evaluate side-chains 125 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN H 84 ASN A 108 ASN D 84 ASN C 38 ASN C 73 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14042 Z= 0.160 Angle : 0.566 10.822 20213 Z= 0.334 Chirality : 0.035 0.194 2311 Planarity : 0.003 0.037 1552 Dihedral : 30.280 171.603 4202 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.44 % Allowed : 15.82 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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 (0.29), residues: 895 helix: 2.07 (0.23), residues: 568 sheet: 0.57 (0.79), residues: 50 loop : -0.25 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.011 0.001 PHE E 67 TYR 0.019 0.001 TYR H 40 ARG 0.003 0.000 ARG F 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 0.991 Fit side-chains REVERT: H 80 LEU cc_start: 0.9102 (tp) cc_final: 0.8844 (tp) REVERT: H 86 ARG cc_start: 0.6943 (mtt-85) cc_final: 0.6684 (mtt-85) REVERT: E 58 THR cc_start: 0.8896 (p) cc_final: 0.8645 (p) REVERT: E 73 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8099 (pp20) REVERT: D 59 MET cc_start: 0.8703 (tpp) cc_final: 0.8077 (tpp) REVERT: D 68 ASP cc_start: 0.8518 (t0) cc_final: 0.8313 (t0) REVERT: B 25 ASN cc_start: 0.8647 (m-40) cc_final: 0.8241 (m-40) outliers start: 11 outliers final: 7 residues processed: 131 average time/residue: 0.2526 time to fit residues: 47.2443 Evaluate side-chains 128 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 73 ASN H 84 ASN A 125 GLN D 84 ASN C 38 ASN C 73 ASN K 41 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.107586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.072772 restraints weight = 31379.421| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.80 r_work: 0.2842 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14042 Z= 0.259 Angle : 0.607 9.279 20213 Z= 0.352 Chirality : 0.038 0.208 2311 Planarity : 0.004 0.036 1552 Dihedral : 30.472 172.039 4202 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.83 % Allowed : 15.42 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 1.74 (0.29), residues: 895 helix: 1.95 (0.23), residues: 567 sheet: 0.56 (0.79), residues: 50 loop : -0.35 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 75 PHE 0.011 0.002 PHE F 61 TYR 0.016 0.002 TYR H 40 ARG 0.003 0.000 ARG D 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2393.62 seconds wall clock time: 44 minutes 9.20 seconds (2649.20 seconds total)