Starting phenix.real_space_refine on Fri Mar 15 08:51:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7on1_12993/03_2024/7on1_12993.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7on1_12993/03_2024/7on1_12993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7on1_12993/03_2024/7on1_12993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7on1_12993/03_2024/7on1_12993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7on1_12993/03_2024/7on1_12993.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7on1_12993/03_2024/7on1_12993.pdb" } resolution = 3.35 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= 0.001 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 35 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 246 5.49 5 S 10 5.16 5 C 6239 2.51 5 N 2069 2.21 5 O 2586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 75": "OE1" <-> "OE2" Residue "d TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 141": "OE1" <-> "OE2" Residue "e TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 150": "OD1" <-> "OD2" Residue "e ASP 167": "OD1" <-> "OD2" Residue "f ASP 86": "OD1" <-> "OD2" Residue "g TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 63": "OE1" <-> "OE2" Residue "g GLU 66": "OE1" <-> "OE2" Residue "h TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 55": "OD1" <-> "OD2" Residue "h GLU 80": "OE1" <-> "OE2" Residue "c TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c ASP 92": "OD1" <-> "OD2" Residue "a ASP 150": "OD1" <-> "OD2" Residue "a GLU 164": "OE1" <-> "OE2" Residue "a ASP 173": "OD1" <-> "OD2" Residue "a ASP 175": "OD1" <-> "OD2" Residue "a GLU 191": "OE1" <-> "OE2" Residue "a GLU 199": "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: 11150 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 169 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 19} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 625 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 735 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "e" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 781 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "f" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "g" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 745 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "h" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 729 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "c" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 742 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2509 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain: "J" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2534 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain: "a" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 781 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 173 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 19} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.43, per 1000 atoms: 0.58 Number of scatterers: 11150 At special positions: 0 Unit cell: (120.7, 115.6, 107.1, 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 10 16.00 P 246 15.00 O 2586 8.00 N 2069 7.00 C 6239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.76 Conformation dependent library (CDL) restraints added in 1.4 seconds 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1466 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 71.6% alpha, 2.1% beta 109 base pairs and 199 stacking pairs defined. Time for finding SS restraints: 5.39 Creating SS restraints... Processing helix chain 'C' and resid 296 through 300 Processing helix chain 'b' and resid 25 through 30 removed outlier: 3.717A pdb=" N ILE b 30 " --> pdb=" O ILE b 27 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 43 Processing helix chain 'b' and resid 50 through 77 removed outlier: 3.909A pdb=" N GLU b 54 " --> pdb=" O LEU b 50 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA b 77 " --> pdb=" O TYR b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 94 removed outlier: 3.690A pdb=" N VAL b 87 " --> pdb=" O THR b 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 53 Processing helix chain 'd' and resid 59 through 88 removed outlier: 3.550A pdb=" N MET d 63 " --> pdb=" O SER d 59 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN d 88 " --> pdb=" O LEU d 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 106 Processing helix chain 'd' and resid 107 through 128 removed outlier: 4.043A pdb=" N HIS d 113 " --> pdb=" O GLU d 109 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER d 128 " --> pdb=" O LYS d 124 " (cutoff:3.500A) Processing helix chain 'e' and resid 134 through 148 Processing helix chain 'e' and resid 154 through 169 removed outlier: 3.922A pdb=" N PHE e 158 " --> pdb=" O SER e 154 " (cutoff:3.500A) Processing helix chain 'e' and resid 180 through 208 removed outlier: 3.521A pdb=" N MET e 184 " --> pdb=" O SER e 180 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA e 208 " --> pdb=" O LEU e 204 " (cutoff:3.500A) Processing helix chain 'e' and resid 214 through 226 removed outlier: 4.082A pdb=" N GLY e 226 " --> pdb=" O ARG e 222 " (cutoff:3.500A) Processing helix chain 'f' and resid 26 through 30 removed outlier: 3.640A pdb=" N GLY f 29 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE f 30 " --> pdb=" O ILE f 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 26 through 30' Processing helix chain 'f' and resid 31 through 43 removed outlier: 3.727A pdb=" N ILE f 35 " --> pdb=" O THR f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 50 through 77 removed outlier: 4.361A pdb=" N GLU f 54 " --> pdb=" O LEU f 50 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA f 77 " --> pdb=" O TYR f 73 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 95 removed outlier: 3.519A pdb=" N VAL f 87 " --> pdb=" O THR f 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 18 through 23 Processing helix chain 'g' and resid 29 through 38 Processing helix chain 'g' and resid 48 through 75 removed outlier: 3.682A pdb=" N ASN g 75 " --> pdb=" O ALA g 71 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 91 Processing helix chain 'g' and resid 92 through 99 Processing helix chain 'h' and resid 41 through 53 removed outlier: 3.751A pdb=" N ILE h 45 " --> pdb=" O TYR h 41 " (cutoff:3.500A) Processing helix chain 'h' and resid 59 through 88 removed outlier: 3.588A pdb=" N ASN h 88 " --> pdb=" O LEU h 84 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 106 removed outlier: 3.586A pdb=" N ILE h 98 " --> pdb=" O SER h 94 " (cutoff:3.500A) Processing helix chain 'h' and resid 107 through 126 removed outlier: 3.507A pdb=" N SER h 116 " --> pdb=" O LYS h 112 " (cutoff:3.500A) Processing helix chain 'c' and resid 18 through 24 Processing helix chain 'c' and resid 29 through 38 Processing helix chain 'c' and resid 47 through 75 removed outlier: 4.523A pdb=" N VAL c 51 " --> pdb=" O SER c 47 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN c 75 " --> pdb=" O ALA c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 91 Processing helix chain 'c' and resid 92 through 99 Processing helix chain 'a' and resid 134 through 148 Processing helix chain 'a' and resid 154 through 168 removed outlier: 3.679A pdb=" N PHE a 158 " --> pdb=" O SER a 154 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU a 168 " --> pdb=" O GLU a 164 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 208 removed outlier: 3.523A pdb=" N ALA a 208 " --> pdb=" O LEU a 204 " (cutoff:3.500A) Processing helix chain 'a' and resid 214 through 226 removed outlier: 3.564A pdb=" N MET a 218 " --> pdb=" O MET a 214 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY a 226 " --> pdb=" O ARG a 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 300 Processing sheet with id=AA1, first strand: chain 'b' and resid 46 through 47 removed outlier: 7.617A pdb=" N ARG b 46 " --> pdb=" O ILE a 213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'b' and resid 81 through 82 Processing sheet with id=AA3, first strand: chain 'b' and resid 97 through 99 removed outlier: 6.722A pdb=" N THR b 97 " --> pdb=" O THR g 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'd' and resid 92 through 93 Processing sheet with id=AA5, first strand: chain 'e' and resid 177 through 178 removed outlier: 6.946A pdb=" N ARG e 177 " --> pdb=" O VAL f 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'f' and resid 98 through 99 Processing sheet with id=AA7, first strand: chain 'g' and resid 79 through 80 390 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 283 hydrogen bonds 550 hydrogen bond angles 0 basepair planarities 109 basepair parallelities 199 stacking parallelities Total time for adding SS restraints: 4.31 Time building geometry restraints manager: 6.18 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: 2072 1.33 - 1.45: 3752 1.45 - 1.57: 5509 1.57 - 1.69: 490 1.69 - 1.80: 20 Bond restraints: 11843 Sorted by residual: bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" C3' DC J 53 " pdb=" C2' DC J 53 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.00e-02 2.50e+03 8.70e-01 bond pdb=" N LYS c 76 " pdb=" CA LYS c 76 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.61e-01 bond pdb=" C3' DT I 1 " pdb=" C2' DT I 1 " ideal model delta sigma weight residual 1.525 1.542 -0.017 2.00e-02 2.50e+03 7.18e-01 ... (remaining 11838 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.25: 1591 106.25 - 113.18: 6372 113.18 - 120.11: 4380 120.11 - 127.03: 4134 127.03 - 133.96: 579 Bond angle restraints: 17056 Sorted by residual: angle pdb=" N LYS f 32 " pdb=" CA LYS f 32 " pdb=" C LYS f 32 " ideal model delta sigma weight residual 109.81 116.33 -6.52 2.21e+00 2.05e-01 8.71e+00 angle pdb=" C ASN g 75 " pdb=" N LYS g 76 " pdb=" CA LYS g 76 " ideal model delta sigma weight residual 122.46 125.27 -2.81 1.41e+00 5.03e-01 3.96e+00 angle pdb=" C ASN d 88 " pdb=" N LYS d 89 " pdb=" CA LYS d 89 " ideal model delta sigma weight residual 122.46 125.26 -2.80 1.41e+00 5.03e-01 3.94e+00 angle pdb=" CA LYS b 32 " pdb=" C LYS b 32 " pdb=" N PRO b 33 " ideal model delta sigma weight residual 118.44 121.54 -3.10 1.59e+00 3.96e-01 3.79e+00 angle pdb=" CA LYS f 32 " pdb=" C LYS f 32 " pdb=" N PRO f 33 " ideal model delta sigma weight residual 118.44 121.51 -3.07 1.59e+00 3.96e-01 3.73e+00 ... (remaining 17051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 5411 35.74 - 71.48: 1054 71.48 - 107.22: 12 107.22 - 142.96: 0 142.96 - 178.70: 2 Dihedral angle restraints: 6479 sinusoidal: 4214 harmonic: 2265 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual -140.00 38.70 -178.70 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 36.57 -176.57 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CB LYS d 50 " pdb=" CG LYS d 50 " pdb=" CD LYS d 50 " pdb=" CE LYS d 50 " ideal model delta sinusoidal sigma weight residual 180.00 122.95 57.05 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 6476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1505 0.028 - 0.056: 326 0.056 - 0.084: 75 0.084 - 0.112: 36 0.112 - 0.140: 13 Chirality restraints: 1955 Sorted by residual: chirality pdb=" CA LYS f 32 " pdb=" N LYS f 32 " pdb=" C LYS f 32 " pdb=" CB LYS f 32 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE c 81 " pdb=" N ILE c 81 " pdb=" C ILE c 81 " pdb=" CB ILE c 81 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA ILE h 58 " pdb=" N ILE h 58 " pdb=" C ILE h 58 " pdb=" CB ILE h 58 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 ... (remaining 1952 not shown) Planarity restraints: 1299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS f 32 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO f 33 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO f 33 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO f 33 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS b 32 " -0.019 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO b 33 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO b 33 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO b 33 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE g 81 " 0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO g 82 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO g 82 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO g 82 " 0.015 5.00e-02 4.00e+02 ... (remaining 1296 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 301 2.68 - 3.23: 9377 3.23 - 3.79: 19631 3.79 - 4.34: 24425 4.34 - 4.90: 36170 Nonbonded interactions: 89904 Sorted by model distance: nonbonded pdb=" O2 DC I -20 " pdb=" N2 DG J 20 " model vdw 2.120 2.496 nonbonded pdb=" N2 DG I -60 " pdb=" O2 DC J 60 " model vdw 2.149 2.496 nonbonded pdb=" O2 DC I -21 " pdb=" N2 DG J 21 " model vdw 2.179 2.496 nonbonded pdb=" OG1 THR e 171 " pdb=" OD1 ASP e 173 " model vdw 2.226 2.440 nonbonded pdb=" OG SER e 148 " pdb=" OD1 ASP e 150 " model vdw 2.292 2.440 ... (remaining 89899 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 'C' selection = (chain 'D' and (resid 284 through 285 or (resid 286 and (name N or name CA or na \ me C or name O or name CB )) or resid 287 through 304)) } ncs_group { reference = chain 'a' selection = chain 'e' } ncs_group { reference = chain 'b' selection = (chain 'f' and (resid 25 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )) or resid 56 through 103)) } ncs_group { reference = chain 'c' selection = (chain 'g' and (resid 17 through 112 or (resid 113 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = (chain 'd' and ((resid 35 through 36 and (name N or name CA or name C or name O \ or name CB )) or resid 37 through 128)) selection = (chain 'h' and (resid 35 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 128)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 7.090 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 38.570 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 : 0.002 0.035 11843 Z= 0.130 Angle : 0.466 6.522 17056 Z= 0.298 Chirality : 0.029 0.140 1955 Planarity : 0.003 0.047 1299 Dihedral : 26.143 178.699 5013 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.27), residues: 757 helix: 0.58 (0.21), residues: 525 sheet: None (None), residues: 0 loop : -1.82 (0.32), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 298 HIS 0.002 0.000 HIS b 76 PHE 0.003 0.000 PHE h 69 TYR 0.006 0.000 TYR g 52 ARG 0.001 0.000 ARG h 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 0.972 Fit side-chains REVERT: C 285 ARG cc_start: 0.6865 (mmt180) cc_final: 0.6594 (ttp-170) REVERT: C 299 ARG cc_start: 0.8319 (mtp85) cc_final: 0.7832 (mtp85) REVERT: d 37 ARG cc_start: 0.6891 (ptp-110) cc_final: 0.6419 (ptp-110) REVERT: d 103 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7967 (ttm110) REVERT: g 38 ARG cc_start: 0.7991 (tpp80) cc_final: 0.7774 (mmt90) REVERT: h 117 GLU cc_start: 0.7575 (tp30) cc_final: 0.7170 (tp30) REVERT: h 120 ARG cc_start: 0.7851 (tmm-80) cc_final: 0.7633 (ttp-110) REVERT: a 147 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7783 (ttp-110) REVERT: a 164 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7996 (tt0) REVERT: a 225 ARG cc_start: 0.8391 (tpp80) cc_final: 0.8093 (mtt180) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.3789 time to fit residues: 90.7984 Evaluate side-chains 142 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN e 187 GLN e 227 GLN f 76 HIS h 51 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11843 Z= 0.356 Angle : 0.604 5.986 17056 Z= 0.351 Chirality : 0.037 0.147 1955 Planarity : 0.005 0.041 1299 Dihedral : 29.605 174.384 3531 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.09 % Allowed : 13.28 % Favored : 85.62 % 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: 1.24 (0.30), residues: 757 helix: 1.78 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.62 (0.36), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP a 178 HIS 0.008 0.001 HIS c 33 PHE 0.019 0.002 PHE d 74 TYR 0.013 0.002 TYR h 125 ARG 0.005 0.001 ARG b 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 157 time to evaluate : 0.935 Fit side-chains REVERT: b 69 ASP cc_start: 0.8674 (m-30) cc_final: 0.8292 (m-30) REVERT: d 87 TYR cc_start: 0.8473 (m-10) cc_final: 0.8238 (m-10) REVERT: d 103 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.8100 (ttm110) REVERT: d 124 LYS cc_start: 0.8768 (tptp) cc_final: 0.8411 (tttt) REVERT: g 76 LYS cc_start: 0.8146 (ptpt) cc_final: 0.7891 (mtpt) REVERT: g 104 ILE cc_start: 0.9587 (mm) cc_final: 0.9322 (mm) REVERT: h 47 LYS cc_start: 0.8813 (mtpt) cc_final: 0.8517 (mttp) REVERT: h 83 LYS cc_start: 0.9155 (ttmt) cc_final: 0.8927 (mtmm) REVERT: h 120 ARG cc_start: 0.7829 (tmm-80) cc_final: 0.7470 (ttp-110) REVERT: c 79 ARG cc_start: 0.8327 (tpp80) cc_final: 0.7936 (mmt90) REVERT: a 147 ARG cc_start: 0.8241 (ttp80) cc_final: 0.7936 (ttm110) REVERT: a 214 MET cc_start: 0.8552 (mpp) cc_final: 0.8113 (mtt) outliers start: 7 outliers final: 3 residues processed: 160 average time/residue: 0.3767 time to fit residues: 76.2017 Evaluate side-chains 149 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 146 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain d residue 123 THR Chi-restraints excluded: chain c residue 103 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN d 88 ASN e 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11843 Z= 0.180 Angle : 0.496 5.714 17056 Z= 0.296 Chirality : 0.032 0.129 1955 Planarity : 0.003 0.039 1299 Dihedral : 29.373 175.171 3531 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.03 % Allowed : 14.84 % Favored : 83.12 % 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: 1.94 (0.31), residues: 757 helix: 2.33 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.45 (0.37), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.003 0.001 HIS f 76 PHE 0.016 0.001 PHE d 74 TYR 0.014 0.001 TYR a 140 ARG 0.004 0.000 ARG g 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 0.920 Fit side-chains REVERT: d 124 LYS cc_start: 0.8648 (tptp) cc_final: 0.8299 (tttt) REVERT: g 76 LYS cc_start: 0.8047 (ptpt) cc_final: 0.7795 (mtpt) REVERT: g 104 ILE cc_start: 0.9538 (mm) cc_final: 0.9306 (mm) REVERT: h 47 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8512 (mttp) REVERT: h 83 LYS cc_start: 0.9098 (ttmt) cc_final: 0.8885 (mtmm) REVERT: h 120 ARG cc_start: 0.7858 (tmm-80) cc_final: 0.7507 (ttp-110) REVERT: c 79 ARG cc_start: 0.8294 (tpp80) cc_final: 0.7842 (mmt90) REVERT: a 147 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7831 (ttm110) REVERT: a 164 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7999 (tt0) REVERT: a 214 MET cc_start: 0.8552 (mpp) cc_final: 0.7942 (mtt) outliers start: 13 outliers final: 7 residues processed: 156 average time/residue: 0.3565 time to fit residues: 70.2491 Evaluate side-chains 151 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 78 LYS Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain e residue 212 THR Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 103 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN d 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11843 Z= 0.371 Angle : 0.600 5.853 17056 Z= 0.351 Chirality : 0.037 0.138 1955 Planarity : 0.004 0.043 1299 Dihedral : 29.788 174.033 3531 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.50 % Allowed : 17.19 % Favored : 80.31 % 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: 1.85 (0.31), residues: 757 helix: 2.29 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.50 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 298 HIS 0.009 0.001 HIS c 33 PHE 0.012 0.002 PHE d 74 TYR 0.013 0.002 TYR a 140 ARG 0.008 0.001 ARG g 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: b 69 ASP cc_start: 0.8631 (m-30) cc_final: 0.8282 (m-30) REVERT: d 124 LYS cc_start: 0.8710 (tptp) cc_final: 0.8377 (tttt) REVERT: h 47 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8519 (mttp) REVERT: h 83 LYS cc_start: 0.9181 (ttmt) cc_final: 0.8940 (mtmm) REVERT: h 120 ARG cc_start: 0.7846 (tmm-80) cc_final: 0.7561 (ttp-110) REVERT: c 79 ARG cc_start: 0.8395 (tpp80) cc_final: 0.7943 (mmt90) REVERT: a 147 ARG cc_start: 0.8282 (ttp80) cc_final: 0.8051 (ttm110) REVERT: a 214 MET cc_start: 0.8646 (mpp) cc_final: 0.8078 (mtt) outliers start: 16 outliers final: 12 residues processed: 155 average time/residue: 0.3369 time to fit residues: 66.2950 Evaluate side-chains 153 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain b residue 78 LYS Chi-restraints excluded: chain d residue 89 LYS Chi-restraints excluded: chain d residue 123 THR Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain e residue 212 THR Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain h residue 37 ARG Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 76 LYS Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 103 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11843 Z= 0.187 Angle : 0.506 5.757 17056 Z= 0.303 Chirality : 0.032 0.136 1955 Planarity : 0.003 0.041 1299 Dihedral : 29.494 175.042 3531 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.19 % Allowed : 17.81 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.31), residues: 757 helix: 2.57 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.37 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 298 HIS 0.003 0.001 HIS c 33 PHE 0.013 0.001 PHE d 74 TYR 0.008 0.001 TYR g 52 ARG 0.004 0.000 ARG e 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: d 124 LYS cc_start: 0.8624 (tptp) cc_final: 0.8270 (tttt) REVERT: g 104 ILE cc_start: 0.9550 (mm) cc_final: 0.9286 (mm) REVERT: h 47 LYS cc_start: 0.8796 (mtpt) cc_final: 0.8520 (mttp) REVERT: h 83 LYS cc_start: 0.9107 (ttmt) cc_final: 0.8883 (mtmm) REVERT: h 120 ARG cc_start: 0.7890 (tmm-80) cc_final: 0.7549 (ttp-110) REVERT: c 79 ARG cc_start: 0.8368 (tpp80) cc_final: 0.7897 (mmt90) REVERT: a 147 ARG cc_start: 0.8183 (ttp80) cc_final: 0.7919 (ttm110) REVERT: a 214 MET cc_start: 0.8661 (mpp) cc_final: 0.7905 (mtt) outliers start: 14 outliers final: 13 residues processed: 153 average time/residue: 0.3297 time to fit residues: 64.8244 Evaluate side-chains 159 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain b residue 78 LYS Chi-restraints excluded: chain d residue 89 LYS Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain e residue 212 THR Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain h residue 37 ARG Chi-restraints excluded: chain h residue 38 LYS Chi-restraints excluded: chain h residue 90 LYS Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 103 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 11843 Z= 0.415 Angle : 0.627 5.909 17056 Z= 0.364 Chirality : 0.039 0.141 1955 Planarity : 0.004 0.044 1299 Dihedral : 29.892 172.815 3531 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.81 % Allowed : 18.28 % Favored : 78.91 % 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: 1.96 (0.31), residues: 757 helix: 2.35 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -1.44 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 298 HIS 0.009 0.001 HIS c 33 PHE 0.011 0.002 PHE a 169 TYR 0.013 0.002 TYR h 41 ARG 0.005 0.001 ARG e 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: b 69 ASP cc_start: 0.8633 (m-30) cc_final: 0.8300 (m-30) REVERT: d 124 LYS cc_start: 0.8732 (tptp) cc_final: 0.8409 (tttt) REVERT: h 47 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8546 (mtmm) REVERT: h 83 LYS cc_start: 0.9179 (ttmt) cc_final: 0.8952 (mtmm) REVERT: h 120 ARG cc_start: 0.7881 (tmm-80) cc_final: 0.7614 (ttp-110) REVERT: c 76 LYS cc_start: 0.8686 (ptpt) cc_final: 0.8352 (mttp) REVERT: c 79 ARG cc_start: 0.8423 (tpp80) cc_final: 0.8006 (mmt90) REVERT: a 147 ARG cc_start: 0.8251 (ttp80) cc_final: 0.8046 (ttm110) REVERT: a 214 MET cc_start: 0.8711 (mpp) cc_final: 0.8069 (mtt) outliers start: 18 outliers final: 14 residues processed: 154 average time/residue: 0.3350 time to fit residues: 65.9297 Evaluate side-chains 155 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain b residue 78 LYS Chi-restraints excluded: chain d residue 89 LYS Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain e residue 212 THR Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain h residue 37 ARG Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 103 THR Chi-restraints excluded: chain a residue 171 THR Chi-restraints excluded: chain a residue 218 MET Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN C 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11843 Z= 0.185 Angle : 0.516 5.843 17056 Z= 0.308 Chirality : 0.032 0.132 1955 Planarity : 0.004 0.042 1299 Dihedral : 29.537 175.345 3531 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.50 % Allowed : 18.91 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.31), residues: 757 helix: 2.65 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.40 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 298 HIS 0.003 0.001 HIS f 76 PHE 0.012 0.001 PHE d 74 TYR 0.007 0.001 TYR g 52 ARG 0.003 0.000 ARG e 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 0.845 Fit side-chains REVERT: d 124 LYS cc_start: 0.8618 (tptp) cc_final: 0.8270 (tttt) REVERT: g 104 ILE cc_start: 0.9548 (mm) cc_final: 0.9272 (mm) REVERT: h 47 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8514 (mttp) REVERT: h 120 ARG cc_start: 0.7885 (tmm-80) cc_final: 0.7572 (ttp-110) REVERT: c 79 ARG cc_start: 0.8401 (tpp80) cc_final: 0.7916 (mmt90) REVERT: a 147 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7922 (ttm110) outliers start: 16 outliers final: 15 residues processed: 156 average time/residue: 0.3357 time to fit residues: 67.4090 Evaluate side-chains 160 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain b residue 78 LYS Chi-restraints excluded: chain d residue 89 LYS Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain e residue 212 THR Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain h residue 37 ARG Chi-restraints excluded: chain h residue 38 LYS Chi-restraints excluded: chain h residue 90 LYS Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 103 THR Chi-restraints excluded: chain a residue 171 THR Chi-restraints excluded: chain a residue 218 MET Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 45 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 88 optimal weight: 0.0570 chunk 80 optimal weight: 4.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11843 Z= 0.162 Angle : 0.496 6.134 17056 Z= 0.295 Chirality : 0.031 0.127 1955 Planarity : 0.003 0.042 1299 Dihedral : 29.416 174.768 3531 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.66 % Allowed : 18.91 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.31), residues: 757 helix: 2.86 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.27 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.002 0.001 HIS f 76 PHE 0.012 0.001 PHE d 74 TYR 0.006 0.001 TYR h 44 ARG 0.003 0.000 ARG g 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 0.847 Fit side-chains REVERT: d 124 LYS cc_start: 0.8613 (tptp) cc_final: 0.8272 (tttt) REVERT: g 104 ILE cc_start: 0.9543 (mm) cc_final: 0.9271 (mm) REVERT: h 47 LYS cc_start: 0.8790 (mtpt) cc_final: 0.8532 (mttp) REVERT: h 120 ARG cc_start: 0.7871 (tmm-80) cc_final: 0.7545 (ttp-110) REVERT: c 63 GLU cc_start: 0.7714 (tp30) cc_final: 0.7501 (tp30) REVERT: c 65 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8826 (mt) REVERT: c 79 ARG cc_start: 0.8400 (tpp80) cc_final: 0.7917 (mmt90) REVERT: a 147 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7846 (ttm110) REVERT: a 164 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7948 (tt0) outliers start: 17 outliers final: 14 residues processed: 158 average time/residue: 0.3260 time to fit residues: 65.7708 Evaluate side-chains 159 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain b residue 78 LYS Chi-restraints excluded: chain b residue 85 LEU Chi-restraints excluded: chain d residue 89 LYS Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain e residue 212 THR Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain h residue 37 ARG Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 65 LEU Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 103 THR Chi-restraints excluded: chain a residue 171 THR Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11843 Z= 0.227 Angle : 0.529 6.577 17056 Z= 0.312 Chirality : 0.033 0.126 1955 Planarity : 0.004 0.042 1299 Dihedral : 29.509 174.559 3531 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.81 % Allowed : 19.22 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.31), residues: 757 helix: 2.78 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.26 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.005 0.001 HIS c 33 PHE 0.011 0.001 PHE d 74 TYR 0.010 0.001 TYR h 41 ARG 0.005 0.000 ARG g 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 0.994 Fit side-chains REVERT: b 69 ASP cc_start: 0.8426 (m-30) cc_final: 0.8113 (m-30) REVERT: d 124 LYS cc_start: 0.8684 (tptp) cc_final: 0.8344 (tttt) REVERT: h 47 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8546 (mttp) REVERT: h 84 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9265 (tp) REVERT: h 120 ARG cc_start: 0.7881 (tmm-80) cc_final: 0.7460 (ttp-170) REVERT: c 65 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8813 (mt) REVERT: c 79 ARG cc_start: 0.8433 (tpp80) cc_final: 0.7981 (mmt90) REVERT: a 147 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7911 (ttm110) REVERT: a 214 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.7918 (mpp) outliers start: 18 outliers final: 14 residues processed: 150 average time/residue: 0.3317 time to fit residues: 63.8705 Evaluate side-chains 154 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain b residue 78 LYS Chi-restraints excluded: chain b residue 85 LEU Chi-restraints excluded: chain d residue 89 LYS Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain e residue 212 THR Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain h residue 37 ARG Chi-restraints excluded: chain h residue 84 LEU Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 65 LEU Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 103 THR Chi-restraints excluded: chain a residue 171 THR Chi-restraints excluded: chain a residue 214 MET Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.2980 chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11843 Z= 0.270 Angle : 0.563 7.747 17056 Z= 0.329 Chirality : 0.034 0.128 1955 Planarity : 0.004 0.042 1299 Dihedral : 29.626 173.727 3531 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.97 % Allowed : 18.91 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.31), residues: 757 helix: 2.67 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -1.27 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 298 HIS 0.006 0.001 HIS c 33 PHE 0.009 0.001 PHE d 74 TYR 0.012 0.001 TYR h 41 ARG 0.004 0.000 ARG g 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 0.923 Fit side-chains REVERT: b 69 ASP cc_start: 0.8549 (m-30) cc_final: 0.8150 (m-30) REVERT: d 124 LYS cc_start: 0.8691 (tptp) cc_final: 0.8356 (tttt) REVERT: h 47 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8548 (mttp) REVERT: h 84 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9291 (tp) REVERT: h 120 ARG cc_start: 0.7889 (tmm-80) cc_final: 0.7469 (ttp-170) REVERT: c 65 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8807 (mt) REVERT: c 79 ARG cc_start: 0.8434 (tpp80) cc_final: 0.7978 (mmt90) REVERT: a 147 ARG cc_start: 0.8213 (ttp80) cc_final: 0.7981 (ttm110) REVERT: a 214 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7967 (mtt) outliers start: 19 outliers final: 15 residues processed: 149 average time/residue: 0.3367 time to fit residues: 64.3160 Evaluate side-chains 156 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain b residue 78 LYS Chi-restraints excluded: chain b residue 85 LEU Chi-restraints excluded: chain d residue 89 LYS Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain e residue 212 THR Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain h residue 37 ARG Chi-restraints excluded: chain h residue 75 GLU Chi-restraints excluded: chain h residue 84 LEU Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 65 LEU Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 103 THR Chi-restraints excluded: chain a residue 171 THR Chi-restraints excluded: chain a residue 214 MET Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 0.4980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.118836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.076484 restraints weight = 19701.970| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.53 r_work: 0.2764 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11843 Z= 0.216 Angle : 0.546 7.694 17056 Z= 0.321 Chirality : 0.033 0.124 1955 Planarity : 0.004 0.042 1299 Dihedral : 29.600 174.124 3531 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.66 % Allowed : 19.38 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.31), residues: 757 helix: 2.66 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.29 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 298 HIS 0.004 0.001 HIS c 33 PHE 0.011 0.001 PHE d 74 TYR 0.008 0.001 TYR h 41 ARG 0.004 0.000 ARG g 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2402.09 seconds wall clock time: 43 minutes 34.03 seconds (2614.03 seconds total)