Starting phenix.real_space_refine on Wed Sep 25 18:26:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7on1_12993/09_2024/7on1_12993.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7on1_12993/09_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_12993/09_2024/7on1_12993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7on1_12993/09_2024/7on1_12993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7on1_12993/09_2024/7on1_12993.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7on1_12993/09_2024/7on1_12993.cif" } 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. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 6.89, per 1000 atoms: 0.62 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 - 3.00 Amino acid : True - 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: 2.75 Conformation dependent library (CDL) restraints added in 821.6 milliseconds 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: 5.14 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: 4.13 Time building geometry restraints manager: 3.18 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: 0.00 - 1.30: 16610 1.30 - 2.61: 402 2.61 - 3.91: 36 3.91 - 5.22: 5 5.22 - 6.52: 3 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 3.040 nonbonded pdb=" OG SER e 148 " pdb=" OD1 ASP e 150 " model vdw 2.292 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 1.380 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.030 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.110 ------------------------------------------------------------------------------- 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 : 0.805 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: 0.3512 time to fit residues: 84.1329 Evaluate side-chains 142 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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: 7.9990 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.8434 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11843 Z= 0.260 Angle : 0.553 6.100 17056 Z= 0.323 Chirality : 0.034 0.142 1955 Planarity : 0.004 0.042 1299 Dihedral : 29.397 175.103 3531 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.94 % Allowed : 10.47 % Favored : 88.59 % 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: 1.42 (0.30), residues: 757 helix: 1.90 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -1.52 (0.36), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 178 HIS 0.005 0.001 HIS c 33 PHE 0.018 0.002 PHE d 74 TYR 0.012 0.001 TYR h 41 ARG 0.004 0.001 ARG g 31 *********************** 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 159 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 153 time to evaluate : 1.093 Fit side-chains REVERT: C 299 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7712 (mtp85) REVERT: b 69 ASP cc_start: 0.8562 (m-30) cc_final: 0.8159 (m-30) REVERT: d 37 ARG cc_start: 0.6914 (ptp-110) cc_final: 0.6513 (ptp-110) REVERT: d 87 TYR cc_start: 0.8294 (m-10) cc_final: 0.7911 (m-10) REVERT: d 103 ARG cc_start: 0.8412 (ttm-80) cc_final: 0.8110 (ttm110) REVERT: d 124 LYS cc_start: 0.8750 (tptp) cc_final: 0.8385 (tttt) REVERT: g 76 LYS cc_start: 0.7821 (ptpt) cc_final: 0.7455 (mtpt) REVERT: g 104 ILE cc_start: 0.9567 (mm) cc_final: 0.9334 (mm) REVERT: h 47 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8512 (mttp) REVERT: h 83 LYS cc_start: 0.9151 (ttmt) cc_final: 0.8880 (mtmm) REVERT: h 120 ARG cc_start: 0.7934 (tmm-80) cc_final: 0.7671 (ttp-110) REVERT: c 77 LYS cc_start: 0.8017 (mtpp) cc_final: 0.7788 (mttp) REVERT: c 79 ARG cc_start: 0.8229 (tpp80) cc_final: 0.7914 (mmt90) REVERT: a 147 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7786 (ttm110) REVERT: a 164 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8073 (tt0) REVERT: a 214 MET cc_start: 0.8554 (mpp) cc_final: 0.8042 (mtt) REVERT: a 225 ARG cc_start: 0.8630 (tpp80) cc_final: 0.8344 (tpp80) outliers start: 6 outliers final: 2 residues processed: 155 average time/residue: 0.3847 time to fit residues: 75.1823 Evaluate side-chains 145 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 292 VAL 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: 0.0010 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.3192 ------------------------------------------------------------------------------- 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 e 219 GLN a 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11843 Z= 0.229 Angle : 0.518 5.775 17056 Z= 0.306 Chirality : 0.033 0.141 1955 Planarity : 0.004 0.040 1299 Dihedral : 29.404 174.870 3531 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.72 % Allowed : 13.12 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.31), residues: 757 helix: 2.29 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -1.34 (0.37), residues: 222 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 0.015 0.001 PHE d 74 TYR 0.013 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 160 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 149 time to evaluate : 0.844 Fit side-chains REVERT: d 124 LYS cc_start: 0.8702 (tptp) cc_final: 0.8344 (tttt) REVERT: e 227 GLN cc_start: 0.7756 (mt0) cc_final: 0.7548 (mt0) REVERT: g 76 LYS cc_start: 0.8106 (ptpt) cc_final: 0.7877 (mtpt) REVERT: g 104 ILE cc_start: 0.9541 (mm) cc_final: 0.9307 (mm) REVERT: h 47 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8530 (mttp) REVERT: h 83 LYS cc_start: 0.9098 (ttmt) cc_final: 0.8817 (mtmm) REVERT: h 120 ARG cc_start: 0.7916 (tmm-80) cc_final: 0.7616 (ttp-110) REVERT: c 79 ARG cc_start: 0.8275 (tpp80) cc_final: 0.7869 (mmt90) REVERT: a 147 ARG cc_start: 0.8160 (ttp80) cc_final: 0.7860 (ttm110) REVERT: a 164 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8026 (tt0) REVERT: a 214 MET cc_start: 0.8590 (mpp) cc_final: 0.7973 (mtt) outliers start: 11 outliers final: 8 residues processed: 153 average time/residue: 0.3542 time to fit residues: 68.5571 Evaluate side-chains 149 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 141 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain b residue 78 LYS 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 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: 1.9990 chunk 65 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 0.0970 chunk 77 optimal weight: 5.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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: 0.8528 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11843 Z= 0.295 Angle : 0.572 5.759 17056 Z= 0.336 Chirality : 0.036 0.139 1955 Planarity : 0.004 0.041 1299 Dihedral : 29.635 173.904 3531 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.50 % Allowed : 15.47 % Favored : 82.03 % 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: 1.98 (0.31), residues: 757 helix: 2.34 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.34 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 298 HIS 0.007 0.001 HIS c 33 PHE 0.013 0.002 PHE a 169 TYR 0.014 0.001 TYR a 140 ARG 0.006 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 169 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 1.244 Fit side-chains REVERT: d 124 LYS cc_start: 0.8724 (tptp) cc_final: 0.8376 (tttt) REVERT: g 104 ILE cc_start: 0.9574 (mm) cc_final: 0.9310 (mm) REVERT: h 47 LYS cc_start: 0.8825 (mtpt) cc_final: 0.8543 (mttp) REVERT: h 83 LYS cc_start: 0.9173 (ttmt) cc_final: 0.8917 (mtmm) REVERT: h 120 ARG cc_start: 0.7931 (tmm-80) cc_final: 0.7629 (ttp-110) REVERT: c 79 ARG cc_start: 0.8389 (tpp80) cc_final: 0.7945 (mmt90) REVERT: a 147 ARG cc_start: 0.8226 (ttp80) cc_final: 0.7995 (ttm110) REVERT: a 214 MET cc_start: 0.8667 (mpp) cc_final: 0.8033 (mtt) outliers start: 16 outliers final: 10 residues processed: 159 average time/residue: 0.3616 time to fit residues: 73.4112 Evaluate side-chains 156 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 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 76 LYS 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: 2.9990 chunk 1 optimal weight: 0.2980 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN a 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11843 Z= 0.197 Angle : 0.511 5.623 17056 Z= 0.305 Chirality : 0.032 0.130 1955 Planarity : 0.003 0.041 1299 Dihedral : 29.459 174.821 3531 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.88 % Allowed : 15.94 % Favored : 82.19 % 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: 2.25 (0.31), residues: 757 helix: 2.55 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.27 (0.38), residues: 224 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 0.015 0.001 TYR a 140 ARG 0.004 0.000 ARG g 73 *********************** 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 164 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 152 time to evaluate : 0.894 Fit side-chains REVERT: d 124 LYS cc_start: 0.8643 (tptp) cc_final: 0.8293 (tttt) REVERT: g 104 ILE cc_start: 0.9549 (mm) cc_final: 0.9280 (mm) REVERT: h 47 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8501 (mttp) REVERT: h 83 LYS cc_start: 0.9114 (ttmt) cc_final: 0.8891 (mtmm) REVERT: h 120 ARG cc_start: 0.7936 (tmm-80) cc_final: 0.7603 (ttp-110) REVERT: c 79 ARG cc_start: 0.8379 (tpp80) cc_final: 0.7915 (mmt90) REVERT: a 147 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7907 (ttm110) REVERT: a 164 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8020 (tt0) REVERT: a 214 MET cc_start: 0.8672 (mpp) cc_final: 0.7902 (mtt) outliers start: 12 outliers final: 11 residues processed: 158 average time/residue: 0.3403 time to fit residues: 68.7226 Evaluate side-chains 159 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 g residue 94 GLU 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 218 MET Chi-restraints excluded: chain D residue 290 VAL 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: 2.9990 chunk 54 optimal weight: 0.0870 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 89 optimal weight: 0.7980 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN h 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11843 Z= 0.203 Angle : 0.513 5.676 17056 Z= 0.306 Chirality : 0.032 0.129 1955 Planarity : 0.003 0.041 1299 Dihedral : 29.472 174.588 3531 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.19 % Allowed : 16.88 % Favored : 80.94 % 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: 2.38 (0.31), residues: 757 helix: 2.65 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.24 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.004 0.001 HIS c 33 PHE 0.011 0.001 PHE d 74 TYR 0.015 0.001 TYR a 140 ARG 0.005 0.000 ARG g 73 *********************** 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 160 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 0.958 Fit side-chains REVERT: d 124 LYS cc_start: 0.8668 (tptp) cc_final: 0.8318 (tttt) REVERT: g 104 ILE cc_start: 0.9552 (mm) cc_final: 0.9279 (mm) REVERT: h 47 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8501 (mttp) REVERT: h 83 LYS cc_start: 0.9110 (ttmt) cc_final: 0.8891 (mtmm) REVERT: h 120 ARG cc_start: 0.7940 (tmm-80) cc_final: 0.7589 (ttp-110) REVERT: c 79 ARG cc_start: 0.8412 (tpp80) cc_final: 0.7896 (mmt90) REVERT: a 147 ARG cc_start: 0.8109 (ttp80) cc_final: 0.7900 (ttm110) REVERT: a 164 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7993 (tt0) REVERT: a 214 MET cc_start: 0.8682 (mpp) cc_final: 0.7880 (mtt) outliers start: 14 outliers final: 14 residues processed: 154 average time/residue: 0.3648 time to fit residues: 72.1049 Evaluate side-chains 158 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 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 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 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: 0.0770 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN h 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3695 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= 0.164 Angle : 0.497 7.039 17056 Z= 0.297 Chirality : 0.031 0.126 1955 Planarity : 0.003 0.041 1299 Dihedral : 29.374 175.040 3531 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.03 % Allowed : 18.12 % Favored : 79.84 % 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: 2.53 (0.31), residues: 757 helix: 2.76 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -1.20 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.003 0.001 HIS c 33 PHE 0.013 0.001 PHE d 74 TYR 0.017 0.001 TYR a 140 ARG 0.007 0.000 ARG g 73 *********************** 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 166 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 0.890 Fit side-chains REVERT: d 124 LYS cc_start: 0.8615 (tptp) cc_final: 0.8267 (tttt) REVERT: h 47 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8531 (mttp) REVERT: h 83 LYS cc_start: 0.9076 (ttmt) cc_final: 0.8768 (mtmm) REVERT: h 120 ARG cc_start: 0.7934 (tmm-80) cc_final: 0.7599 (ttp-110) REVERT: c 79 ARG cc_start: 0.8399 (tpp80) cc_final: 0.7886 (mmt90) REVERT: a 147 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7854 (ttm110) REVERT: a 164 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8012 (tt0) outliers start: 13 outliers final: 12 residues processed: 160 average time/residue: 0.3597 time to fit residues: 72.6868 Evaluate side-chains 161 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 199 GLU 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: 2.9990 chunk 18 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 0.0040 chunk 63 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- 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: 0.8442 moved from start: 0.3713 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= 0.183 Angle : 0.504 6.168 17056 Z= 0.300 Chirality : 0.032 0.130 1955 Planarity : 0.003 0.041 1299 Dihedral : 29.405 174.727 3531 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.19 % Allowed : 18.28 % Favored : 79.53 % 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: 2.62 (0.31), residues: 757 helix: 2.83 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -1.16 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 298 HIS 0.003 0.001 HIS c 33 PHE 0.011 0.001 PHE d 74 TYR 0.016 0.001 TYR a 140 ARG 0.006 0.000 ARG g 73 *********************** 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 161 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 0.895 Fit side-chains REVERT: d 124 LYS cc_start: 0.8650 (tptp) cc_final: 0.8302 (tttt) REVERT: h 47 LYS cc_start: 0.8809 (mtpt) cc_final: 0.8533 (mttp) REVERT: h 83 LYS cc_start: 0.9086 (ttmt) cc_final: 0.8872 (mtmm) REVERT: h 120 ARG cc_start: 0.7936 (tmm-80) cc_final: 0.7594 (ttp-110) REVERT: c 66 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8482 (tm-30) REVERT: c 79 ARG cc_start: 0.8422 (tpp80) cc_final: 0.7909 (mmt90) REVERT: a 164 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7989 (tt0) outliers start: 14 outliers final: 12 residues processed: 154 average time/residue: 0.3436 time to fit residues: 67.4617 Evaluate side-chains 158 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 218 MET 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: 2.9990 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN h 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3768 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= 0.189 Angle : 0.505 5.895 17056 Z= 0.300 Chirality : 0.032 0.131 1955 Planarity : 0.003 0.041 1299 Dihedral : 29.397 174.653 3531 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.03 % Allowed : 18.12 % Favored : 79.84 % 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: 2.63 (0.31), residues: 757 helix: 2.83 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -1.13 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.003 0.001 HIS c 33 PHE 0.011 0.001 PHE d 74 TYR 0.016 0.001 TYR a 140 ARG 0.006 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 158 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 0.807 Fit side-chains REVERT: d 124 LYS cc_start: 0.8652 (tptp) cc_final: 0.8309 (tttt) REVERT: h 47 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8521 (mttp) REVERT: h 83 LYS cc_start: 0.9094 (ttmt) cc_final: 0.8883 (mtmm) REVERT: h 120 ARG cc_start: 0.7937 (tmm-80) cc_final: 0.7590 (ttp-110) REVERT: c 66 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8498 (tm-30) REVERT: c 79 ARG cc_start: 0.8428 (tpp80) cc_final: 0.7921 (mmt90) REVERT: a 164 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7994 (tt0) outliers start: 13 outliers final: 13 residues processed: 151 average time/residue: 0.3470 time to fit residues: 66.7922 Evaluate side-chains 157 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 218 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: 0.3980 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.8474 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11843 Z= 0.217 Angle : 0.523 5.617 17056 Z= 0.310 Chirality : 0.033 0.132 1955 Planarity : 0.003 0.042 1299 Dihedral : 29.460 174.368 3531 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.88 % Allowed : 17.97 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.31), residues: 757 helix: 2.78 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.08 (0.39), residues: 221 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 0.010 0.001 PHE d 74 TYR 0.016 0.001 TYR a 140 ARG 0.005 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 159 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 147 time to evaluate : 0.911 Fit side-chains REVERT: d 124 LYS cc_start: 0.8681 (tptp) cc_final: 0.8333 (tttt) REVERT: h 47 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8518 (mttp) REVERT: h 83 LYS cc_start: 0.9112 (ttmt) cc_final: 0.8805 (mtmm) REVERT: h 120 ARG cc_start: 0.7937 (tmm-80) cc_final: 0.7509 (ttp-170) REVERT: c 79 ARG cc_start: 0.8427 (tpp80) cc_final: 0.7924 (mmt90) REVERT: a 164 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7984 (tt0) outliers start: 12 outliers final: 12 residues processed: 153 average time/residue: 0.3446 time to fit residues: 67.4385 Evaluate side-chains 156 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 218 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: 0.8980 chunk 70 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 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: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN h 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.117442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.074614 restraints weight = 19656.753| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.56 r_work: 0.2728 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11843 Z= 0.315 Angle : 0.582 5.728 17056 Z= 0.341 Chirality : 0.036 0.136 1955 Planarity : 0.004 0.042 1299 Dihedral : 29.688 173.585 3531 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.88 % Allowed : 17.97 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.31), residues: 757 helix: 2.64 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.19 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 298 HIS 0.007 0.001 HIS c 33 PHE 0.009 0.002 PHE d 74 TYR 0.016 0.001 TYR a 140 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: 2463.61 seconds wall clock time: 48 minutes 32.32 seconds (2912.32 seconds total)