Starting phenix.real_space_refine on Fri Mar 15 19:16:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f33_28830/03_2024/8f33_28830_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f33_28830/03_2024/8f33_28830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f33_28830/03_2024/8f33_28830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f33_28830/03_2024/8f33_28830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f33_28830/03_2024/8f33_28830_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f33_28830/03_2024/8f33_28830_updated.pdb" } resolution = 3.28 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 8180 2.51 5 N 2085 2.21 5 O 2250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 64": "OE1" <-> "OE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12545 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "D" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "C" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "B" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.46, per 1000 atoms: 0.51 Number of scatterers: 12545 At special positions: 0 Unit cell: (86.724, 86.724, 123.516, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 2250 8.00 N 2085 7.00 C 8180 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: 4.08 Conformation dependent library (CDL) restraints added in 2.2 seconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 20 sheets defined 30.0% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'E' and resid 63 through 69 Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'E' and resid 210 through 224 removed outlier: 5.167A pdb=" N PHE E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N TRP E 224 " --> pdb=" O TRP E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 248 Processing helix chain 'E' and resid 261 through 286 Processing helix chain 'E' and resid 303 through 316 Processing helix chain 'D' and resid 63 through 69 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 202 through 207 Processing helix chain 'D' and resid 210 through 224 removed outlier: 5.167A pdb=" N PHE D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N TRP D 224 " --> pdb=" O TRP D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 248 Processing helix chain 'D' and resid 261 through 286 Processing helix chain 'D' and resid 303 through 316 Processing helix chain 'C' and resid 63 through 69 Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 202 through 207 Processing helix chain 'C' and resid 210 through 224 removed outlier: 5.167A pdb=" N PHE C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N TRP C 224 " --> pdb=" O TRP C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 248 Processing helix chain 'C' and resid 261 through 286 Processing helix chain 'C' and resid 303 through 316 Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 210 through 224 removed outlier: 5.166A pdb=" N PHE B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N TRP B 224 " --> pdb=" O TRP B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 248 Processing helix chain 'B' and resid 261 through 286 Processing helix chain 'B' and resid 303 through 316 Processing helix chain 'A' and resid 63 through 69 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 210 through 224 removed outlier: 5.167A pdb=" N PHE A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N TRP A 224 " --> pdb=" O TRP A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 248 Processing helix chain 'A' and resid 261 through 286 Processing helix chain 'A' and resid 303 through 316 Processing sheet with id= A, first strand: chain 'E' and resid 12 through 14 Processing sheet with id= B, first strand: chain 'E' and resid 145 through 148 removed outlier: 7.228A pdb=" N VAL E 16 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N TYR E 148 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE E 18 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= D, first strand: chain 'E' and resid 167 through 174 Processing sheet with id= E, first strand: chain 'D' and resid 12 through 14 Processing sheet with id= F, first strand: chain 'D' and resid 145 through 148 removed outlier: 7.228A pdb=" N VAL D 16 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N TYR D 148 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE D 18 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= H, first strand: chain 'D' and resid 167 through 174 Processing sheet with id= I, first strand: chain 'C' and resid 12 through 14 Processing sheet with id= J, first strand: chain 'C' and resid 145 through 148 removed outlier: 7.228A pdb=" N VAL C 16 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N TYR C 148 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE C 18 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 76 through 78 Processing sheet with id= L, first strand: chain 'C' and resid 167 through 174 Processing sheet with id= M, first strand: chain 'B' and resid 12 through 14 Processing sheet with id= N, first strand: chain 'B' and resid 145 through 148 removed outlier: 7.229A pdb=" N VAL B 16 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N TYR B 148 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 18 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 76 through 78 Processing sheet with id= P, first strand: chain 'B' and resid 167 through 174 Processing sheet with id= Q, first strand: chain 'A' and resid 12 through 14 Processing sheet with id= R, first strand: chain 'A' and resid 145 through 148 removed outlier: 7.228A pdb=" N VAL A 16 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N TYR A 148 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE A 18 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 76 through 78 Processing sheet with id= T, first strand: chain 'A' and resid 167 through 174 560 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3991 1.34 - 1.46: 2739 1.46 - 1.57: 6100 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 12880 Sorted by residual: bond pdb=" CG1 ILE D 215 " pdb=" CD1 ILE D 215 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.13e+00 bond pdb=" CG1 ILE E 215 " pdb=" CD1 ILE E 215 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.12e+00 bond pdb=" CG1 ILE B 215 " pdb=" CD1 ILE B 215 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.10e+00 bond pdb=" CG1 ILE A 215 " pdb=" CD1 ILE A 215 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.09e+00 bond pdb=" CG1 ILE C 215 " pdb=" CD1 ILE C 215 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.08e+00 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.12: 327 106.12 - 113.13: 6780 113.13 - 120.14: 4653 120.14 - 127.15: 5605 127.15 - 134.17: 180 Bond angle restraints: 17545 Sorted by residual: angle pdb=" C ASN A 60 " pdb=" N THR A 61 " pdb=" CA THR A 61 " ideal model delta sigma weight residual 121.54 130.60 -9.06 1.91e+00 2.74e-01 2.25e+01 angle pdb=" C ASN B 60 " pdb=" N THR B 61 " pdb=" CA THR B 61 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" C ASN E 60 " pdb=" N THR E 61 " pdb=" CA THR E 61 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" C ASN D 60 " pdb=" N THR D 61 " pdb=" CA THR D 61 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C ASN C 60 " pdb=" N THR C 61 " pdb=" CA THR C 61 " ideal model delta sigma weight residual 121.54 130.48 -8.94 1.91e+00 2.74e-01 2.19e+01 ... (remaining 17540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 6810 17.22 - 34.45: 570 34.45 - 51.67: 125 51.67 - 68.90: 15 68.90 - 86.12: 10 Dihedral angle restraints: 7530 sinusoidal: 3025 harmonic: 4505 Sorted by residual: dihedral pdb=" CA PHE B 106 " pdb=" C PHE B 106 " pdb=" N LEU B 107 " pdb=" CA LEU B 107 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA PHE C 106 " pdb=" C PHE C 106 " pdb=" N LEU C 107 " pdb=" CA LEU C 107 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA PHE A 106 " pdb=" C PHE A 106 " pdb=" N LEU A 107 " pdb=" CA LEU A 107 " ideal model delta harmonic sigma weight residual 180.00 163.03 16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 7527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1138 0.042 - 0.084: 572 0.084 - 0.126: 186 0.126 - 0.168: 32 0.168 - 0.210: 22 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CB ILE C 39 " pdb=" CA ILE C 39 " pdb=" CG1 ILE C 39 " pdb=" CG2 ILE C 39 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB ILE D 39 " pdb=" CA ILE D 39 " pdb=" CG1 ILE D 39 " pdb=" CG2 ILE D 39 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB ILE A 39 " pdb=" CA ILE A 39 " pdb=" CG1 ILE A 39 " pdb=" CG2 ILE A 39 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1947 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 206 " -0.013 2.00e-02 2.50e+03 1.27e-02 4.04e+00 pdb=" CG TRP B 206 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 206 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 206 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 206 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 206 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 206 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 206 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 206 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 206 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 206 " -0.012 2.00e-02 2.50e+03 1.25e-02 3.93e+00 pdb=" CG TRP A 206 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 206 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 206 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 206 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 206 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 206 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 206 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 206 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 206 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 206 " -0.013 2.00e-02 2.50e+03 1.25e-02 3.93e+00 pdb=" CG TRP E 206 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP E 206 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP E 206 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 206 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 206 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 206 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 206 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 206 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP E 206 " -0.003 2.00e-02 2.50e+03 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4456 2.87 - 3.38: 10956 3.38 - 3.88: 21055 3.88 - 4.39: 23272 4.39 - 4.90: 42764 Nonbonded interactions: 102503 Sorted by model distance: nonbonded pdb=" O LEU D 225 " pdb=" NH2 ARG D 231 " model vdw 2.359 2.520 nonbonded pdb=" O LEU C 225 " pdb=" NH2 ARG C 231 " model vdw 2.360 2.520 nonbonded pdb=" O LEU A 225 " pdb=" NH2 ARG A 231 " model vdw 2.360 2.520 nonbonded pdb=" O LEU E 225 " pdb=" NH2 ARG E 231 " model vdw 2.360 2.520 nonbonded pdb=" O LEU B 225 " pdb=" NH2 ARG B 231 " model vdw 2.360 2.520 ... (remaining 102498 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.010 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.300 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 33.700 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 : 0.005 0.069 12880 Z= 0.333 Angle : 0.801 9.490 17545 Z= 0.425 Chirality : 0.056 0.210 1950 Planarity : 0.006 0.045 2235 Dihedral : 13.623 86.122 4620 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -1.40 (0.20), residues: 1525 helix: -0.47 (0.20), residues: 545 sheet: 0.83 (0.24), residues: 435 loop : -2.94 (0.22), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 206 HIS 0.002 0.001 HIS B 177 PHE 0.025 0.003 PHE B 247 TYR 0.023 0.003 TYR C 148 ARG 0.006 0.001 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.544 Fit side-chains REVERT: D 30 GLU cc_start: 0.5858 (tp30) cc_final: 0.5525 (mm-30) REVERT: A 30 GLU cc_start: 0.5801 (tp30) cc_final: 0.5458 (mm-30) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2743 time to fit residues: 54.7980 Evaluate side-chains 97 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 12880 Z= 0.344 Angle : 0.603 6.542 17545 Z= 0.308 Chirality : 0.049 0.153 1950 Planarity : 0.004 0.037 2235 Dihedral : 4.771 21.669 1690 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.73 % Allowed : 6.69 % Favored : 92.58 % 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: -0.89 (0.20), residues: 1525 helix: 0.11 (0.21), residues: 560 sheet: 0.94 (0.24), residues: 435 loop : -2.73 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 206 HIS 0.003 0.001 HIS C 177 PHE 0.032 0.002 PHE C 247 TYR 0.015 0.002 TYR C 245 ARG 0.003 0.000 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.321 Fit side-chains REVERT: E 159 GLU cc_start: 0.7172 (pm20) cc_final: 0.6264 (tt0) REVERT: C 245 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.7809 (t80) REVERT: B 247 PHE cc_start: 0.5840 (p90) cc_final: 0.5215 (p90) REVERT: A 30 GLU cc_start: 0.5900 (tp30) cc_final: 0.5528 (mm-30) outliers start: 10 outliers final: 8 residues processed: 122 average time/residue: 0.2507 time to fit residues: 42.8183 Evaluate side-chains 119 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 277 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 135 optimal weight: 0.0470 chunk 46 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 12880 Z= 0.244 Angle : 0.534 9.994 17545 Z= 0.270 Chirality : 0.046 0.141 1950 Planarity : 0.004 0.035 2235 Dihedral : 4.552 23.098 1690 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.38 % Allowed : 10.40 % Favored : 88.22 % 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: -0.55 (0.21), residues: 1525 helix: 0.68 (0.22), residues: 555 sheet: 1.01 (0.25), residues: 405 loop : -2.57 (0.22), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 206 HIS 0.002 0.001 HIS C 177 PHE 0.032 0.002 PHE D 247 TYR 0.016 0.002 TYR C 245 ARG 0.003 0.000 ARG E 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 1.373 Fit side-chains REVERT: E 159 GLU cc_start: 0.7272 (pm20) cc_final: 0.6414 (tt0) REVERT: E 245 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7760 (t80) REVERT: D 245 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.7814 (t80) REVERT: C 159 GLU cc_start: 0.7359 (pm20) cc_final: 0.6555 (tt0) REVERT: C 245 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7792 (t80) REVERT: B 245 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7865 (t80) REVERT: A 245 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.7774 (t80) outliers start: 19 outliers final: 10 residues processed: 134 average time/residue: 0.2861 time to fit residues: 53.8207 Evaluate side-chains 132 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 277 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 20.0000 chunk 102 optimal weight: 0.2980 chunk 70 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 129 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 12880 Z= 0.294 Angle : 0.551 8.185 17545 Z= 0.281 Chirality : 0.047 0.150 1950 Planarity : 0.004 0.033 2235 Dihedral : 4.624 19.986 1690 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.64 % Allowed : 9.53 % Favored : 86.84 % 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: -0.37 (0.21), residues: 1525 helix: 0.81 (0.23), residues: 560 sheet: 1.17 (0.25), residues: 395 loop : -2.47 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 206 HIS 0.003 0.001 HIS C 177 PHE 0.031 0.002 PHE B 247 TYR 0.019 0.002 TYR C 245 ARG 0.003 0.000 ARG E 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 128 time to evaluate : 1.353 Fit side-chains REVERT: E 97 ASP cc_start: 0.6422 (OUTLIER) cc_final: 0.5867 (p0) REVERT: E 245 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7829 (t80) REVERT: D 245 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7703 (t80) REVERT: C 97 ASP cc_start: 0.6448 (OUTLIER) cc_final: 0.5952 (p0) REVERT: C 159 GLU cc_start: 0.7388 (pm20) cc_final: 0.6643 (tt0) REVERT: C 245 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.7933 (t80) REVERT: B 97 ASP cc_start: 0.6215 (OUTLIER) cc_final: 0.5651 (p0) REVERT: B 245 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7746 (t80) REVERT: B 247 PHE cc_start: 0.6087 (p90) cc_final: 0.5520 (p90) REVERT: A 97 ASP cc_start: 0.6460 (OUTLIER) cc_final: 0.5985 (p0) REVERT: A 245 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7867 (t80) outliers start: 50 outliers final: 18 residues processed: 169 average time/residue: 0.2475 time to fit residues: 60.1893 Evaluate side-chains 147 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 277 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12880 Z= 0.170 Angle : 0.489 7.945 17545 Z= 0.248 Chirality : 0.045 0.135 1950 Planarity : 0.004 0.035 2235 Dihedral : 4.218 16.877 1690 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.47 % Allowed : 11.56 % Favored : 85.96 % 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: -0.17 (0.22), residues: 1525 helix: 1.09 (0.23), residues: 555 sheet: 1.17 (0.26), residues: 405 loop : -2.42 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 206 HIS 0.002 0.001 HIS E 177 PHE 0.030 0.001 PHE D 247 TYR 0.013 0.001 TYR C 245 ARG 0.001 0.000 ARG E 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 1.340 Fit side-chains REVERT: E 97 ASP cc_start: 0.6499 (OUTLIER) cc_final: 0.6018 (p0) REVERT: E 159 GLU cc_start: 0.7126 (pm20) cc_final: 0.6363 (tt0) REVERT: E 245 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7789 (t80) REVERT: D 245 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.7715 (t80) REVERT: C 97 ASP cc_start: 0.6427 (OUTLIER) cc_final: 0.6021 (p0) REVERT: C 159 GLU cc_start: 0.7296 (pm20) cc_final: 0.6549 (tt0) REVERT: C 245 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7818 (t80) REVERT: B 97 ASP cc_start: 0.6225 (OUTLIER) cc_final: 0.5714 (p0) REVERT: B 245 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7707 (t80) REVERT: B 247 PHE cc_start: 0.5993 (p90) cc_final: 0.5314 (p90) REVERT: A 97 ASP cc_start: 0.6510 (OUTLIER) cc_final: 0.6043 (p0) REVERT: A 245 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7721 (t80) outliers start: 34 outliers final: 21 residues processed: 152 average time/residue: 0.2663 time to fit residues: 57.5780 Evaluate side-chains 149 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 119 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 277 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 0.4980 chunk 12 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 139 optimal weight: 0.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 12880 Z= 0.301 Angle : 0.558 9.103 17545 Z= 0.283 Chirality : 0.047 0.152 1950 Planarity : 0.004 0.033 2235 Dihedral : 4.557 20.310 1690 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.20 % Allowed : 11.64 % 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: -0.25 (0.21), residues: 1525 helix: 0.95 (0.23), residues: 560 sheet: 1.23 (0.26), residues: 395 loop : -2.43 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 206 HIS 0.003 0.001 HIS B 177 PHE 0.032 0.002 PHE B 247 TYR 0.019 0.002 TYR C 245 ARG 0.003 0.000 ARG E 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 125 time to evaluate : 1.555 Fit side-chains REVERT: E 97 ASP cc_start: 0.6400 (OUTLIER) cc_final: 0.5869 (p0) REVERT: E 159 GLU cc_start: 0.7267 (pm20) cc_final: 0.7043 (pm20) REVERT: E 245 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.7729 (t80) REVERT: D 245 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7697 (t80) REVERT: C 97 ASP cc_start: 0.6360 (OUTLIER) cc_final: 0.5870 (p0) REVERT: C 159 GLU cc_start: 0.7356 (pm20) cc_final: 0.6612 (tt0) REVERT: C 245 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7925 (t80) REVERT: B 97 ASP cc_start: 0.6149 (OUTLIER) cc_final: 0.5595 (p0) REVERT: B 245 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7701 (t80) REVERT: A 97 ASP cc_start: 0.6416 (OUTLIER) cc_final: 0.5948 (p0) REVERT: A 245 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7684 (t80) outliers start: 44 outliers final: 23 residues processed: 162 average time/residue: 0.2641 time to fit residues: 61.4512 Evaluate side-chains 153 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 277 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 12880 Z= 0.339 Angle : 0.591 12.189 17545 Z= 0.300 Chirality : 0.048 0.156 1950 Planarity : 0.004 0.032 2235 Dihedral : 4.698 21.517 1690 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.13 % Allowed : 12.44 % Favored : 84.44 % 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: -0.41 (0.21), residues: 1525 helix: 0.72 (0.23), residues: 560 sheet: 1.13 (0.26), residues: 395 loop : -2.41 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 220 HIS 0.003 0.001 HIS B 177 PHE 0.032 0.002 PHE B 247 TYR 0.020 0.002 TYR C 245 ARG 0.004 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 127 time to evaluate : 1.258 Fit side-chains REVERT: E 97 ASP cc_start: 0.6273 (OUTLIER) cc_final: 0.5693 (p0) REVERT: E 159 GLU cc_start: 0.7242 (pm20) cc_final: 0.6985 (pm20) REVERT: E 223 PHE cc_start: 0.6777 (m-80) cc_final: 0.6527 (m-80) REVERT: E 245 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.7781 (t80) REVERT: D 245 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.7655 (t80) REVERT: C 97 ASP cc_start: 0.6313 (OUTLIER) cc_final: 0.5841 (p0) REVERT: C 159 GLU cc_start: 0.7390 (pm20) cc_final: 0.6635 (tt0) REVERT: C 245 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.8015 (t80) REVERT: B 97 ASP cc_start: 0.6146 (OUTLIER) cc_final: 0.5578 (p0) REVERT: B 245 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.7690 (t80) REVERT: A 97 ASP cc_start: 0.6321 (OUTLIER) cc_final: 0.5932 (p0) REVERT: A 245 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7730 (t80) outliers start: 43 outliers final: 24 residues processed: 163 average time/residue: 0.2477 time to fit residues: 57.6035 Evaluate side-chains 157 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 124 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 277 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 91 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 233 GLN D 233 GLN A 284 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12880 Z= 0.139 Angle : 0.480 9.691 17545 Z= 0.245 Chirality : 0.044 0.129 1950 Planarity : 0.004 0.034 2235 Dihedral : 4.074 16.327 1690 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.47 % Allowed : 13.09 % Favored : 84.44 % 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: -0.17 (0.22), residues: 1525 helix: 0.85 (0.23), residues: 560 sheet: 1.35 (0.26), residues: 395 loop : -2.28 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 220 HIS 0.001 0.000 HIS B 177 PHE 0.028 0.001 PHE E 247 TYR 0.011 0.001 TYR C 245 ARG 0.001 0.000 ARG D 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: E 97 ASP cc_start: 0.6376 (OUTLIER) cc_final: 0.5922 (p0) REVERT: E 159 GLU cc_start: 0.7214 (pm20) cc_final: 0.6943 (pm20) REVERT: E 245 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.7745 (t80) REVERT: D 245 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7736 (t80) REVERT: C 97 ASP cc_start: 0.6412 (OUTLIER) cc_final: 0.5996 (p0) REVERT: C 159 GLU cc_start: 0.7357 (pm20) cc_final: 0.6441 (tt0) REVERT: C 245 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.7813 (t80) REVERT: B 97 ASP cc_start: 0.6186 (OUTLIER) cc_final: 0.5684 (p0) REVERT: B 245 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.7616 (t80) REVERT: A 97 ASP cc_start: 0.6481 (OUTLIER) cc_final: 0.6047 (p0) REVERT: A 245 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7726 (t80) outliers start: 34 outliers final: 21 residues processed: 144 average time/residue: 0.2661 time to fit residues: 54.0479 Evaluate side-chains 147 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 12880 Z= 0.356 Angle : 0.593 10.814 17545 Z= 0.302 Chirality : 0.048 0.162 1950 Planarity : 0.004 0.031 2235 Dihedral : 4.651 22.223 1690 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.33 % Allowed : 13.45 % Favored : 84.22 % 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: -0.33 (0.21), residues: 1525 helix: 0.73 (0.23), residues: 560 sheet: 1.15 (0.26), residues: 395 loop : -2.27 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 220 HIS 0.003 0.001 HIS A 284 PHE 0.034 0.002 PHE B 247 TYR 0.021 0.002 TYR C 245 ARG 0.003 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 127 time to evaluate : 1.458 Fit side-chains REVERT: E 97 ASP cc_start: 0.6283 (OUTLIER) cc_final: 0.5742 (p0) REVERT: E 159 GLU cc_start: 0.7223 (pm20) cc_final: 0.6944 (pm20) REVERT: E 245 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7781 (t80) REVERT: D 245 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.7683 (t80) REVERT: C 97 ASP cc_start: 0.6323 (OUTLIER) cc_final: 0.5840 (p0) REVERT: C 245 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.7940 (t80) REVERT: B 97 ASP cc_start: 0.6127 (OUTLIER) cc_final: 0.5579 (p0) REVERT: B 245 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7644 (t80) REVERT: A 97 ASP cc_start: 0.6350 (OUTLIER) cc_final: 0.5951 (p0) REVERT: A 245 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.7687 (t80) outliers start: 32 outliers final: 17 residues processed: 153 average time/residue: 0.2694 time to fit residues: 58.5863 Evaluate side-chains 152 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 118 optimal weight: 0.0000 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 72 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 284 HIS C 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12880 Z= 0.136 Angle : 0.482 9.179 17545 Z= 0.247 Chirality : 0.044 0.126 1950 Planarity : 0.004 0.034 2235 Dihedral : 4.000 16.103 1690 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.24 % Allowed : 14.84 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1525 helix: 0.92 (0.23), residues: 555 sheet: 1.37 (0.26), residues: 395 loop : -2.21 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 220 HIS 0.001 0.000 HIS B 177 PHE 0.028 0.001 PHE E 247 TYR 0.010 0.001 TYR C 245 ARG 0.001 0.000 ARG C 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.494 Fit side-chains REVERT: E 97 ASP cc_start: 0.6428 (OUTLIER) cc_final: 0.5978 (p0) REVERT: E 159 GLU cc_start: 0.7185 (pm20) cc_final: 0.6921 (pm20) REVERT: E 245 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7669 (t80) REVERT: D 228 PHE cc_start: 0.5735 (t80) cc_final: 0.5327 (t80) REVERT: D 245 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7649 (t80) REVERT: C 97 ASP cc_start: 0.6407 (OUTLIER) cc_final: 0.6015 (p0) REVERT: C 245 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.7750 (t80) REVERT: B 97 ASP cc_start: 0.6194 (OUTLIER) cc_final: 0.5735 (p0) REVERT: B 245 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.7658 (t80) REVERT: A 97 ASP cc_start: 0.6456 (OUTLIER) cc_final: 0.5960 (p0) REVERT: A 245 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.7689 (t80) outliers start: 17 outliers final: 7 residues processed: 133 average time/residue: 0.2811 time to fit residues: 52.6949 Evaluate side-chains 136 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.150168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.114880 restraints weight = 15322.465| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.82 r_work: 0.3120 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 12880 Z= 0.365 Angle : 0.604 10.553 17545 Z= 0.307 Chirality : 0.049 0.163 1950 Planarity : 0.004 0.031 2235 Dihedral : 4.665 22.350 1690 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.82 % Allowed : 14.40 % Favored : 83.78 % 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: -0.30 (0.21), residues: 1525 helix: 0.76 (0.23), residues: 555 sheet: 1.12 (0.25), residues: 395 loop : -2.21 (0.22), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 220 HIS 0.003 0.001 HIS B 177 PHE 0.034 0.002 PHE B 247 TYR 0.021 0.002 TYR C 245 ARG 0.003 0.000 ARG C 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2423.77 seconds wall clock time: 45 minutes 43.06 seconds (2743.06 seconds total)