Starting phenix.real_space_refine on Sat Dec 9 23:11:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k11_8193/12_2023/5k11_8193_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k11_8193/12_2023/5k11_8193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k11_8193/12_2023/5k11_8193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k11_8193/12_2023/5k11_8193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k11_8193/12_2023/5k11_8193_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k11_8193/12_2023/5k11_8193_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6334 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 6 5.49 5 S 38 5.16 5 C 4016 2.51 5 N 1074 2.21 5 O 1204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6338 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3121 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3121 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.88, per 1000 atoms: 0.61 Number of scatterers: 6338 At special positions: 0 Unit cell: (103.455, 73.755, 82.17, 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 38 16.00 P 6 15.00 O 1204 8.00 N 1074 7.00 C 4016 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: 2.42 Conformation dependent library (CDL) restraints added in 1.3 seconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1464 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 8 sheets defined 42.1% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 17 through 30 removed outlier: 3.526A pdb=" N GLU A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 55 through 67 removed outlier: 3.681A pdb=" N ALA A 63 " --> pdb=" O ASP A 59 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 186 through 203 Processing helix chain 'A' and resid 217 through 231 removed outlier: 3.591A pdb=" N ASP A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.610A pdb=" N MET A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 330 through 346 removed outlier: 3.803A pdb=" N TRP A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 368 removed outlier: 3.786A pdb=" N PHE A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 380 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 394 through 412 removed outlier: 3.879A pdb=" N MET A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 30 removed outlier: 3.526A pdb=" N GLU B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 55 through 67 removed outlier: 3.681A pdb=" N ALA B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS B 66 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 186 through 203 Processing helix chain 'B' and resid 217 through 231 removed outlier: 3.591A pdb=" N ASP B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 251 through 260 removed outlier: 3.610A pdb=" N MET B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 330 through 346 removed outlier: 3.803A pdb=" N TRP B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 368 removed outlier: 3.786A pdb=" N PHE B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 380 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 394 through 412 removed outlier: 3.878A pdb=" N MET B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 9 through 14 removed outlier: 5.919A pdb=" N ASP A 38 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU A 12 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N HIS A 40 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLN A 14 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR A 42 " --> pdb=" O GLN A 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 69 through 72 removed outlier: 5.885A pdb=" N VAL A 303 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LYS A 72 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 305 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL A 107 " --> pdb=" O CYS A 132 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS A 132 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 141 through 144 removed outlier: 3.554A pdb=" N THR A 142 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 150 through 152 Processing sheet with id= E, first strand: chain 'B' and resid 9 through 14 removed outlier: 5.920A pdb=" N ASP B 38 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU B 12 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N HIS B 40 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLN B 14 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TYR B 42 " --> pdb=" O GLN B 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 69 through 72 removed outlier: 5.886A pdb=" N VAL B 303 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LYS B 72 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA B 305 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL B 107 " --> pdb=" O CYS B 132 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS B 132 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 141 through 144 removed outlier: 3.554A pdb=" N THR B 142 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 150 through 152 230 hydrogen bonds defined for protein. 666 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: 1.63 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1988 1.34 - 1.46: 1296 1.46 - 1.58: 3112 1.58 - 1.70: 10 1.70 - 1.82: 64 Bond restraints: 6470 Sorted by residual: bond pdb=" O2B NDP A 501 " pdb=" P2B NDP A 501 " ideal model delta sigma weight residual 1.833 1.610 0.223 3.80e-02 6.93e+02 3.45e+01 bond pdb=" O2B NDP B 501 " pdb=" P2B NDP B 501 " ideal model delta sigma weight residual 1.833 1.611 0.222 3.80e-02 6.93e+02 3.43e+01 bond pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.757 1.609 0.148 3.50e-02 8.16e+02 1.79e+01 bond pdb=" O5D NDP B 501 " pdb=" PN NDP B 501 " ideal model delta sigma weight residual 1.757 1.610 0.147 3.50e-02 8.16e+02 1.77e+01 bond pdb=" C2B NDP A 501 " pdb=" O2B NDP A 501 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.90e-02 1.19e+03 1.10e+01 ... (remaining 6465 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.93: 144 105.93 - 113.46: 3635 113.46 - 120.99: 3102 120.99 - 128.52: 1795 128.52 - 136.05: 60 Bond angle restraints: 8736 Sorted by residual: angle pdb=" C5B NDP B 501 " pdb=" O5B NDP B 501 " pdb=" PA NDP B 501 " ideal model delta sigma weight residual 103.84 120.43 -16.59 1.91e+00 2.73e-01 7.51e+01 angle pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " ideal model delta sigma weight residual 103.84 120.40 -16.56 1.91e+00 2.73e-01 7.48e+01 angle pdb=" PA NDP B 501 " pdb=" O3 NDP B 501 " pdb=" PN NDP B 501 " ideal model delta sigma weight residual 107.74 120.34 -12.60 1.95e+00 2.62e-01 4.16e+01 angle pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 107.74 120.31 -12.57 1.95e+00 2.62e-01 4.14e+01 angle pdb=" C5D NDP B 501 " pdb=" O5D NDP B 501 " pdb=" PN NDP B 501 " ideal model delta sigma weight residual 104.93 120.48 -15.55 2.66e+00 1.41e-01 3.42e+01 ... (remaining 8731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.22: 3786 29.22 - 58.44: 42 58.44 - 87.66: 12 87.66 - 116.88: 0 116.88 - 146.11: 2 Dihedral angle restraints: 3842 sinusoidal: 1564 harmonic: 2278 Sorted by residual: dihedral pdb=" CA PHE B 334 " pdb=" C PHE B 334 " pdb=" N ALA B 335 " pdb=" CA ALA B 335 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA PHE A 334 " pdb=" C PHE A 334 " pdb=" N ALA A 335 " pdb=" CA ALA A 335 " ideal model delta harmonic sigma weight residual 180.00 155.14 24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ALA B 241 " pdb=" C ALA B 241 " pdb=" N GLN B 242 " pdb=" CA GLN B 242 " ideal model delta harmonic sigma weight residual -180.00 -155.49 -24.51 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 3839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 595 0.050 - 0.100: 279 0.100 - 0.151: 66 0.151 - 0.201: 10 0.201 - 0.251: 4 Chirality restraints: 954 Sorted by residual: chirality pdb=" CB ILE A 244 " pdb=" CA ILE A 244 " pdb=" CG1 ILE A 244 " pdb=" CG2 ILE A 244 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB ILE B 244 " pdb=" CA ILE B 244 " pdb=" CG1 ILE B 244 " pdb=" CG2 ILE B 244 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB VAL A 255 " pdb=" CA VAL A 255 " pdb=" CG1 VAL A 255 " pdb=" CG2 VAL A 255 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 951 not shown) Planarity restraints: 1104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 192 " -0.022 2.00e-02 2.50e+03 2.06e-02 7.41e+00 pdb=" CG PHE A 192 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A 192 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 192 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 192 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 192 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 192 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 192 " 0.022 2.00e-02 2.50e+03 2.03e-02 7.23e+00 pdb=" CG PHE B 192 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 192 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 192 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 192 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 192 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 192 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 32 " 0.013 2.00e-02 2.50e+03 1.67e-02 4.90e+00 pdb=" CG PHE A 32 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 32 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 32 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 32 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 32 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 32 " 0.001 2.00e-02 2.50e+03 ... (remaining 1101 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 164 2.63 - 3.20: 6475 3.20 - 3.76: 10444 3.76 - 4.33: 15325 4.33 - 4.90: 23430 Nonbonded interactions: 55838 Sorted by model distance: nonbonded pdb=" NZ LYS A 29 " pdb=" OD1 ASP A 399 " model vdw 2.061 2.520 nonbonded pdb=" NZ LYS B 29 " pdb=" OD1 ASP B 399 " model vdw 2.061 2.520 nonbonded pdb=" ND2 ASN B 184 " pdb=" OH TYR B 219 " model vdw 2.137 2.520 nonbonded pdb=" ND2 ASN A 184 " pdb=" OH TYR A 219 " model vdw 2.138 2.520 nonbonded pdb=" ND2 ASN B 116 " pdb=" O ILE B 367 " model vdw 2.148 2.520 ... (remaining 55833 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 2.080 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 20.660 Find NCS groups from input model: 0.350 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 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 : 0.012 0.223 6470 Z= 0.749 Angle : 1.235 16.593 8736 Z= 0.649 Chirality : 0.059 0.251 954 Planarity : 0.006 0.050 1104 Dihedral : 12.123 146.105 2378 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 29.53 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.14 % Favored : 93.35 % Rotamer: Outliers : 0.30 % Allowed : 1.21 % Favored : 98.49 % 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: -4.89 (0.22), residues: 782 helix: -3.96 (0.17), residues: 326 sheet: -2.87 (0.31), residues: 144 loop : -2.27 (0.29), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.005 TRP A 92 HIS 0.012 0.004 HIS B 170 PHE 0.047 0.005 PHE A 192 TYR 0.035 0.004 TYR B 231 ARG 0.011 0.002 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 205 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 205 average time/residue: 0.2818 time to fit residues: 69.3131 Evaluate side-chains 105 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.724 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 30.0000 chunk 59 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 96 ASN A 101 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN A 184 ASN A 228 GLN A 271 ASN ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 HIS A 385 ASN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS B 96 ASN ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN B 228 GLN ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 HIS B 385 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6470 Z= 0.304 Angle : 0.805 6.543 8736 Z= 0.419 Chirality : 0.048 0.172 954 Planarity : 0.005 0.034 1104 Dihedral : 10.784 150.991 860 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 28.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.66 % Allowed : 13.29 % Favored : 85.05 % 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: -2.67 (0.26), residues: 782 helix: -1.64 (0.25), residues: 336 sheet: -2.59 (0.31), residues: 180 loop : -0.85 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 23 HIS 0.009 0.002 HIS B 248 PHE 0.024 0.003 PHE B 227 TYR 0.018 0.002 TYR A 34 ARG 0.005 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 127 average time/residue: 0.2026 time to fit residues: 33.2294 Evaluate side-chains 106 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.711 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0632 time to fit residues: 2.0228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 40.0000 chunk 21 optimal weight: 30.0000 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 0.0970 chunk 63 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 53 optimal weight: 40.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6470 Z= 0.220 Angle : 0.729 15.090 8736 Z= 0.368 Chirality : 0.045 0.182 954 Planarity : 0.004 0.034 1104 Dihedral : 10.272 146.610 860 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.72 % Allowed : 14.50 % Favored : 82.78 % 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: -1.38 (0.29), residues: 782 helix: -0.66 (0.26), residues: 352 sheet: -1.48 (0.36), residues: 168 loop : -0.47 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 23 HIS 0.005 0.001 HIS B 248 PHE 0.023 0.002 PHE A 227 TYR 0.009 0.001 TYR B 219 ARG 0.005 0.001 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 132 average time/residue: 0.2285 time to fit residues: 38.2037 Evaluate side-chains 106 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.705 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0595 time to fit residues: 1.9129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 37 optimal weight: 0.0870 chunk 67 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 42 optimal weight: 30.0000 overall best weight: 6.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6470 Z= 0.293 Angle : 0.728 6.092 8736 Z= 0.378 Chirality : 0.044 0.182 954 Planarity : 0.004 0.039 1104 Dihedral : 10.082 142.063 860 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 25.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.76 % Allowed : 16.92 % Favored : 82.33 % 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: -0.93 (0.29), residues: 782 helix: -0.25 (0.26), residues: 354 sheet: -1.38 (0.37), residues: 168 loop : -0.22 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 205 HIS 0.005 0.002 HIS B 248 PHE 0.018 0.002 PHE A 227 TYR 0.016 0.002 TYR A 391 ARG 0.002 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 98 average time/residue: 0.2206 time to fit residues: 27.6431 Evaluate side-chains 81 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.696 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0904 time to fit residues: 1.2757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 40.0000 chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6470 Z= 0.258 Angle : 0.706 6.638 8736 Z= 0.364 Chirality : 0.044 0.167 954 Planarity : 0.004 0.044 1104 Dihedral : 9.849 136.906 860 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.36 % Allowed : 17.22 % Favored : 81.42 % 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 (0.30), residues: 782 helix: 0.22 (0.27), residues: 352 sheet: -1.31 (0.36), residues: 168 loop : -0.20 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 23 HIS 0.004 0.001 HIS B 248 PHE 0.016 0.002 PHE A 265 TYR 0.012 0.001 TYR A 391 ARG 0.003 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 93 average time/residue: 0.2127 time to fit residues: 25.6653 Evaluate side-chains 84 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.704 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0575 time to fit residues: 1.1266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 40.0000 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 40.0000 chunk 42 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.6513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6470 Z= 0.290 Angle : 0.710 7.434 8736 Z= 0.367 Chirality : 0.044 0.222 954 Planarity : 0.004 0.047 1104 Dihedral : 9.708 133.935 860 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 24.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.76 % Allowed : 18.28 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.30), residues: 782 helix: 0.53 (0.27), residues: 362 sheet: -1.33 (0.39), residues: 148 loop : -0.48 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 205 HIS 0.005 0.001 HIS A 170 PHE 0.014 0.002 PHE A 265 TYR 0.011 0.001 TYR A 391 ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 94 average time/residue: 0.2088 time to fit residues: 25.7618 Evaluate side-chains 80 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.803 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0621 time to fit residues: 1.2564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 40.0000 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 47 optimal weight: 40.0000 chunk 45 optimal weight: 0.0970 chunk 34 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 overall best weight: 5.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.6718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6470 Z= 0.255 Angle : 0.703 9.981 8736 Z= 0.357 Chirality : 0.045 0.221 954 Planarity : 0.004 0.040 1104 Dihedral : 9.537 132.393 860 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 22.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.76 % Allowed : 18.43 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.30), residues: 782 helix: 0.70 (0.27), residues: 364 sheet: -1.15 (0.40), residues: 144 loop : -0.56 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 23 HIS 0.004 0.001 HIS A 170 PHE 0.014 0.002 PHE A 371 TYR 0.009 0.001 TYR A 208 ARG 0.002 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 101 average time/residue: 0.1967 time to fit residues: 26.2308 Evaluate side-chains 88 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.668 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0624 time to fit residues: 1.1052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 30.0000 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 68 optimal weight: 30.0000 chunk 72 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.6927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6470 Z= 0.267 Angle : 0.730 7.989 8736 Z= 0.372 Chirality : 0.044 0.213 954 Planarity : 0.004 0.040 1104 Dihedral : 9.501 131.707 860 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.91 % Allowed : 20.09 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.30), residues: 782 helix: 0.61 (0.27), residues: 370 sheet: -1.12 (0.40), residues: 144 loop : -0.57 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 23 HIS 0.005 0.001 HIS A 170 PHE 0.014 0.002 PHE A 355 TYR 0.011 0.001 TYR A 208 ARG 0.003 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 0.2135 time to fit residues: 25.8708 Evaluate side-chains 90 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 0.728 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0587 time to fit residues: 1.3233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 30.0000 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.7145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6470 Z= 0.245 Angle : 0.763 13.995 8736 Z= 0.380 Chirality : 0.044 0.208 954 Planarity : 0.004 0.034 1104 Dihedral : 9.351 130.504 860 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 24.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.76 % Allowed : 20.69 % Favored : 78.55 % 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 (0.30), residues: 782 helix: 0.52 (0.27), residues: 372 sheet: -1.20 (0.39), residues: 152 loop : -0.44 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 23 HIS 0.004 0.001 HIS A 248 PHE 0.014 0.002 PHE A 144 TYR 0.012 0.001 TYR A 34 ARG 0.003 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 95 average time/residue: 0.1975 time to fit residues: 24.8792 Evaluate side-chains 88 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.742 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0601 time to fit residues: 1.0573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 overall best weight: 7.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.7349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6470 Z= 0.290 Angle : 0.812 14.223 8736 Z= 0.402 Chirality : 0.045 0.257 954 Planarity : 0.004 0.043 1104 Dihedral : 9.378 130.968 860 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 26.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.15 % Allowed : 21.30 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.30), residues: 782 helix: 0.44 (0.27), residues: 368 sheet: -0.93 (0.40), residues: 144 loop : -0.54 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 23 HIS 0.006 0.001 HIS A 170 PHE 0.013 0.002 PHE A 355 TYR 0.036 0.002 TYR A 42 ARG 0.005 0.000 ARG B 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 86 average time/residue: 0.1970 time to fit residues: 22.6096 Evaluate side-chains 82 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.669 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0563 time to fit residues: 1.0375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.060906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.049712 restraints weight = 32677.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.051401 restraints weight = 21586.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.052647 restraints weight = 15739.976| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.7518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6470 Z= 0.211 Angle : 0.804 15.155 8736 Z= 0.390 Chirality : 0.046 0.289 954 Planarity : 0.004 0.044 1104 Dihedral : 9.075 128.235 860 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.15 % Allowed : 22.21 % Favored : 77.64 % 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: -0.28 (0.31), residues: 782 helix: 0.41 (0.27), residues: 372 sheet: -0.83 (0.41), residues: 146 loop : -0.41 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 267 HIS 0.006 0.001 HIS B 248 PHE 0.018 0.002 PHE A 397 TYR 0.028 0.001 TYR A 42 ARG 0.002 0.000 ARG B 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1526.86 seconds wall clock time: 28 minutes 59.51 seconds (1739.51 seconds total)