Starting phenix.real_space_refine on Mon Apr 8 05:32:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k11_8193/04_2024/5k11_8193_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k11_8193/04_2024/5k11_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_8193/04_2024/5k11_8193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k11_8193/04_2024/5k11_8193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k11_8193/04_2024/5k11_8193_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k11_8193/04_2024/5k11_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 3.95, per 1000 atoms: 0.62 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: 2.55 Conformation dependent library (CDL) restraints added in 1.2 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: 1.29 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: 1.67 Time building geometry restraints manager: 2.75 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 2.220 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 21.360 Find NCS groups from input model: 0.310 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.230 ------------------------------------------------------------------------------- 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 : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 VAL cc_start: 0.8490 (m) cc_final: 0.8000 (p) REVERT: A 257 GLN cc_start: 0.8598 (tp-100) cc_final: 0.8344 (tp-100) REVERT: B 255 VAL cc_start: 0.8493 (m) cc_final: 0.8022 (p) REVERT: B 257 GLN cc_start: 0.8577 (tp-100) cc_final: 0.8323 (tp-100) outliers start: 2 outliers final: 0 residues processed: 205 average time/residue: 0.2865 time to fit residues: 70.2596 Evaluate side-chains 107 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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: 20.0000 chunk 59 optimal weight: 9.9990 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: 5.9990 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: 5.5388 ------------------------------------------------------------------------------- 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 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 48 ASN B 96 ASN ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN B 228 GLN B 271 ASN ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 HIS B 385 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6470 Z= 0.298 Angle : 0.809 6.460 8736 Z= 0.422 Chirality : 0.048 0.182 954 Planarity : 0.005 0.034 1104 Dihedral : 10.820 150.430 860 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 27.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.06 % Allowed : 13.75 % Favored : 85.20 % 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: -2.87 (0.26), residues: 782 helix: -1.81 (0.24), residues: 340 sheet: -2.60 (0.31), residues: 180 loop : -1.02 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 23 HIS 0.009 0.002 HIS B 248 PHE 0.024 0.003 PHE B 227 TYR 0.020 0.002 TYR A 34 ARG 0.009 0.001 ARG A 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 129 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 VAL cc_start: 0.8423 (m) cc_final: 0.7971 (p) REVERT: A 257 GLN cc_start: 0.8651 (tp-100) cc_final: 0.8187 (tp-100) REVERT: A 291 MET cc_start: 0.8445 (mmm) cc_final: 0.8228 (mmm) REVERT: B 255 VAL cc_start: 0.8431 (m) cc_final: 0.7965 (p) REVERT: B 257 GLN cc_start: 0.8646 (tp-100) cc_final: 0.8187 (tp-100) REVERT: B 291 MET cc_start: 0.8439 (mmm) cc_final: 0.8185 (mmm) outliers start: 7 outliers final: 7 residues processed: 128 average time/residue: 0.2187 time to fit residues: 35.8072 Evaluate side-chains 110 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 182 MET 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: 5.9990 chunk 58 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 309 HIS ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 309 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.5223 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= 0.291 Angle : 0.734 11.366 8736 Z= 0.377 Chirality : 0.045 0.158 954 Planarity : 0.004 0.031 1104 Dihedral : 10.328 147.763 860 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 27.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.53 % Allowed : 14.35 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.29), residues: 782 helix: -0.79 (0.26), residues: 350 sheet: -1.93 (0.36), residues: 170 loop : -0.34 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 23 HIS 0.006 0.002 HIS B 248 PHE 0.020 0.003 PHE B 227 TYR 0.010 0.002 TYR A 34 ARG 0.002 0.001 ARG B 338 *********************** 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 141 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 111 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: A 199 MET cc_start: 0.5928 (tpt) cc_final: 0.4756 (tpt) REVERT: A 255 VAL cc_start: 0.8534 (m) cc_final: 0.8202 (p) REVERT: B 112 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.6910 (mp) REVERT: B 255 VAL cc_start: 0.8545 (m) cc_final: 0.8122 (p) outliers start: 30 outliers final: 16 residues processed: 135 average time/residue: 0.2274 time to fit residues: 38.4444 Evaluate side-chains 101 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 390 ASP 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: 9.9990 chunk 33 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 67 optimal weight: 0.4980 chunk 20 optimal weight: 20.0000 chunk 62 optimal weight: 0.0040 chunk 42 optimal weight: 20.0000 overall best weight: 4.0998 ------------------------------------------------------------------------------- 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: 0.6394 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6470 Z= 0.241 Angle : 0.738 7.658 8736 Z= 0.376 Chirality : 0.045 0.166 954 Planarity : 0.004 0.044 1104 Dihedral : 10.118 142.709 860 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 24.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.32 % Allowed : 16.16 % Favored : 80.51 % 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: -1.16 (0.29), residues: 782 helix: -0.37 (0.27), residues: 352 sheet: -1.48 (0.37), residues: 166 loop : -0.48 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 23 HIS 0.004 0.001 HIS B 248 PHE 0.018 0.002 PHE B 227 TYR 0.012 0.001 TYR B 391 ARG 0.002 0.001 ARG A 82 *********************** 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 123 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.8441 (pttm) cc_final: 0.8238 (pttm) outliers start: 22 outliers final: 17 residues processed: 117 average time/residue: 0.2254 time to fit residues: 33.7379 Evaluate side-chains 97 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 390 ASP 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: 0.9990 chunk 64 optimal weight: 10.0000 chunk 52 optimal weight: 30.0000 chunk 0 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 67 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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** B 133 HIS B 228 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.6332 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= 0.229 Angle : 0.718 7.041 8736 Z= 0.366 Chirality : 0.044 0.175 954 Planarity : 0.004 0.044 1104 Dihedral : 9.865 135.938 860 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.72 % Allowed : 16.92 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.69 (0.30), residues: 782 helix: 0.02 (0.27), residues: 360 sheet: -1.16 (0.37), residues: 164 loop : -0.32 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 23 HIS 0.003 0.001 HIS A 248 PHE 0.018 0.002 PHE B 227 TYR 0.009 0.001 TYR A 391 ARG 0.002 0.000 ARG A 82 *********************** 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 118 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 MET cc_start: 0.6507 (mmm) cc_final: 0.6290 (mpp) outliers start: 18 outliers final: 13 residues processed: 111 average time/residue: 0.2384 time to fit residues: 33.8691 Evaluate side-chains 98 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 390 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 30.0000 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 40.0000 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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** B 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.6563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6470 Z= 0.259 Angle : 0.721 7.622 8736 Z= 0.366 Chirality : 0.045 0.223 954 Planarity : 0.004 0.040 1104 Dihedral : 9.738 134.074 860 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 22.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.02 % Allowed : 17.82 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.51 (0.30), residues: 782 helix: 0.31 (0.27), residues: 360 sheet: -1.26 (0.36), residues: 170 loop : -0.30 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 23 HIS 0.004 0.001 HIS A 248 PHE 0.015 0.002 PHE B 227 TYR 0.012 0.001 TYR B 34 ARG 0.002 0.000 ARG A 82 *********************** 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 116 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 107 average time/residue: 0.1946 time to fit residues: 27.6027 Evaluate side-chains 96 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 390 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 75 optimal weight: 40.0000 chunk 47 optimal weight: 30.0000 chunk 45 optimal weight: 5.9990 chunk 34 optimal weight: 30.0000 chunk 46 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.6811 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= 0.244 Angle : 0.745 9.974 8736 Z= 0.376 Chirality : 0.046 0.225 954 Planarity : 0.003 0.031 1104 Dihedral : 9.564 132.508 860 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.72 % Allowed : 17.52 % Favored : 79.76 % 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: 0.57 (0.27), residues: 364 sheet: -1.14 (0.40), residues: 148 loop : -0.45 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 23 HIS 0.006 0.001 HIS A 248 PHE 0.014 0.002 PHE A 355 TYR 0.008 0.001 TYR B 34 ARG 0.008 0.001 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 116 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 107 average time/residue: 0.1999 time to fit residues: 28.1399 Evaluate side-chains 101 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 390 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 8.9990 chunk 47 optimal weight: 40.0000 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 59 optimal weight: 30.0000 chunk 68 optimal weight: 30.0000 chunk 72 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.7046 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= 0.262 Angle : 0.750 9.236 8736 Z= 0.376 Chirality : 0.045 0.255 954 Planarity : 0.004 0.056 1104 Dihedral : 9.460 131.059 860 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 24.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.57 % Allowed : 18.73 % Favored : 78.70 % 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: -0.23 (0.30), residues: 782 helix: 0.65 (0.27), residues: 370 sheet: -1.08 (0.39), residues: 148 loop : -0.51 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 23 HIS 0.006 0.001 HIS A 248 PHE 0.014 0.002 PHE A 227 TYR 0.027 0.002 TYR A 42 ARG 0.004 0.001 ARG B 249 *********************** 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 107 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 14 residues processed: 101 average time/residue: 0.2118 time to fit residues: 27.7469 Evaluate side-chains 96 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 390 ASP 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: 10.0000 chunk 21 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 chunk 45 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 overall best weight: 8.1994 ------------------------------------------------------------------------------- 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** B 68 ASN B 171 ASN B 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.7192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 6470 Z= 0.316 Angle : 0.782 10.848 8736 Z= 0.397 Chirality : 0.045 0.252 954 Planarity : 0.004 0.040 1104 Dihedral : 9.451 131.251 860 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 27.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.87 % Allowed : 20.39 % Favored : 76.74 % 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 (0.30), residues: 782 helix: 0.62 (0.27), residues: 370 sheet: -1.21 (0.39), residues: 148 loop : -0.54 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 23 HIS 0.013 0.002 HIS A 248 PHE 0.015 0.002 PHE A 227 TYR 0.023 0.002 TYR B 42 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 107 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 98 average time/residue: 0.1938 time to fit residues: 25.4101 Evaluate side-chains 100 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 390 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** B 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 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 : 0.004 0.052 6470 Z= 0.265 Angle : 0.784 9.773 8736 Z= 0.393 Chirality : 0.046 0.254 954 Planarity : 0.004 0.042 1104 Dihedral : 9.294 130.026 860 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 26.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.11 % Allowed : 21.30 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.30), residues: 782 helix: 0.65 (0.27), residues: 372 sheet: -1.27 (0.38), residues: 152 loop : -0.56 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 23 HIS 0.009 0.001 HIS A 248 PHE 0.017 0.002 PHE A 227 TYR 0.022 0.002 TYR B 42 ARG 0.003 0.000 ARG A 222 ********************** 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 99 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 254 MET cc_start: 0.6850 (mtp) cc_final: 0.6172 (mtm) outliers start: 14 outliers final: 14 residues processed: 93 average time/residue: 0.1828 time to fit residues: 22.7038 Evaluate side-chains 96 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 390 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 54 optimal weight: 0.2980 chunk 3 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 overall best weight: 5.4588 ------------------------------------------------------------------------------- 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** B 68 ASN B 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.059415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.048228 restraints weight = 33243.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.049895 restraints weight = 21830.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.051149 restraints weight = 15885.027| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.7507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6470 Z= 0.260 Angle : 0.777 9.705 8736 Z= 0.391 Chirality : 0.045 0.255 954 Planarity : 0.004 0.043 1104 Dihedral : 9.227 130.196 860 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 26.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.11 % Allowed : 22.05 % Favored : 75.83 % 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: -0.23 (0.30), residues: 782 helix: 0.65 (0.27), residues: 372 sheet: -1.03 (0.40), residues: 146 loop : -0.57 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 23 HIS 0.009 0.001 HIS A 248 PHE 0.016 0.002 PHE A 227 TYR 0.019 0.002 TYR A 42 ARG 0.005 0.001 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1635.85 seconds wall clock time: 31 minutes 7.05 seconds (1867.05 seconds total)