Starting phenix.real_space_refine on Thu Feb 15 05:07:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udb_26455/02_2024/7udb_26455.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udb_26455/02_2024/7udb_26455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udb_26455/02_2024/7udb_26455.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udb_26455/02_2024/7udb_26455.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udb_26455/02_2024/7udb_26455.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udb_26455/02_2024/7udb_26455.pdb" } resolution = 3.5 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= 0.013 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 4776 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 4064 2.51 5 N 1114 2.21 5 O 1259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 197": "OD1" <-> "OD2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 231": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6472 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4424 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 27, 'TRANS': 523} Chain breaks: 3 Chain: "B" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1675 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 205} Chain breaks: 4 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 373 Classifications: {'peptide': 48} Link IDs: {'TRANS': 47} Time building chain proxies: 3.92, per 1000 atoms: 0.61 Number of scatterers: 6472 At special positions: 0 Unit cell: (92.88, 112.32, 89.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1259 8.00 N 1114 7.00 C 4064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS C 36 " distance=2.03 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 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 65.3% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 5 through 20 Processing helix chain 'A' and resid 34 through 45 removed outlier: 3.789A pdb=" N CYS A 44 " --> pdb=" O MET A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.743A pdb=" N ILE A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 91 removed outlier: 4.108A pdb=" N PHE A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 Proline residue: A 95 - end of helix No H-bonds generated for 'chain 'A' and resid 92 through 97' Processing helix chain 'A' and resid 111 through 121 Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.199A pdb=" N VAL A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 151 through 157 removed outlier: 3.927A pdb=" N SER A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 162 removed outlier: 3.792A pdb=" N ALA A 162 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 184 removed outlier: 3.606A pdb=" N ILE A 168 " --> pdb=" O MET A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 216 removed outlier: 3.934A pdb=" N LEU A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 removed outlier: 3.528A pdb=" N LEU A 244 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 295 through 314 Processing helix chain 'A' and resid 327 through 359 Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 361 through 375 Processing helix chain 'A' and resid 385 through 395 removed outlier: 3.959A pdb=" N ALA A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 415 removed outlier: 3.743A pdb=" N ILE A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 431 Processing helix chain 'A' and resid 434 through 436 No H-bonds generated for 'chain 'A' and resid 434 through 436' Processing helix chain 'A' and resid 437 through 443 removed outlier: 3.765A pdb=" N THR A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 447 Processing helix chain 'A' and resid 480 through 491 removed outlier: 3.909A pdb=" N ASP A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 561 removed outlier: 4.034A pdb=" N ARG A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 584 removed outlier: 3.675A pdb=" N LEU A 579 " --> pdb=" O PRO A 575 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 12 Processing helix chain 'B' and resid 30 through 64 removed outlier: 3.565A pdb=" N SER B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 105 removed outlier: 3.566A pdb=" N GLU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 149 Processing helix chain 'B' and resid 163 through 169 Processing helix chain 'B' and resid 178 through 196 removed outlier: 3.520A pdb=" N ILE B 187 " --> pdb=" O MET B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 223 removed outlier: 3.994A pdb=" N ASP B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N MET B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 38 through 74 removed outlier: 4.129A pdb=" N VAL C 42 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 60 " --> pdb=" O ARG C 56 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SER C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 60 removed outlier: 7.033A pdb=" N LYS A 29 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLU A 59 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A 31 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL A 30 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU A 76 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL A 32 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA A 73 " --> pdb=" O HIS A 103 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE A 105 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR A 75 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ALA A 102 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 130 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A 104 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU A 132 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE A 106 " --> pdb=" O GLU A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 6.696A pdb=" N TYR A 145 " --> pdb=" O SER A 569 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 266 Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 546 removed outlier: 6.267A pdb=" N VAL A 545 " --> pdb=" O LEU A 573 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 367 hydrogen bonds defined for protein. 1077 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: 1.82 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2162 1.34 - 1.46: 1266 1.46 - 1.58: 3074 1.58 - 1.70: 0 1.70 - 1.81: 61 Bond restraints: 6563 Sorted by residual: bond pdb=" CB ASP B 140 " pdb=" CG ASP B 140 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.10e+00 bond pdb=" CB ASP B 27 " pdb=" CG ASP B 27 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.08e+00 bond pdb=" CA ASP B 27 " pdb=" CB ASP B 27 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 8.13e-01 bond pdb=" CA THR A 455 " pdb=" CB THR A 455 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.43e-01 bond pdb=" CA VAL A 391 " pdb=" C VAL A 391 " ideal model delta sigma weight residual 1.520 1.527 -0.007 8.80e-03 1.29e+04 6.40e-01 ... (remaining 6558 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.83: 121 105.83 - 112.85: 3620 112.85 - 119.88: 2186 119.88 - 126.91: 2849 126.91 - 133.94: 52 Bond angle restraints: 8828 Sorted by residual: angle pdb=" N GLY B 227 " pdb=" CA GLY B 227 " pdb=" C GLY B 227 " ideal model delta sigma weight residual 110.63 115.64 -5.01 1.45e+00 4.76e-01 1.19e+01 angle pdb=" C SER A 454 " pdb=" N THR A 455 " pdb=" CA THR A 455 " ideal model delta sigma weight residual 121.54 126.05 -4.51 1.91e+00 2.74e-01 5.57e+00 angle pdb=" CB MET B 219 " pdb=" CG MET B 219 " pdb=" SD MET B 219 " ideal model delta sigma weight residual 112.70 105.75 6.95 3.00e+00 1.11e-01 5.36e+00 angle pdb=" C ARG A 275 " pdb=" N VAL A 276 " pdb=" CA VAL A 276 " ideal model delta sigma weight residual 121.97 126.12 -4.15 1.80e+00 3.09e-01 5.32e+00 angle pdb=" CA ASP B 27 " pdb=" CB ASP B 27 " pdb=" CG ASP B 27 " ideal model delta sigma weight residual 112.60 114.64 -2.04 1.00e+00 1.00e+00 4.18e+00 ... (remaining 8823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3629 17.96 - 35.92: 390 35.92 - 53.89: 85 53.89 - 71.85: 10 71.85 - 89.81: 13 Dihedral angle restraints: 4127 sinusoidal: 1738 harmonic: 2389 Sorted by residual: dihedral pdb=" CB CYS B 205 " pdb=" SG CYS B 205 " pdb=" SG CYS C 36 " pdb=" CB CYS C 36 " ideal model delta sinusoidal sigma weight residual -86.00 -162.62 76.62 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB GLU A 12 " pdb=" CG GLU A 12 " pdb=" CD GLU A 12 " pdb=" OE1 GLU A 12 " ideal model delta sinusoidal sigma weight residual 0.00 89.81 -89.81 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA LEU A 573 " pdb=" C LEU A 573 " pdb=" N THR A 574 " pdb=" CA THR A 574 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 4124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 670 0.030 - 0.060: 215 0.060 - 0.090: 85 0.090 - 0.120: 34 0.120 - 0.150: 4 Chirality restraints: 1008 Sorted by residual: chirality pdb=" CB VAL A 451 " pdb=" CA VAL A 451 " pdb=" CG1 VAL A 451 " pdb=" CG2 VAL A 451 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ASP B 27 " pdb=" N ASP B 27 " pdb=" C ASP B 27 " pdb=" CB ASP B 27 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE A 135 " pdb=" N ILE A 135 " pdb=" C ILE A 135 " pdb=" CB ILE A 135 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 1005 not shown) Planarity restraints: 1132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 16 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.37e+00 pdb=" C HIS A 16 " 0.044 2.00e-02 2.50e+03 pdb=" O HIS A 16 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP A 17 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 58 " -0.016 2.00e-02 2.50e+03 1.84e-02 5.09e+00 pdb=" CG HIS B 58 " 0.039 2.00e-02 2.50e+03 pdb=" ND1 HIS B 58 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS B 58 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 HIS B 58 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS B 58 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 94 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO A 95 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.032 5.00e-02 4.00e+02 ... (remaining 1129 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 257 2.73 - 3.27: 6529 3.27 - 3.81: 10336 3.81 - 4.36: 11980 4.36 - 4.90: 21091 Nonbonded interactions: 50193 Sorted by model distance: nonbonded pdb=" O ILE A 541 " pdb=" OG SER A 569 " model vdw 2.182 2.440 nonbonded pdb=" OH TYR A 75 " pdb=" OD2 ASP A 90 " model vdw 2.223 2.440 nonbonded pdb=" OH TYR A 186 " pdb=" OD1 ASP A 210 " model vdw 2.243 2.440 nonbonded pdb=" OH TYR A 264 " pdb=" OD2 ASP A 353 " model vdw 2.269 2.440 nonbonded pdb=" OH TYR A 358 " pdb=" OD1 ASP A 363 " model vdw 2.288 2.440 ... (remaining 50188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.360 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: 1.600 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 20.950 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.003 0.027 6563 Z= 0.165 Angle : 0.499 6.947 8828 Z= 0.269 Chirality : 0.038 0.150 1008 Planarity : 0.004 0.056 1132 Dihedral : 15.554 89.809 2558 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.72 % 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: 1.74 (0.30), residues: 787 helix: 2.32 (0.24), residues: 462 sheet: -0.28 (0.71), residues: 56 loop : -0.61 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 563 HIS 0.022 0.001 HIS B 58 PHE 0.012 0.001 PHE A 237 TYR 0.021 0.001 TYR B 141 ARG 0.006 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.942 Fit side-chains REVERT: B 30 MET cc_start: 0.6985 (mtt) cc_final: 0.6483 (mtt) REVERT: B 224 GLU cc_start: 0.7041 (tt0) cc_final: 0.6762 (mm-30) REVERT: C 71 GLN cc_start: 0.7914 (tt0) cc_final: 0.7662 (tt0) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.1873 time to fit residues: 31.0607 Evaluate side-chains 98 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6563 Z= 0.260 Angle : 0.518 6.016 8828 Z= 0.274 Chirality : 0.040 0.141 1008 Planarity : 0.004 0.060 1132 Dihedral : 3.566 16.825 870 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.97 % Allowed : 7.32 % Favored : 91.71 % 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: 1.80 (0.30), residues: 787 helix: 2.43 (0.24), residues: 467 sheet: -0.82 (0.66), residues: 56 loop : -0.63 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 478 HIS 0.005 0.001 HIS A 347 PHE 0.010 0.001 PHE B 216 TYR 0.010 0.001 TYR B 141 ARG 0.004 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 0.747 Fit side-chains REVERT: B 138 GLN cc_start: 0.8771 (mm110) cc_final: 0.8553 (mm-40) outliers start: 7 outliers final: 4 residues processed: 104 average time/residue: 0.1761 time to fit residues: 24.9580 Evaluate side-chains 99 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 80 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 64 optimal weight: 0.0670 chunk 24 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 54 optimal weight: 0.0170 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6563 Z= 0.154 Angle : 0.459 6.675 8828 Z= 0.243 Chirality : 0.038 0.139 1008 Planarity : 0.004 0.060 1132 Dihedral : 3.402 15.292 870 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.69 % Allowed : 8.70 % Favored : 90.61 % 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: 2.06 (0.30), residues: 787 helix: 2.67 (0.24), residues: 462 sheet: -0.75 (0.66), residues: 56 loop : -0.52 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 478 HIS 0.003 0.001 HIS B 58 PHE 0.007 0.001 PHE A 310 TYR 0.016 0.001 TYR B 141 ARG 0.004 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 0.795 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 105 average time/residue: 0.1678 time to fit residues: 24.3696 Evaluate side-chains 95 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 39 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.0170 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6563 Z= 0.169 Angle : 0.463 5.839 8828 Z= 0.245 Chirality : 0.038 0.143 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.340 14.809 870 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.08 % Rotamer: Outliers : 0.83 % Allowed : 10.64 % Favored : 88.54 % 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: 2.12 (0.30), residues: 787 helix: 2.71 (0.24), residues: 462 sheet: -0.87 (0.64), residues: 58 loop : -0.43 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 478 HIS 0.007 0.001 HIS B 58 PHE 0.006 0.001 PHE A 310 TYR 0.012 0.001 TYR B 141 ARG 0.003 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.797 Fit side-chains REVERT: B 98 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7911 (mt0) outliers start: 6 outliers final: 4 residues processed: 99 average time/residue: 0.1615 time to fit residues: 22.3572 Evaluate side-chains 97 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 80 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6563 Z= 0.332 Angle : 0.537 6.122 8828 Z= 0.283 Chirality : 0.041 0.159 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.588 16.535 870 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.24 % Allowed : 12.43 % Favored : 86.33 % 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: 1.92 (0.30), residues: 787 helix: 2.58 (0.24), residues: 462 sheet: -1.04 (0.62), residues: 58 loop : -0.55 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 478 HIS 0.007 0.001 HIS A 347 PHE 0.007 0.001 PHE B 216 TYR 0.010 0.001 TYR A 501 ARG 0.004 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.802 Fit side-chains REVERT: B 98 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7971 (mt0) outliers start: 9 outliers final: 7 residues processed: 96 average time/residue: 0.1776 time to fit residues: 23.3364 Evaluate side-chains 97 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 80 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6563 Z= 0.266 Angle : 0.528 10.734 8828 Z= 0.273 Chirality : 0.040 0.153 1008 Planarity : 0.004 0.062 1132 Dihedral : 3.598 16.394 870 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.24 % Allowed : 13.81 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.30), residues: 787 helix: 2.55 (0.24), residues: 462 sheet: -1.03 (0.61), residues: 58 loop : -0.55 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 478 HIS 0.006 0.001 HIS A 347 PHE 0.005 0.001 PHE B 216 TYR 0.014 0.001 TYR B 141 ARG 0.003 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.778 Fit side-chains REVERT: B 98 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7930 (mt0) outliers start: 9 outliers final: 6 residues processed: 100 average time/residue: 0.1704 time to fit residues: 23.4691 Evaluate side-chains 99 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 80 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.0060 chunk 64 optimal weight: 7.9990 chunk 42 optimal weight: 0.1980 chunk 76 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6563 Z= 0.146 Angle : 0.466 6.241 8828 Z= 0.246 Chirality : 0.038 0.153 1008 Planarity : 0.004 0.062 1132 Dihedral : 3.404 14.886 870 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.07 % Allowed : 12.71 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.31), residues: 787 helix: 2.68 (0.24), residues: 462 sheet: -0.65 (0.69), residues: 53 loop : -0.48 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 478 HIS 0.004 0.001 HIS B 58 PHE 0.005 0.001 PHE A 137 TYR 0.021 0.001 TYR B 141 ARG 0.002 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.784 Fit side-chains REVERT: B 98 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: B 239 HIS cc_start: 0.7921 (m170) cc_final: 0.7714 (m170) outliers start: 15 outliers final: 8 residues processed: 106 average time/residue: 0.1578 time to fit residues: 23.4945 Evaluate side-chains 104 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 80 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 51 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6563 Z= 0.179 Angle : 0.496 7.490 8828 Z= 0.262 Chirality : 0.039 0.152 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.380 14.474 870 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.24 % Allowed : 14.78 % Favored : 83.98 % 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: 2.07 (0.30), residues: 787 helix: 2.64 (0.24), residues: 463 sheet: -0.60 (0.69), residues: 53 loop : -0.48 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 478 HIS 0.009 0.001 HIS B 213 PHE 0.007 0.001 PHE A 310 TYR 0.020 0.001 TYR B 141 ARG 0.002 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.772 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 102 average time/residue: 0.1660 time to fit residues: 23.5107 Evaluate side-chains 99 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 80 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 75 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6563 Z= 0.194 Angle : 0.499 8.249 8828 Z= 0.263 Chirality : 0.039 0.148 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.400 14.561 870 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.24 % Allowed : 14.64 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.30), residues: 787 helix: 2.62 (0.24), residues: 463 sheet: -0.77 (0.63), residues: 58 loop : -0.50 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 478 HIS 0.006 0.001 HIS B 213 PHE 0.005 0.001 PHE B 29 TYR 0.019 0.001 TYR B 141 ARG 0.002 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.768 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 102 average time/residue: 0.1715 time to fit residues: 24.1413 Evaluate side-chains 99 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 80 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 38 optimal weight: 0.0470 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6563 Z= 0.169 Angle : 0.521 14.553 8828 Z= 0.270 Chirality : 0.038 0.147 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.380 14.322 870 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.10 % Allowed : 15.19 % Favored : 83.70 % 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: 2.13 (0.30), residues: 787 helix: 2.66 (0.24), residues: 463 sheet: -0.55 (0.69), residues: 53 loop : -0.41 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 28 HIS 0.005 0.001 HIS B 213 PHE 0.006 0.001 PHE B 216 TYR 0.019 0.001 TYR B 141 ARG 0.002 0.000 ARG A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.718 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 97 average time/residue: 0.1617 time to fit residues: 21.8624 Evaluate side-chains 98 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 80 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.175042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.131408 restraints weight = 7515.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.131955 restraints weight = 6464.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.134459 restraints weight = 5832.449| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6563 Z= 0.195 Angle : 0.528 16.080 8828 Z= 0.271 Chirality : 0.039 0.149 1008 Planarity : 0.004 0.061 1132 Dihedral : 3.384 14.401 870 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.38 % Allowed : 14.78 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.30), residues: 787 helix: 2.66 (0.24), residues: 463 sheet: -0.56 (0.69), residues: 53 loop : -0.41 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 478 HIS 0.005 0.001 HIS B 213 PHE 0.006 0.001 PHE B 216 TYR 0.019 0.001 TYR B 141 ARG 0.002 0.000 ARG A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1417.98 seconds wall clock time: 26 minutes 35.72 seconds (1595.72 seconds total)