Starting phenix.real_space_refine (version: dev) on Thu Jun 2 18:18:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udb_26455/06_2022/7udb_26455.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udb_26455/06_2022/7udb_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_26455/06_2022/7udb_26455.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udb_26455/06_2022/7udb_26455.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udb_26455/06_2022/7udb_26455.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udb_26455/06_2022/7udb_26455.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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-4617/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: 4.31, per 1000 atoms: 0.67 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: 2.62 Conformation dependent library (CDL) restraints added in 1.0 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: 0.33 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: 1.86 Time building geometry restraints manager: 2.87 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 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. 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: 0.010 Normalize map: mean=0, sd=1: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 1.860 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.060 Process input model: 21.460 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 % 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 *********************** 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 : 0.812 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.1877 time to fit residues: 31.2252 Evaluate side-chains 97 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.865 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2011 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.0894 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= 0.262 Angle : 0.524 6.273 8828 Z= 0.277 Chirality : 0.040 0.140 1008 Planarity : 0.004 0.060 1132 Dihedral : 3.567 16.827 870 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.83 % 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: 1.90 (0.30), residues: 787 helix: 2.52 (0.24), residues: 461 sheet: -0.82 (0.66), residues: 56 loop : -0.53 (0.36), residues: 270 *********************** 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: 6 poor density : 103 time to evaluate : 0.912 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 105 average time/residue: 0.1820 time to fit residues: 26.1082 Evaluate side-chains 98 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0640 time to fit residues: 1.5712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 24 optimal weight: 0.0020 chunk 57 optimal weight: 4.9990 chunk 54 optimal weight: 0.1980 overall best weight: 1.2390 ------------------------------------------------------------------------------- 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: 0.8234 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 6563 Z= 0.239 Angle : 0.499 6.590 8828 Z= 0.263 Chirality : 0.039 0.143 1008 Planarity : 0.004 0.059 1132 Dihedral : 3.552 16.584 870 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.30), residues: 787 helix: 2.49 (0.24), residues: 468 sheet: -0.89 (0.65), residues: 56 loop : -0.68 (0.36), residues: 263 *********************** 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 103 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.898 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 102 average time/residue: 0.1688 time to fit residues: 23.8225 Evaluate side-chains 97 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0607 time to fit residues: 1.4827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.0030 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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: 0.8209 moved from start: 0.1135 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= 0.168 Angle : 0.462 6.499 8828 Z= 0.246 Chirality : 0.038 0.146 1008 Planarity : 0.004 0.059 1132 Dihedral : 3.437 15.671 870 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.30), residues: 787 helix: 2.57 (0.24), residues: 468 sheet: -0.95 (0.64), residues: 58 loop : -0.61 (0.36), residues: 261 *********************** 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 104 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.830 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 101 average time/residue: 0.1620 time to fit residues: 22.9961 Evaluate side-chains 94 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0615 time to fit residues: 1.3946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.0670 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.0170 chunk 44 optimal weight: 4.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- 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: 0.8254 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 6563 Z= 0.288 Angle : 0.516 6.164 8828 Z= 0.272 Chirality : 0.040 0.157 1008 Planarity : 0.004 0.058 1132 Dihedral : 3.567 16.533 870 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.14 % 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: 1.83 (0.30), residues: 787 helix: 2.48 (0.24), residues: 468 sheet: -1.10 (0.62), residues: 58 loop : -0.62 (0.36), residues: 261 *********************** 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 97 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.820 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 96 average time/residue: 0.1737 time to fit residues: 22.9316 Evaluate side-chains 93 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0598 time to fit residues: 1.2523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 73 optimal weight: 0.0870 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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: 0.8215 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 6563 Z= 0.172 Angle : 0.479 6.911 8828 Z= 0.254 Chirality : 0.038 0.150 1008 Planarity : 0.004 0.057 1132 Dihedral : 3.441 15.393 870 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.41 % 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: 2.00 (0.30), residues: 787 helix: 2.64 (0.24), residues: 463 sheet: -0.97 (0.63), residues: 58 loop : -0.55 (0.36), residues: 266 *********************** 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 97 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.894 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 97 average time/residue: 0.1827 time to fit residues: 24.5303 Evaluate side-chains 92 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.860 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0640 time to fit residues: 1.3158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.0470 chunk 64 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- 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: 0.8222 moved from start: 0.1367 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= 0.194 Angle : 0.498 9.776 8828 Z= 0.259 Chirality : 0.039 0.155 1008 Planarity : 0.004 0.058 1132 Dihedral : 3.434 15.230 870 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.69 % 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: 2.51 (0.24), residues: 469 sheet: -0.93 (0.64), residues: 58 loop : -0.58 (0.36), residues: 260 *********************** 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 97 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.844 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 95 average time/residue: 0.1649 time to fit residues: 21.9258 Evaluate side-chains 92 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 0.818 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0578 time to fit residues: 1.3136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 0.0060 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 42 optimal weight: 0.0970 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 6563 Z= 0.147 Angle : 0.484 10.324 8828 Z= 0.252 Chirality : 0.038 0.148 1008 Planarity : 0.004 0.059 1132 Dihedral : 3.340 14.277 870 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.30), residues: 787 helix: 2.59 (0.24), residues: 469 sheet: -0.62 (0.70), residues: 53 loop : -0.51 (0.36), residues: 265 *********************** 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 96 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.855 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1640 time to fit residues: 22.0169 Evaluate side-chains 91 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.807 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8223 moved from start: 0.1475 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= 0.217 Angle : 0.537 12.159 8828 Z= 0.273 Chirality : 0.039 0.149 1008 Planarity : 0.004 0.055 1132 Dihedral : 3.395 14.900 870 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.14 % 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: 1.96 (0.30), residues: 787 helix: 2.55 (0.24), residues: 469 sheet: -0.83 (0.63), residues: 58 loop : -0.55 (0.36), residues: 260 *********************** 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 92 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.828 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.1774 time to fit residues: 22.5555 Evaluate side-chains 89 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.864 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8215 moved from start: 0.1501 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= 0.193 Angle : 0.541 13.456 8828 Z= 0.274 Chirality : 0.039 0.150 1008 Planarity : 0.004 0.068 1132 Dihedral : 3.409 14.677 870 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.30), residues: 787 helix: 2.53 (0.24), residues: 469 sheet: -0.65 (0.69), residues: 53 loop : -0.53 (0.36), residues: 265 ********************** 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 92 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.760 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 91 average time/residue: 0.1849 time to fit residues: 22.8851 Evaluate side-chains 90 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.175445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.131357 restraints weight = 7467.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.131721 restraints weight = 6063.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.133942 restraints weight = 5851.734| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1525 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= 0.184 Angle : 0.520 11.685 8828 Z= 0.267 Chirality : 0.039 0.147 1008 Planarity : 0.004 0.058 1132 Dihedral : 3.399 14.367 870 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.30), residues: 787 helix: 2.55 (0.24), residues: 469 sheet: -0.62 (0.69), residues: 53 loop : -0.55 (0.36), residues: 265 =============================================================================== Job complete usr+sys time: 1316.12 seconds wall clock time: 24 minutes 45.05 seconds (1485.05 seconds total)