Starting phenix.real_space_refine on Sat Aug 23 22:30:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eup_19979/08_2025/9eup_19979_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eup_19979/08_2025/9eup_19979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eup_19979/08_2025/9eup_19979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eup_19979/08_2025/9eup_19979.map" model { file = "/net/cci-nas-00/data/ceres_data/9eup_19979/08_2025/9eup_19979_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eup_19979/08_2025/9eup_19979_trim.cif" } resolution = 3.0 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 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 4957 2.51 5 N 1213 2.21 5 O 1395 1.98 5 H 7364 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14966 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8423 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 23, 'TRANS': 508} Chain: "H" Number of atoms: 3279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3279 Classifications: {'peptide': 219} Link IDs: {'CIS': 3, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 204} Chain: "L" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3190 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 203} Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 74 Unusual residues: {' CL': 1, ' NA': 2, '144': 1, 'CLR': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 2.32, per 1000 atoms: 0.16 Number of scatterers: 14966 At special positions: 0 Unit cell: (77.64, 82.816, 152.692, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 34 16.00 Na 2 11.00 O 1395 8.00 N 1213 7.00 C 4957 6.00 H 7364 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.23 Conformation dependent library (CDL) restraints added in 292.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 12 sheets defined 49.3% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 removed outlier: 3.527A pdb=" N PHE A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 76 through 92 removed outlier: 3.599A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 107 through 138 removed outlier: 3.795A pdb=" N TYR A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR A 123 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 removed outlier: 4.049A pdb=" N SER A 147 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 219 Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 236 through 255 Processing helix chain 'A' and resid 257 through 269 removed outlier: 4.518A pdb=" N LYS A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TRP A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 4.167A pdb=" N ILE A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 298 removed outlier: 3.609A pdb=" N GLY A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.751A pdb=" N TRP A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 340 through 373 removed outlier: 3.550A pdb=" N ASP A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.599A pdb=" N VAL A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.708A pdb=" N VAL A 389 " --> pdb=" O GLY A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 398 Processing helix chain 'A' and resid 402 through 437 removed outlier: 4.083A pdb=" N ASP A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 442 Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 466 through 478 removed outlier: 3.690A pdb=" N PHE A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 516 through 541 removed outlier: 4.609A pdb=" N ALA A 527 " --> pdb=" O TRP A 523 " (cutoff:3.500A) Proline residue: A 528 - end of helix removed outlier: 3.725A pdb=" N GLY A 541 " --> pdb=" O TYR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 582 removed outlier: 3.869A pdb=" N MET A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE A 571 " --> pdb=" O SER A 567 " (cutoff:3.500A) Proline residue: A 572 - end of helix Processing helix chain 'A' and resid 585 through 595 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 101 through 105 removed outlier: 3.638A pdb=" N GLY H 105 " --> pdb=" O ARG H 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.937A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 Processing helix chain 'L' and resid 184 through 190 removed outlier: 3.822A pdb=" N HIS L 190 " --> pdb=" O GLU L 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 158 Processing sheet with id=AA2, first strand: chain 'A' and resid 546 through 547 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.950A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.023A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 128 through 130 removed outlier: 3.678A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N TYR H 181 " --> pdb=" O GLY H 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 128 through 130 removed outlier: 3.678A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N TYR H 181 " --> pdb=" O GLY H 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 157 through 160 Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.265A pdb=" N MET L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 116 through 119 removed outlier: 3.994A pdb=" N ASN L 139 " --> pdb=" O TYR L 174 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 154 through 156 removed outlier: 4.595A pdb=" N TRP L 149 " --> pdb=" O ARG L 156 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N TYR L 193 " --> pdb=" O LYS L 208 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LYS L 208 " --> pdb=" O TYR L 193 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS L 195 " --> pdb=" O ILE L 206 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE L 206 " --> pdb=" O CYS L 195 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ALA L 197 " --> pdb=" O SER L 204 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N SER L 204 " --> pdb=" O ALA L 197 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS L 199 " --> pdb=" O SER L 202 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7350 1.03 - 1.22: 44 1.22 - 1.42: 3407 1.42 - 1.61: 4331 1.61 - 1.81: 55 Bond restraints: 15187 Sorted by residual: bond pdb=" CAI Y01 A 701 " pdb=" CAZ Y01 A 701 " ideal model delta sigma weight residual 1.332 1.090 0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" CAI Y01 A 701 " pdb=" CAK Y01 A 701 " ideal model delta sigma weight residual 1.492 1.274 0.218 2.00e-02 2.50e+03 1.18e+02 bond pdb=" CAZ Y01 A 701 " pdb=" CBH Y01 A 701 " ideal model delta sigma weight residual 1.519 1.362 0.157 2.00e-02 2.50e+03 6.17e+01 bond pdb=" CAS Y01 A 701 " pdb=" CAU Y01 A 701 " ideal model delta sigma weight residual 1.530 1.685 -0.155 2.00e-02 2.50e+03 6.00e+01 bond pdb=" CBD Y01 A 701 " pdb=" CBG Y01 A 701 " ideal model delta sigma weight residual 1.520 1.380 0.140 2.00e-02 2.50e+03 4.92e+01 ... (remaining 15182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 27056 2.47 - 4.93: 186 4.93 - 7.40: 30 7.40 - 9.87: 4 9.87 - 12.33: 2 Bond angle restraints: 27278 Sorted by residual: angle pdb=" O ILE A 351 " pdb=" C ILE A 351 " pdb=" N ASN A 352 " ideal model delta sigma weight residual 121.87 116.23 5.64 9.70e-01 1.06e+00 3.39e+01 angle pdb=" CA PRO L 120 " pdb=" N PRO L 120 " pdb=" CD PRO L 120 " ideal model delta sigma weight residual 112.00 103.89 8.11 1.40e+00 5.10e-01 3.36e+01 angle pdb=" CA ILE A 351 " pdb=" C ILE A 351 " pdb=" N ASN A 352 " ideal model delta sigma weight residual 117.15 123.31 -6.16 1.14e+00 7.69e-01 2.92e+01 angle pdb=" C GLY H 135 " pdb=" N ASP H 136 " pdb=" CA ASP H 136 " ideal model delta sigma weight residual 121.70 129.99 -8.29 1.80e+00 3.09e-01 2.12e+01 angle pdb=" CA PRO H 129 " pdb=" N PRO H 129 " pdb=" CD PRO H 129 " ideal model delta sigma weight residual 112.00 106.24 5.76 1.40e+00 5.10e-01 1.69e+01 ... (remaining 27273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 6640 17.01 - 34.02: 501 34.02 - 51.02: 160 51.02 - 68.03: 69 68.03 - 85.04: 16 Dihedral angle restraints: 7386 sinusoidal: 3884 harmonic: 3502 Sorted by residual: dihedral pdb=" CA SER H 7 " pdb=" C SER H 7 " pdb=" N GLY H 8 " pdb=" CA GLY H 8 " ideal model delta harmonic sigma weight residual -180.00 -153.28 -26.72 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA VAL H 187 " pdb=" C VAL H 187 " pdb=" N THR H 188 " pdb=" CA THR H 188 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA THR A 146 " pdb=" C THR A 146 " pdb=" N SER A 147 " pdb=" CA SER A 147 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 7383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1076 0.083 - 0.167: 99 0.167 - 0.250: 5 0.250 - 0.334: 2 0.334 - 0.417: 2 Chirality restraints: 1184 Sorted by residual: chirality pdb=" CBF Y01 A 701 " pdb=" CAS Y01 A 701 " pdb=" CBD Y01 A 701 " pdb=" CBH Y01 A 701 " both_signs ideal model delta sigma weight residual False -2.45 -2.86 0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CBI Y01 A 701 " pdb=" CAU Y01 A 701 " pdb=" CBE Y01 A 701 " pdb=" CBG Y01 A 701 " both_signs ideal model delta sigma weight residual False 2.94 2.56 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CBE Y01 A 701 " pdb=" CAP Y01 A 701 " pdb=" CBB Y01 A 701 " pdb=" CBI Y01 A 701 " both_signs ideal model delta sigma weight residual False 2.57 2.86 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 1181 not shown) Planarity restraints: 2238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 352 " 0.120 2.00e-02 2.50e+03 1.17e-01 2.06e+02 pdb=" CG ASN A 352 " -0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN A 352 " -0.119 2.00e-02 2.50e+03 pdb=" ND2 ASN A 352 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 352 " 0.165 2.00e-02 2.50e+03 pdb="HD22 ASN A 352 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR H 128 " 0.074 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO H 129 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO H 129 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO H 129 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 72 " 0.293 9.50e-02 1.11e+02 9.88e-02 1.38e+01 pdb=" NE ARG H 72 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG H 72 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG H 72 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG H 72 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG H 72 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG H 72 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG H 72 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 72 " 0.001 2.00e-02 2.50e+03 ... (remaining 2235 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.12: 415 2.12 - 2.74: 27363 2.74 - 3.36: 43571 3.36 - 3.98: 58231 3.98 - 4.60: 90689 Nonbonded interactions: 220269 Sorted by model distance: nonbonded pdb=" O TYR H 32 " pdb="HH22 ARG H 72 " model vdw 1.505 2.450 nonbonded pdb=" HH TYR H 151 " pdb=" OE2 GLU H 154 " model vdw 1.629 2.450 nonbonded pdb=" OD1 ASP A 506 " pdb="HH12 ARG H 56 " model vdw 1.634 2.450 nonbonded pdb=" HE ARG A 52 " pdb=" OE1 GLU A 384 " model vdw 1.635 2.450 nonbonded pdb=" HH TYR A 498 " pdb=" OD2 ASP A 506 " model vdw 1.637 2.450 ... (remaining 220264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.180 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:5.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 : 0.010 0.242 7825 Z= 0.468 Angle : 0.824 12.331 10676 Z= 0.440 Chirality : 0.053 0.417 1184 Planarity : 0.009 0.132 1320 Dihedral : 13.766 85.039 2810 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.12 % Allowed : 6.91 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.25), residues: 959 helix: -1.32 (0.22), residues: 398 sheet: -0.53 (0.37), residues: 191 loop : -0.48 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.003 ARG H 72 TYR 0.020 0.003 TYR A 498 PHE 0.028 0.003 PHE A 357 TRP 0.030 0.003 TRP A 255 HIS 0.010 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.01038 ( 7823) covalent geometry : angle 0.82388 (10672) SS BOND : bond 0.00195 ( 2) SS BOND : angle 1.13378 ( 4) hydrogen bonds : bond 0.14440 ( 412) hydrogen bonds : angle 7.18102 ( 1191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 211 ASN cc_start: 0.7256 (m-40) cc_final: 0.6909 (t0) outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 1.0592 time to fit residues: 82.2268 Evaluate side-chains 63 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 352 ASN A 443 ASN H 170 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN L 146 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.138685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.098321 restraints weight = 25106.307| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.60 r_work: 0.2990 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7825 Z= 0.166 Angle : 0.587 6.806 10676 Z= 0.316 Chirality : 0.041 0.178 1184 Planarity : 0.005 0.052 1320 Dihedral : 5.661 47.426 1194 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.49 % Allowed : 8.63 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.27), residues: 959 helix: 0.01 (0.25), residues: 401 sheet: -0.37 (0.38), residues: 186 loop : -0.16 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 76 TYR 0.012 0.001 TYR A 498 PHE 0.025 0.002 PHE A 357 TRP 0.013 0.001 TRP A 255 HIS 0.009 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 7823) covalent geometry : angle 0.58735 (10672) SS BOND : bond 0.00060 ( 2) SS BOND : angle 0.59238 ( 4) hydrogen bonds : bond 0.04583 ( 412) hydrogen bonds : angle 5.41534 ( 1191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: L 2 ASN cc_start: 0.7737 (t0) cc_final: 0.7515 (t0) outliers start: 4 outliers final: 4 residues processed: 71 average time/residue: 1.1465 time to fit residues: 86.6415 Evaluate side-chains 63 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain H residue 162 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 37 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.138362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.098146 restraints weight = 25327.526| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.61 r_work: 0.2991 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7825 Z= 0.179 Angle : 0.554 6.322 10676 Z= 0.296 Chirality : 0.040 0.144 1184 Planarity : 0.005 0.047 1320 Dihedral : 5.316 45.428 1194 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.74 % Allowed : 9.74 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.27), residues: 959 helix: 0.35 (0.26), residues: 399 sheet: -0.29 (0.38), residues: 182 loop : -0.01 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 508 TYR 0.011 0.001 TYR A 537 PHE 0.021 0.002 PHE A 357 TRP 0.010 0.001 TRP A 255 HIS 0.007 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 7823) covalent geometry : angle 0.55419 (10672) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.60485 ( 4) hydrogen bonds : bond 0.04346 ( 412) hydrogen bonds : angle 5.10892 ( 1191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8166 (tp) cc_final: 0.7878 (tp) REVERT: H 104 ARG cc_start: 0.8120 (mtp-110) cc_final: 0.7810 (mtp180) REVERT: L 2 ASN cc_start: 0.7771 (t0) cc_final: 0.7548 (t0) REVERT: L 106 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7549 (mt-10) outliers start: 6 outliers final: 4 residues processed: 72 average time/residue: 1.2064 time to fit residues: 92.5591 Evaluate side-chains 66 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain H residue 162 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 46 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.138766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.098576 restraints weight = 25184.377| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.60 r_work: 0.2998 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7825 Z= 0.155 Angle : 0.525 6.591 10676 Z= 0.280 Chirality : 0.039 0.139 1184 Planarity : 0.004 0.037 1320 Dihedral : 5.070 45.525 1194 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.99 % Allowed : 10.23 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.27), residues: 959 helix: 0.52 (0.26), residues: 399 sheet: -0.04 (0.38), residues: 183 loop : -0.04 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 589 TYR 0.014 0.001 TYR A 455 PHE 0.017 0.001 PHE A 357 TRP 0.008 0.001 TRP A 255 HIS 0.006 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 7823) covalent geometry : angle 0.52460 (10672) SS BOND : bond 0.00124 ( 2) SS BOND : angle 0.67529 ( 4) hydrogen bonds : bond 0.04011 ( 412) hydrogen bonds : angle 4.85556 ( 1191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8163 (tp) cc_final: 0.7856 (tp) REVERT: H 104 ARG cc_start: 0.8094 (mtp-110) cc_final: 0.7745 (mtp180) REVERT: L 2 ASN cc_start: 0.7779 (t0) cc_final: 0.7560 (t0) REVERT: L 106 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7676 (mt-10) outliers start: 8 outliers final: 6 residues processed: 75 average time/residue: 1.1979 time to fit residues: 95.6965 Evaluate side-chains 70 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 33 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.139064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.098814 restraints weight = 25269.833| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.61 r_work: 0.3007 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7825 Z= 0.154 Angle : 0.522 6.096 10676 Z= 0.278 Chirality : 0.039 0.138 1184 Planarity : 0.005 0.080 1320 Dihedral : 4.993 51.246 1194 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.99 % Allowed : 10.73 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.27), residues: 959 helix: 0.66 (0.26), residues: 398 sheet: 0.05 (0.38), residues: 183 loop : -0.08 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 156 TYR 0.017 0.001 TYR A 455 PHE 0.015 0.001 PHE A 530 TRP 0.009 0.001 TRP A 255 HIS 0.005 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 7823) covalent geometry : angle 0.52207 (10672) SS BOND : bond 0.00077 ( 2) SS BOND : angle 0.59748 ( 4) hydrogen bonds : bond 0.03960 ( 412) hydrogen bonds : angle 4.79307 ( 1191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8366 (t0) REVERT: H 18 LEU cc_start: 0.8177 (tp) cc_final: 0.7926 (tp) REVERT: H 104 ARG cc_start: 0.8083 (mtp-110) cc_final: 0.7778 (mtp180) REVERT: L 2 ASN cc_start: 0.7780 (t0) cc_final: 0.7558 (t0) REVERT: L 106 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7732 (mt-10) outliers start: 8 outliers final: 6 residues processed: 73 average time/residue: 1.2067 time to fit residues: 93.9095 Evaluate side-chains 69 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.139055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.098848 restraints weight = 24979.131| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.59 r_work: 0.2994 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7825 Z= 0.158 Angle : 0.520 6.309 10676 Z= 0.277 Chirality : 0.039 0.139 1184 Planarity : 0.004 0.045 1320 Dihedral : 4.935 55.927 1194 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.86 % Allowed : 11.10 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.28), residues: 959 helix: 0.73 (0.26), residues: 398 sheet: 0.07 (0.38), residues: 183 loop : -0.12 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 156 TYR 0.009 0.001 TYR A 537 PHE 0.015 0.001 PHE A 530 TRP 0.009 0.001 TRP A 255 HIS 0.005 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7823) covalent geometry : angle 0.52044 (10672) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.57952 ( 4) hydrogen bonds : bond 0.03939 ( 412) hydrogen bonds : angle 4.73177 ( 1191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8110 (tp) cc_final: 0.7816 (tp) REVERT: H 104 ARG cc_start: 0.8049 (mtp-110) cc_final: 0.7722 (mtp180) REVERT: L 2 ASN cc_start: 0.7770 (t0) cc_final: 0.7549 (t0) REVERT: L 10 ILE cc_start: 0.8769 (mt) cc_final: 0.8536 (mt) REVERT: L 106 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7501 (mt-10) outliers start: 7 outliers final: 7 residues processed: 71 average time/residue: 1.2473 time to fit residues: 94.3489 Evaluate side-chains 68 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 8 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 13 optimal weight: 0.0570 chunk 77 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.139437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.099476 restraints weight = 24938.359| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.59 r_work: 0.3004 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7825 Z= 0.146 Angle : 0.515 5.870 10676 Z= 0.274 Chirality : 0.039 0.138 1184 Planarity : 0.005 0.057 1320 Dihedral : 4.851 57.767 1194 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.11 % Allowed : 10.97 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.28), residues: 959 helix: 0.82 (0.26), residues: 398 sheet: 0.16 (0.39), residues: 180 loop : -0.17 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 76 TYR 0.009 0.001 TYR A 537 PHE 0.016 0.001 PHE A 530 TRP 0.008 0.001 TRP A 255 HIS 0.005 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7823) covalent geometry : angle 0.51526 (10672) SS BOND : bond 0.00103 ( 2) SS BOND : angle 0.55446 ( 4) hydrogen bonds : bond 0.03847 ( 412) hydrogen bonds : angle 4.65180 ( 1191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8320 (t0) REVERT: H 18 LEU cc_start: 0.8106 (tp) cc_final: 0.7808 (tp) REVERT: H 217 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6808 (mm-30) REVERT: L 2 ASN cc_start: 0.7779 (t0) cc_final: 0.7560 (t0) REVERT: L 10 ILE cc_start: 0.8779 (mt) cc_final: 0.8556 (mt) REVERT: L 106 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7505 (mt-10) outliers start: 9 outliers final: 7 residues processed: 72 average time/residue: 1.2206 time to fit residues: 93.7159 Evaluate side-chains 69 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 74 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 0.0770 chunk 33 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.099777 restraints weight = 25163.641| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.60 r_work: 0.3010 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7825 Z= 0.142 Angle : 0.515 5.802 10676 Z= 0.273 Chirality : 0.039 0.138 1184 Planarity : 0.005 0.111 1320 Dihedral : 4.705 49.954 1194 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.36 % Allowed : 11.34 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.28), residues: 959 helix: 0.87 (0.26), residues: 398 sheet: 0.22 (0.39), residues: 180 loop : -0.13 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 156 TYR 0.009 0.001 TYR A 537 PHE 0.016 0.001 PHE A 530 TRP 0.008 0.001 TRP A 237 HIS 0.005 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7823) covalent geometry : angle 0.51466 (10672) SS BOND : bond 0.00121 ( 2) SS BOND : angle 0.59097 ( 4) hydrogen bonds : bond 0.03791 ( 412) hydrogen bonds : angle 4.60792 ( 1191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8316 (t0) REVERT: H 18 LEU cc_start: 0.8079 (tp) cc_final: 0.7780 (tp) REVERT: H 76 ARG cc_start: 0.7804 (mtt-85) cc_final: 0.7526 (mtt90) REVERT: L 2 ASN cc_start: 0.7791 (t0) cc_final: 0.7557 (t0) REVERT: L 10 ILE cc_start: 0.8809 (mt) cc_final: 0.8585 (mt) REVERT: L 106 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7521 (mt-10) outliers start: 11 outliers final: 10 residues processed: 71 average time/residue: 1.2202 time to fit residues: 92.5358 Evaluate side-chains 70 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 93 optimal weight: 9.9990 chunk 75 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.139586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.099613 restraints weight = 25243.432| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.59 r_work: 0.3005 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7825 Z= 0.152 Angle : 0.514 5.719 10676 Z= 0.273 Chirality : 0.039 0.138 1184 Planarity : 0.005 0.071 1320 Dihedral : 4.600 42.896 1194 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.36 % Allowed : 11.10 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.28), residues: 959 helix: 0.83 (0.26), residues: 400 sheet: 0.20 (0.39), residues: 183 loop : -0.20 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 156 TYR 0.022 0.001 TYR A 455 PHE 0.016 0.001 PHE A 530 TRP 0.009 0.001 TRP A 255 HIS 0.004 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7823) covalent geometry : angle 0.51442 (10672) SS BOND : bond 0.00133 ( 2) SS BOND : angle 0.62101 ( 4) hydrogen bonds : bond 0.03837 ( 412) hydrogen bonds : angle 4.58843 ( 1191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8352 (t0) REVERT: H 18 LEU cc_start: 0.8112 (tp) cc_final: 0.7801 (tp) REVERT: H 76 ARG cc_start: 0.7866 (mtt-85) cc_final: 0.7590 (mtt90) REVERT: L 2 ASN cc_start: 0.7829 (t0) cc_final: 0.7592 (t0) REVERT: L 10 ILE cc_start: 0.8825 (mt) cc_final: 0.8607 (mt) REVERT: L 106 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7539 (mt-10) REVERT: L 170 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8178 (ttmt) outliers start: 11 outliers final: 9 residues processed: 74 average time/residue: 1.2359 time to fit residues: 97.5321 Evaluate side-chains 72 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.139879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.099885 restraints weight = 25209.737| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.61 r_work: 0.3031 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7825 Z= 0.146 Angle : 0.513 5.888 10676 Z= 0.272 Chirality : 0.039 0.138 1184 Planarity : 0.005 0.083 1320 Dihedral : 4.496 38.276 1194 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.36 % Allowed : 11.34 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.28), residues: 959 helix: 0.89 (0.26), residues: 400 sheet: 0.24 (0.39), residues: 183 loop : -0.16 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 156 TYR 0.008 0.001 TYR A 342 PHE 0.016 0.001 PHE A 530 TRP 0.008 0.001 TRP A 237 HIS 0.005 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7823) covalent geometry : angle 0.51287 (10672) SS BOND : bond 0.00133 ( 2) SS BOND : angle 0.61806 ( 4) hydrogen bonds : bond 0.03783 ( 412) hydrogen bonds : angle 4.55486 ( 1191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8315 (t0) REVERT: H 18 LEU cc_start: 0.8158 (tp) cc_final: 0.7922 (tp) REVERT: H 76 ARG cc_start: 0.7806 (mtt-85) cc_final: 0.7546 (mtt90) REVERT: L 2 ASN cc_start: 0.7825 (t0) cc_final: 0.7598 (t0) REVERT: L 10 ILE cc_start: 0.8836 (mt) cc_final: 0.8614 (mt) REVERT: L 106 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7555 (mt-10) REVERT: L 170 LYS cc_start: 0.8549 (ttpp) cc_final: 0.8168 (ttmt) REVERT: L 176 MET cc_start: 0.7449 (ttt) cc_final: 0.6606 (tpt) outliers start: 11 outliers final: 9 residues processed: 72 average time/residue: 1.0009 time to fit residues: 77.8312 Evaluate side-chains 71 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 64 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.140385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.100456 restraints weight = 24950.895| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.59 r_work: 0.3021 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7825 Z= 0.136 Angle : 0.504 5.231 10676 Z= 0.267 Chirality : 0.039 0.138 1184 Planarity : 0.005 0.073 1320 Dihedral : 4.399 37.179 1194 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.23 % Allowed : 11.47 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.28), residues: 959 helix: 0.93 (0.26), residues: 400 sheet: 0.28 (0.40), residues: 183 loop : -0.14 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 156 TYR 0.008 0.001 TYR A 342 PHE 0.016 0.001 PHE A 530 TRP 0.009 0.001 TRP A 237 HIS 0.005 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7823) covalent geometry : angle 0.50435 (10672) SS BOND : bond 0.00145 ( 2) SS BOND : angle 0.61954 ( 4) hydrogen bonds : bond 0.03717 ( 412) hydrogen bonds : angle 4.52285 ( 1191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4517.55 seconds wall clock time: 77 minutes 26.97 seconds (4646.97 seconds total)