Starting phenix.real_space_refine on Fri Jun 13 14:45:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eup_19979/06_2025/9eup_19979_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eup_19979/06_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_19979/06_2025/9eup_19979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eup_19979/06_2025/9eup_19979.map" model { file = "/net/cci-nas-00/data/ceres_data/9eup_19979/06_2025/9eup_19979_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eup_19979/06_2025/9eup_19979_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.83, per 1000 atoms: 0.52 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: 4.18 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.37 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: 5.76 Time building geometry restraints manager: 4.89 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: 1.220 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: 0.270 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.510 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.460 ------------------------------------------------------------------------------- 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 (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: -1.46 (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 TRP 0.030 0.003 TRP A 255 HIS 0.010 0.002 HIS A 90 PHE 0.028 0.003 PHE A 357 TYR 0.020 0.003 TYR A 498 ARG 0.031 0.003 ARG H 72 Details of bonding type rmsd hydrogen bonds : bond 0.14440 ( 412) hydrogen bonds : angle 7.18102 ( 1191) SS BOND : bond 0.00195 ( 2) SS BOND : angle 1.13378 ( 4) covalent geometry : bond 0.01038 ( 7823) covalent geometry : angle 0.82388 (10672) *********************** 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 : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 211 ASN cc_start: 0.7256 (m-40) cc_final: 0.6559 (t0) outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 2.4150 time to fit residues: 188.2825 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 : 1.212 ------------------------------------------------------------------------------- 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 80 optimal weight: 0.0050 chunk 72 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.139452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.099039 restraints weight = 24986.915| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.61 r_work: 0.3003 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7825 Z= 0.140 Angle : 0.577 6.530 10676 Z= 0.310 Chirality : 0.041 0.187 1184 Planarity : 0.005 0.055 1320 Dihedral : 5.688 48.797 1194 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.37 % Allowed : 8.38 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.27), residues: 959 helix: 0.03 (0.25), residues: 401 sheet: -0.36 (0.38), residues: 186 loop : -0.12 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 255 HIS 0.009 0.001 HIS A 90 PHE 0.025 0.002 PHE A 357 TYR 0.010 0.001 TYR L 95 ARG 0.004 0.001 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 412) hydrogen bonds : angle 5.43131 ( 1191) SS BOND : bond 0.00093 ( 2) SS BOND : angle 0.54200 ( 4) covalent geometry : bond 0.00308 ( 7823) covalent geometry : angle 0.57712 (10672) *********************** 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 74 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 73 average time/residue: 2.4594 time to fit residues: 191.3691 Evaluate side-chains 63 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 352 ASN 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 78 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 0.0970 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 L 2 ASN L 6 GLN L 146 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.139490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.099334 restraints weight = 25065.388| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.59 r_work: 0.3003 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1326 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= 0.153 Angle : 0.541 6.190 10676 Z= 0.289 Chirality : 0.039 0.144 1184 Planarity : 0.005 0.049 1320 Dihedral : 5.303 48.387 1194 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.62 % Allowed : 9.62 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.27), residues: 959 helix: 0.46 (0.26), residues: 399 sheet: -0.28 (0.38), residues: 182 loop : 0.07 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.006 0.001 HIS A 90 PHE 0.022 0.002 PHE A 357 TYR 0.010 0.001 TYR A 537 ARG 0.003 0.000 ARG A 508 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 412) hydrogen bonds : angle 5.04967 ( 1191) SS BOND : bond 0.00178 ( 2) SS BOND : angle 0.66684 ( 4) covalent geometry : bond 0.00351 ( 7823) covalent geometry : angle 0.54139 (10672) *********************** 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 76 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8139 (tp) cc_final: 0.7854 (tp) REVERT: H 104 ARG cc_start: 0.8119 (mtp-110) cc_final: 0.7849 (mtp180) REVERT: L 106 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7573 (mt-10) outliers start: 5 outliers final: 4 residues processed: 74 average time/residue: 2.6294 time to fit residues: 206.4524 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 : 1.177 ------------------------------------------------------------------------------- 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 73 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 86 optimal weight: 0.0070 chunk 21 optimal weight: 0.8980 chunk 75 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.141095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.100941 restraints weight = 24927.741| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.60 r_work: 0.3029 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7825 Z= 0.107 Angle : 0.499 5.281 10676 Z= 0.265 Chirality : 0.038 0.138 1184 Planarity : 0.004 0.038 1320 Dihedral : 5.009 47.703 1194 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.74 % Allowed : 9.99 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.27), residues: 959 helix: 0.72 (0.26), residues: 399 sheet: 0.01 (0.38), residues: 183 loop : 0.12 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 237 HIS 0.006 0.001 HIS A 90 PHE 0.018 0.001 PHE A 357 TYR 0.009 0.001 TYR A 455 ARG 0.002 0.000 ARG A 589 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 412) hydrogen bonds : angle 4.72988 ( 1191) SS BOND : bond 0.00145 ( 2) SS BOND : angle 0.54410 ( 4) covalent geometry : bond 0.00233 ( 7823) covalent geometry : angle 0.49885 (10672) *********************** 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: 6 poor density : 72 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8119 (tp) cc_final: 0.7885 (tp) REVERT: H 104 ARG cc_start: 0.8068 (mtp-110) cc_final: 0.7730 (mtp180) REVERT: L 10 ILE cc_start: 0.8758 (mt) cc_final: 0.8523 (mt) REVERT: L 106 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7563 (mt-10) outliers start: 6 outliers final: 4 residues processed: 77 average time/residue: 2.2721 time to fit residues: 187.3702 Evaluate side-chains 69 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 L residue 70 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 93 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.139160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.098806 restraints weight = 25215.064| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.62 r_work: 0.2997 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7825 Z= 0.178 Angle : 0.530 6.785 10676 Z= 0.282 Chirality : 0.039 0.138 1184 Planarity : 0.005 0.075 1320 Dihedral : 5.022 47.047 1194 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.74 % Allowed : 10.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.28), residues: 959 helix: 0.77 (0.26), residues: 398 sheet: 0.08 (0.38), residues: 183 loop : 0.01 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 255 HIS 0.006 0.001 HIS A 90 PHE 0.015 0.002 PHE A 530 TYR 0.015 0.001 TYR A 455 ARG 0.012 0.001 ARG L 156 Details of bonding type rmsd hydrogen bonds : bond 0.04033 ( 412) hydrogen bonds : angle 4.78279 ( 1191) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.65602 ( 4) covalent geometry : bond 0.00417 ( 7823) covalent geometry : angle 0.52954 (10672) *********************** 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 70 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8160 (tp) cc_final: 0.7864 (tp) REVERT: H 104 ARG cc_start: 0.8057 (mtp-110) cc_final: 0.7729 (mtp180) REVERT: L 10 ILE cc_start: 0.8760 (mt) cc_final: 0.8518 (mt) REVERT: L 106 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7447 (mt-10) outliers start: 6 outliers final: 5 residues processed: 68 average time/residue: 2.4658 time to fit residues: 180.0012 Evaluate side-chains 68 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 L residue 34 LEU 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 3 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.139808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.099436 restraints weight = 25046.753| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.61 r_work: 0.3007 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1806 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= 0.147 Angle : 0.515 6.059 10676 Z= 0.273 Chirality : 0.039 0.138 1184 Planarity : 0.005 0.056 1320 Dihedral : 4.889 51.413 1194 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.99 % Allowed : 10.48 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.28), residues: 959 helix: 0.86 (0.26), residues: 398 sheet: 0.17 (0.39), residues: 183 loop : -0.03 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.006 0.001 HIS A 90 PHE 0.016 0.001 PHE A 530 TYR 0.019 0.001 TYR A 455 ARG 0.009 0.001 ARG L 156 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 412) hydrogen bonds : angle 4.64258 ( 1191) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.63841 ( 4) covalent geometry : bond 0.00338 ( 7823) covalent geometry : angle 0.51449 (10672) *********************** 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 75 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7122 (mt0) REVERT: H 18 LEU cc_start: 0.8167 (tp) cc_final: 0.7893 (tp) REVERT: H 104 ARG cc_start: 0.8049 (mtp-110) cc_final: 0.7724 (mtp180) REVERT: L 10 ILE cc_start: 0.8758 (mt) cc_final: 0.8533 (mt) REVERT: L 106 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7500 (mt-10) outliers start: 8 outliers final: 7 residues processed: 73 average time/residue: 2.5227 time to fit residues: 197.3565 Evaluate side-chains 67 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 46 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.140020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.099889 restraints weight = 25209.715| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.60 r_work: 0.3020 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1870 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= 0.148 Angle : 0.514 5.872 10676 Z= 0.273 Chirality : 0.039 0.138 1184 Planarity : 0.005 0.055 1320 Dihedral : 4.851 56.908 1194 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.86 % Allowed : 11.34 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.28), residues: 959 helix: 0.91 (0.26), residues: 398 sheet: 0.19 (0.39), residues: 183 loop : -0.06 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.005 0.001 HIS A 90 PHE 0.016 0.001 PHE A 530 TYR 0.009 0.001 TYR A 537 ARG 0.007 0.000 ARG L 156 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 412) hydrogen bonds : angle 4.60141 ( 1191) SS BOND : bond 0.00125 ( 2) SS BOND : angle 0.63673 ( 4) covalent geometry : bond 0.00343 ( 7823) covalent geometry : angle 0.51362 (10672) *********************** 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 69 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7146 (mt0) REVERT: H 18 LEU cc_start: 0.8125 (tp) cc_final: 0.7798 (tp) REVERT: H 104 ARG cc_start: 0.8069 (mtp-110) cc_final: 0.7737 (mtp180) REVERT: L 10 ILE cc_start: 0.8776 (mt) cc_final: 0.8558 (mt) REVERT: L 106 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7545 (mt-10) outliers start: 7 outliers final: 6 residues processed: 68 average time/residue: 2.4111 time to fit residues: 175.3646 Evaluate side-chains 66 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 70 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 90 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.140068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.099587 restraints weight = 24974.031| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.62 r_work: 0.3010 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7825 Z= 0.139 Angle : 0.511 5.941 10676 Z= 0.271 Chirality : 0.039 0.139 1184 Planarity : 0.005 0.057 1320 Dihedral : 4.749 56.424 1194 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.11 % Allowed : 11.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.28), residues: 959 helix: 0.93 (0.26), residues: 400 sheet: 0.31 (0.39), residues: 180 loop : -0.16 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.005 0.001 HIS A 90 PHE 0.016 0.001 PHE A 530 TYR 0.008 0.001 TYR A 342 ARG 0.007 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 412) hydrogen bonds : angle 4.54723 ( 1191) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.63554 ( 4) covalent geometry : bond 0.00322 ( 7823) covalent geometry : angle 0.51056 (10672) *********************** 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 70 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7105 (mt0) REVERT: H 18 LEU cc_start: 0.8101 (tp) cc_final: 0.7805 (tp) REVERT: H 76 ARG cc_start: 0.7808 (mtt-85) cc_final: 0.7539 (mtt90) REVERT: L 10 ILE cc_start: 0.8800 (mt) cc_final: 0.8580 (mt) REVERT: L 106 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7545 (mt-10) REVERT: L 170 LYS cc_start: 0.8554 (ttpp) cc_final: 0.8148 (ttmt) outliers start: 9 outliers final: 8 residues processed: 69 average time/residue: 2.3732 time to fit residues: 174.9730 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 : 1.137 ------------------------------------------------------------------------------- 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 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 60 optimal weight: 0.1980 chunk 92 optimal weight: 10.0000 chunk 85 optimal weight: 0.0970 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.141223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.101121 restraints weight = 25020.106| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.59 r_work: 0.3040 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7825 Z= 0.116 Angle : 0.498 5.190 10676 Z= 0.264 Chirality : 0.038 0.137 1184 Planarity : 0.006 0.124 1320 Dihedral : 4.582 48.572 1194 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.99 % Allowed : 11.84 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.28), residues: 959 helix: 1.02 (0.26), residues: 400 sheet: 0.33 (0.40), residues: 183 loop : -0.08 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 237 HIS 0.005 0.001 HIS A 90 PHE 0.016 0.001 PHE A 530 TYR 0.008 0.001 TYR A 342 ARG 0.015 0.001 ARG L 156 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 412) hydrogen bonds : angle 4.45864 ( 1191) SS BOND : bond 0.00153 ( 2) SS BOND : angle 0.61346 ( 4) covalent geometry : bond 0.00263 ( 7823) covalent geometry : angle 0.49811 (10672) *********************** 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 71 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7125 (mt0) REVERT: H 18 LEU cc_start: 0.8113 (tp) cc_final: 0.7810 (tp) REVERT: H 76 ARG cc_start: 0.7771 (mtt-85) cc_final: 0.7530 (mtt90) REVERT: L 10 ILE cc_start: 0.8840 (mt) cc_final: 0.8629 (mt) REVERT: L 106 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7594 (mt-10) REVERT: L 170 LYS cc_start: 0.8545 (ttpp) cc_final: 0.8133 (ttmt) REVERT: L 176 MET cc_start: 0.7477 (ttt) cc_final: 0.6577 (tpt) outliers start: 8 outliers final: 7 residues processed: 70 average time/residue: 2.5165 time to fit residues: 187.5242 Evaluate side-chains 66 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 65 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.139780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.099306 restraints weight = 25181.461| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.61 r_work: 0.3006 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2065 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 : 0.521 5.659 10676 Z= 0.276 Chirality : 0.039 0.137 1184 Planarity : 0.005 0.085 1320 Dihedral : 4.576 43.744 1194 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.99 % Allowed : 11.84 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.28), residues: 959 helix: 0.98 (0.26), residues: 400 sheet: 0.34 (0.40), residues: 183 loop : -0.10 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.005 0.001 HIS A 90 PHE 0.016 0.001 PHE A 530 TYR 0.022 0.001 TYR A 455 ARG 0.014 0.001 ARG L 156 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 412) hydrogen bonds : angle 4.52070 ( 1191) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.66000 ( 4) covalent geometry : bond 0.00370 ( 7823) covalent geometry : angle 0.52109 (10672) ********************** 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 69 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7082 (mt0) REVERT: H 18 LEU cc_start: 0.8087 (tp) cc_final: 0.7785 (tp) REVERT: H 76 ARG cc_start: 0.7792 (mtt-85) cc_final: 0.7547 (mtt90) REVERT: L 106 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7698 (mt-10) REVERT: L 170 LYS cc_start: 0.8549 (ttpp) cc_final: 0.8136 (ttmt) REVERT: L 176 MET cc_start: 0.7442 (ttt) cc_final: 0.6526 (tpt) outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 2.4598 time to fit residues: 178.4404 Evaluate side-chains 65 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 3 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 60 optimal weight: 0.4980 chunk 74 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.140740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.100576 restraints weight = 25039.255| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.59 r_work: 0.3033 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7825 Z= 0.132 Angle : 0.501 5.667 10676 Z= 0.266 Chirality : 0.039 0.138 1184 Planarity : 0.005 0.090 1320 Dihedral : 4.441 40.286 1194 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.86 % Allowed : 12.21 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.28), residues: 959 helix: 1.02 (0.26), residues: 400 sheet: 0.40 (0.40), residues: 183 loop : -0.07 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 237 HIS 0.005 0.001 HIS A 90 PHE 0.016 0.001 PHE A 530 TYR 0.008 0.001 TYR A 342 ARG 0.014 0.001 ARG L 156 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 412) hydrogen bonds : angle 4.48110 ( 1191) SS BOND : bond 0.00148 ( 2) SS BOND : angle 0.63596 ( 4) covalent geometry : bond 0.00304 ( 7823) covalent geometry : angle 0.50108 (10672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9171.41 seconds wall clock time: 156 minutes 21.34 seconds (9381.34 seconds total)