Starting phenix.real_space_refine on Tue Aug 6 02:47:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eup_19979/08_2024/9eup_19979_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eup_19979/08_2024/9eup_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eup_19979/08_2024/9eup_19979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eup_19979/08_2024/9eup_19979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eup_19979/08_2024/9eup_19979_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eup_19979/08_2024/9eup_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 Residue "A GLU 543": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "L GLU 1": "OE1" <-> "OE2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "L GLU 186": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 7.65, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.54 Conformation dependent library (CDL) restraints added in 1.6 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: 1.41 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: 5.36 Time building geometry restraints manager: 13.19 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: 97.60 - 104.90: 163 104.90 - 112.19: 16726 112.19 - 119.49: 3887 119.49 - 126.78: 6364 126.78 - 134.08: 138 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: 0.760 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: 0.240 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 51.680 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.050 ------------------------------------------------------------------------------- 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 7823 Z= 0.693 Angle : 0.824 12.331 10672 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 1.202 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: 2.4285 time to fit residues: 189.3543 Evaluate side-chains 63 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7823 Z= 0.195 Angle : 0.577 6.529 10672 Z= 0.310 Chirality : 0.040 0.188 1184 Planarity : 0.005 0.055 1320 Dihedral : 5.685 48.729 1194 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.37 % Allowed : 8.51 % Favored : 91.12 % 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 *********************** 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 fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 73 average time/residue: 2.4881 time to fit residues: 193.4938 Evaluate side-chains 63 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 47 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7823 Z= 0.238 Angle : 0.548 6.283 10672 Z= 0.292 Chirality : 0.040 0.144 1184 Planarity : 0.005 0.050 1320 Dihedral : 5.328 48.310 1194 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.49 % Allowed : 9.74 % 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: 0.08 (0.27), residues: 959 helix: 0.41 (0.26), residues: 401 sheet: -0.28 (0.38), residues: 182 loop : 0.07 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8387 (tp) cc_final: 0.8181 (tp) REVERT: H 104 ARG cc_start: 0.8358 (mtp-110) cc_final: 0.8107 (mtp180) REVERT: L 106 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7509 (mt-10) outliers start: 4 outliers final: 4 residues processed: 75 average time/residue: 2.4937 time to fit residues: 198.9558 Evaluate side-chains 68 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 85 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7823 Z= 0.263 Angle : 0.541 6.024 10672 Z= 0.289 Chirality : 0.040 0.140 1184 Planarity : 0.004 0.037 1320 Dihedral : 5.149 47.433 1194 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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 (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: 0.16 (0.27), residues: 959 helix: 0.51 (0.26), residues: 399 sheet: -0.09 (0.38), residues: 183 loop : -0.03 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 255 HIS 0.006 0.001 HIS A 90 PHE 0.018 0.002 PHE A 357 TYR 0.012 0.001 TYR A 455 ARG 0.003 0.000 ARG A 508 *********************** 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 77 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8415 (tp) cc_final: 0.8188 (tp) REVERT: H 104 ARG cc_start: 0.8332 (mtp-110) cc_final: 0.8057 (mtp180) outliers start: 8 outliers final: 5 residues processed: 75 average time/residue: 2.4286 time to fit residues: 194.9650 Evaluate side-chains 69 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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 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 76 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7823 Z= 0.235 Angle : 0.526 6.732 10672 Z= 0.280 Chirality : 0.039 0.138 1184 Planarity : 0.005 0.080 1320 Dihedral : 5.039 48.340 1194 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.99 % Allowed : 10.97 % 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 (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: 0.26 (0.27), residues: 959 helix: 0.65 (0.26), residues: 398 sheet: 0.02 (0.38), residues: 183 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 0.015 0.001 PHE A 530 TYR 0.014 0.001 TYR A 455 ARG 0.010 0.001 ARG L 156 *********************** 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 76 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8422 (tp) cc_final: 0.8183 (tp) REVERT: H 104 ARG cc_start: 0.8329 (mtp-110) cc_final: 0.7950 (mtp180) outliers start: 8 outliers final: 7 residues processed: 74 average time/residue: 2.3232 time to fit residues: 183.9839 Evaluate side-chains 71 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7823 Z= 0.253 Angle : 0.532 6.695 10672 Z= 0.283 Chirality : 0.039 0.139 1184 Planarity : 0.005 0.049 1320 Dihedral : 4.988 52.958 1194 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.86 % Allowed : 11.47 % Favored : 87.67 % 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: 0.25 (0.27), residues: 959 helix: 0.67 (0.26), residues: 398 sheet: 0.03 (0.38), residues: 183 loop : -0.12 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 255 HIS 0.006 0.001 HIS A 90 PHE 0.016 0.001 PHE A 530 TYR 0.018 0.001 TYR A 455 ARG 0.007 0.000 ARG L 156 *********************** 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 71 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8435 (tp) cc_final: 0.8209 (tp) REVERT: H 104 ARG cc_start: 0.8323 (mtp-110) cc_final: 0.8063 (mtp180) outliers start: 7 outliers final: 7 residues processed: 70 average time/residue: 2.3547 time to fit residues: 176.3203 Evaluate side-chains 67 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 10 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7823 Z= 0.257 Angle : 0.531 6.678 10672 Z= 0.283 Chirality : 0.039 0.139 1184 Planarity : 0.005 0.060 1320 Dihedral : 4.971 59.771 1194 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.99 % Allowed : 12.08 % 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: 0.26 (0.27), residues: 959 helix: 0.70 (0.26), residues: 398 sheet: 0.05 (0.39), residues: 183 loop : -0.16 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 255 HIS 0.005 0.001 HIS A 90 PHE 0.016 0.001 PHE A 530 TYR 0.010 0.001 TYR A 537 ARG 0.007 0.001 ARG L 156 *********************** 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 70 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8682 (t0) REVERT: H 18 LEU cc_start: 0.8361 (tp) cc_final: 0.8144 (tp) REVERT: H 104 ARG cc_start: 0.8336 (mtp-110) cc_final: 0.8061 (mtp180) REVERT: H 217 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6915 (mm-30) outliers start: 8 outliers final: 7 residues processed: 69 average time/residue: 2.3708 time to fit residues: 174.8959 Evaluate side-chains 67 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 34 LEU 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 54 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7823 Z= 0.221 Angle : 0.520 6.117 10672 Z= 0.276 Chirality : 0.039 0.138 1184 Planarity : 0.005 0.057 1320 Dihedral : 4.763 51.740 1194 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.11 % Allowed : 11.96 % 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: 0.35 (0.28), residues: 959 helix: 0.79 (0.26), residues: 398 sheet: 0.17 (0.39), residues: 180 loop : -0.18 (0.34), residues: 381 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 0.009 0.001 TYR A 537 ARG 0.006 0.001 ARG H 76 *********************** 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 68 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: A 475 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8661 (t0) REVERT: H 18 LEU cc_start: 0.8361 (tp) cc_final: 0.8144 (tp) outliers start: 9 outliers final: 8 residues processed: 67 average time/residue: 2.2731 time to fit residues: 163.2268 Evaluate side-chains 65 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 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 85 optimal weight: 0.2980 chunk 87 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7823 Z= 0.229 Angle : 0.523 5.874 10672 Z= 0.277 Chirality : 0.039 0.137 1184 Planarity : 0.005 0.114 1320 Dihedral : 4.692 46.366 1194 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.99 % Allowed : 12.33 % Favored : 86.68 % 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: 0.39 (0.28), residues: 959 helix: 0.84 (0.26), residues: 398 sheet: 0.16 (0.39), residues: 183 loop : -0.14 (0.34), residues: 378 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 0.009 0.001 TYR A 537 ARG 0.017 0.001 ARG L 156 *********************** 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 66 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8667 (t0) REVERT: H 18 LEU cc_start: 0.8374 (tp) cc_final: 0.8137 (tp) REVERT: L 176 MET cc_start: 0.8108 (ttt) cc_final: 0.7281 (tpt) outliers start: 8 outliers final: 7 residues processed: 65 average time/residue: 2.3809 time to fit residues: 165.7691 Evaluate side-chains 65 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 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 42 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7823 Z= 0.214 Angle : 0.520 5.587 10672 Z= 0.275 Chirality : 0.039 0.139 1184 Planarity : 0.005 0.085 1320 Dihedral : 4.553 39.871 1194 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.23 % Allowed : 11.84 % 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: 0.38 (0.28), residues: 959 helix: 0.85 (0.26), residues: 400 sheet: 0.18 (0.39), residues: 183 loop : -0.21 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 99 HIS 0.005 0.001 HIS A 90 PHE 0.016 0.001 PHE A 530 TYR 0.019 0.001 TYR A 455 ARG 0.014 0.001 ARG L 156 ********************** 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 fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8650 (t0) REVERT: H 18 LEU cc_start: 0.8413 (tp) cc_final: 0.8152 (tp) REVERT: L 170 LYS cc_start: 0.8462 (ttpp) cc_final: 0.8172 (ttmt) REVERT: L 176 MET cc_start: 0.8063 (ttt) cc_final: 0.7315 (tpt) outliers start: 10 outliers final: 8 residues processed: 68 average time/residue: 2.1186 time to fit residues: 155.1500 Evaluate side-chains 68 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 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 69 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 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 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.099383 restraints weight = 25173.460| |-----------------------------------------------------------------------------| 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: 0.2900 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7823 Z= 0.218 Angle : 0.514 6.028 10672 Z= 0.272 Chirality : 0.039 0.164 1184 Planarity : 0.005 0.090 1320 Dihedral : 4.473 38.838 1194 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.36 % Allowed : 11.96 % Favored : 86.68 % 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: 0.43 (0.28), residues: 959 helix: 0.89 (0.26), residues: 400 sheet: 0.23 (0.40), residues: 183 loop : -0.20 (0.34), residues: 376 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 0.009 0.001 TYR A 537 ARG 0.014 0.001 ARG L 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5138.58 seconds wall clock time: 89 minutes 27.10 seconds (5367.10 seconds total)