Starting phenix.real_space_refine on Wed Jun 26 02:02:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y93_39068/06_2024/8y93_39068_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y93_39068/06_2024/8y93_39068.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/8y93_39068/06_2024/8y93_39068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y93_39068/06_2024/8y93_39068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y93_39068/06_2024/8y93_39068_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y93_39068/06_2024/8y93_39068_updated.pdb" } 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= 0.055 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: 6 Type Number sf(0) Gaussians S 40 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 6072 2.51 5 N 1413 2.21 5 O 1528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 81": "NH1" <-> "NH2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E ARG 216": "NH1" <-> "NH2" Residue "E ARG 301": "NH1" <-> "NH2" Residue "E ARG 341": "NH1" <-> "NH2" Residue "E ARG 440": "NH1" <-> "NH2" Residue "E ARG 442": "NH1" <-> "NH2" Residue "E ARG 500": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "E ARG 518": "NH1" <-> "NH2" Residue "E ARG 587": "NH1" <-> "NH2" Residue "E ARG 604": "NH1" <-> "NH2" Residue "E ARG 607": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 9055 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "E" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {' CL': 1, ' NA': 1, 'TP0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.57, per 1000 atoms: 0.62 Number of scatterers: 9055 At special positions: 0 Unit cell: (97.09, 85.41, 118.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 40 16.00 Na 1 11.00 O 1528 8.00 N 1413 7.00 C 6072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.13 Conformation dependent library (CDL) restraints added in 1.5 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 0 sheets defined 64.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 62 through 73 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 91 through 103 removed outlier: 3.708A pdb=" N PHE A 94 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 96 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 107 through 119 removed outlier: 4.085A pdb=" N GLU A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 114 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 115 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 166 removed outlier: 4.724A pdb=" N GLY A 136 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 140 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL A 141 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE A 144 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL A 148 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE A 150 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 151 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR A 152 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASN A 153 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 159 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR A 161 " --> pdb=" O TRP A 158 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR A 162 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE A 164 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 165 " --> pdb=" O TYR A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 252 removed outlier: 3.863A pdb=" N CYS A 240 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.595A pdb=" N LYS A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 283 removed outlier: 4.566A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 310 through 319 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 339 through 371 removed outlier: 3.553A pdb=" N PHE A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.772A pdb=" N VAL A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 397 removed outlier: 3.863A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 434 removed outlier: 3.556A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 442 through 457 removed outlier: 3.772A pdb=" N PHE A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 493 Processing helix chain 'A' and resid 498 through 509 Processing helix chain 'A' and resid 515 through 522 Processing helix chain 'A' and resid 524 through 538 Processing helix chain 'A' and resid 552 through 579 removed outlier: 3.797A pdb=" N TRP A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) Proline residue: A 570 - end of helix Processing helix chain 'A' and resid 584 through 588 Processing helix chain 'A' and resid 598 through 602 removed outlier: 3.552A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 598 through 602' Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 611 through 614 No H-bonds generated for 'chain 'A' and resid 611 through 614' Processing helix chain 'E' and resid 62 through 73 removed outlier: 3.616A pdb=" N LEU E 66 " --> pdb=" O LYS E 62 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 104 Processing helix chain 'E' and resid 106 through 120 Processing helix chain 'E' and resid 132 through 167 removed outlier: 3.610A pdb=" N LYS E 135 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY E 136 " --> pdb=" O PHE E 133 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL E 137 " --> pdb=" O PHE E 134 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN E 153 " --> pdb=" O PHE E 150 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE E 167 " --> pdb=" O PHE E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 215 Processing helix chain 'E' and resid 235 through 252 Processing helix chain 'E' and resid 256 through 266 Processing helix chain 'E' and resid 270 through 283 removed outlier: 3.958A pdb=" N LEU E 274 " --> pdb=" O PRO E 270 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR E 283 " --> pdb=" O VAL E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 294 removed outlier: 4.058A pdb=" N SER E 288 " --> pdb=" O PRO E 285 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASN E 289 " --> pdb=" O GLY E 286 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY E 290 " --> pdb=" O ALA E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 319 Processing helix chain 'E' and resid 325 through 332 removed outlier: 3.745A pdb=" N TYR E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 371 Processing helix chain 'E' and resid 386 through 397 Proline residue: E 392 - end of helix Processing helix chain 'E' and resid 401 through 434 Processing helix chain 'E' and resid 436 through 440 Processing helix chain 'E' and resid 442 through 456 Processing helix chain 'E' and resid 465 through 493 Processing helix chain 'E' and resid 498 through 508 Processing helix chain 'E' and resid 515 through 522 Processing helix chain 'E' and resid 524 through 538 Processing helix chain 'E' and resid 552 through 579 removed outlier: 3.525A pdb=" N TRP E 556 " --> pdb=" O PRO E 552 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER E 565 " --> pdb=" O ILE E 561 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU E 568 " --> pdb=" O SER E 564 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL E 569 " --> pdb=" O SER E 565 " (cutoff:3.500A) Proline residue: E 570 - end of helix Processing helix chain 'E' and resid 584 through 592 Processing helix chain 'E' and resid 599 through 602 No H-bonds generated for 'chain 'E' and resid 599 through 602' Processing helix chain 'E' and resid 611 through 615 459 hydrogen bonds defined for protein. 1203 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: 2.33 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1395 1.32 - 1.44: 2870 1.44 - 1.57: 5022 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 9349 Sorted by residual: bond pdb=" CA TRP E 128 " pdb=" C TRP E 128 " ideal model delta sigma weight residual 1.530 1.458 0.072 1.14e-02 7.69e+03 4.02e+01 bond pdb=" C3 TP0 A 701 " pdb=" C6 TP0 A 701 " ideal model delta sigma weight residual 1.483 1.555 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CA VAL E 127 " pdb=" C VAL E 127 " ideal model delta sigma weight residual 1.525 1.481 0.044 1.27e-02 6.20e+03 1.18e+01 bond pdb=" CA ILE E 130 " pdb=" C ILE E 130 " ideal model delta sigma weight residual 1.520 1.470 0.050 1.54e-02 4.22e+03 1.07e+01 bond pdb=" CA LYS E 129 " pdb=" C LYS E 129 " ideal model delta sigma weight residual 1.522 1.485 0.037 1.31e-02 5.83e+03 7.81e+00 ... (remaining 9344 not shown) Histogram of bond angle deviations from ideal: 96.19 - 103.75: 107 103.75 - 111.32: 3990 111.32 - 118.88: 3368 118.88 - 126.44: 5070 126.44 - 134.00: 222 Bond angle restraints: 12757 Sorted by residual: angle pdb=" N LYS E 129 " pdb=" CA LYS E 129 " pdb=" C LYS E 129 " ideal model delta sigma weight residual 113.30 96.19 17.11 1.34e+00 5.57e-01 1.63e+02 angle pdb=" N VAL E 127 " pdb=" CA VAL E 127 " pdb=" C VAL E 127 " ideal model delta sigma weight residual 113.16 102.59 10.57 1.49e+00 4.50e-01 5.03e+01 angle pdb=" N ILE E 130 " pdb=" CA ILE E 130 " pdb=" C ILE E 130 " ideal model delta sigma weight residual 112.83 106.53 6.30 9.90e-01 1.02e+00 4.04e+01 angle pdb=" C14 TP0 A 701 " pdb=" N1 TP0 A 701 " pdb=" C20 TP0 A 701 " ideal model delta sigma weight residual 111.01 99.00 12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" N VAL A 137 " pdb=" CA VAL A 137 " pdb=" C VAL A 137 " ideal model delta sigma weight residual 113.00 108.42 4.58 1.30e+00 5.92e-01 1.24e+01 ... (remaining 12752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.77: 5099 28.77 - 57.55: 111 57.55 - 86.32: 8 86.32 - 115.09: 1 115.09 - 143.87: 2 Dihedral angle restraints: 5221 sinusoidal: 1957 harmonic: 3264 Sorted by residual: dihedral pdb=" C22 TP0 A 701 " pdb=" C21 TP0 A 701 " pdb=" C4 TP0 A 701 " pdb=" C6 TP0 A 701 " ideal model delta sinusoidal sigma weight residual 71.36 -72.51 143.87 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" C10 TP0 A 701 " pdb=" C21 TP0 A 701 " pdb=" C4 TP0 A 701 " pdb=" C22 TP0 A 701 " ideal model delta sinusoidal sigma weight residual 108.73 -108.00 -143.27 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C LYS E 129 " pdb=" N LYS E 129 " pdb=" CA LYS E 129 " pdb=" CB LYS E 129 " ideal model delta harmonic sigma weight residual -122.60 -113.18 -9.42 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 5218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1156 0.045 - 0.090: 231 0.090 - 0.134: 28 0.134 - 0.179: 1 0.179 - 0.224: 2 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CB VAL E 127 " pdb=" CA VAL E 127 " pdb=" CG1 VAL E 127 " pdb=" CG2 VAL E 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA LYS E 129 " pdb=" N LYS E 129 " pdb=" C LYS E 129 " pdb=" CB LYS E 129 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA TRP E 128 " pdb=" N TRP E 128 " pdb=" C TRP E 128 " pdb=" CB TRP E 128 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.54e-01 ... (remaining 1415 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS E 131 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO E 132 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 132 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 132 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 391 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO E 392 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 392 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 392 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 127 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C VAL E 127 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL E 127 " 0.010 2.00e-02 2.50e+03 pdb=" N TRP E 128 " 0.009 2.00e-02 2.50e+03 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 126 2.68 - 3.24: 9084 3.24 - 3.79: 14653 3.79 - 4.35: 19787 4.35 - 4.90: 32803 Nonbonded interactions: 76453 Sorted by model distance: nonbonded pdb=" C20 TP0 A 701 " pdb=" C29 TP0 A 701 " model vdw 2.127 3.088 nonbonded pdb=" OG SER A 318 " pdb="CL CL A 703 " model vdw 2.227 2.590 nonbonded pdb=" N LYS E 129 " pdb=" N ILE E 130 " model vdw 2.244 2.560 nonbonded pdb=" O SER A 251 " pdb=" OG1 THR A 258 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR E 332 " pdb=" OG1 THR E 429 " model vdw 2.295 2.440 ... (remaining 76448 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 53 through 617) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.400 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: 0.010 Extract box with map and model: 7.080 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.360 Find NCS groups from input model: 0.690 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:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9349 Z= 0.205 Angle : 0.603 17.108 12757 Z= 0.367 Chirality : 0.035 0.224 1418 Planarity : 0.004 0.048 1554 Dihedral : 11.793 143.867 3145 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.15 % Allowed : 7.14 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.23), residues: 1126 helix: -0.76 (0.18), residues: 730 sheet: None (None), residues: 0 loop : -1.94 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 128 HIS 0.001 0.000 HIS A 280 PHE 0.011 0.001 PHE A 409 TYR 0.007 0.001 TYR A 340 ARG 0.002 0.000 ARG E 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 249 time to evaluate : 1.030 Fit side-chains REVERT: A 147 TYR cc_start: 0.8334 (m-10) cc_final: 0.7725 (m-10) REVERT: A 271 TYR cc_start: 0.8411 (m-80) cc_final: 0.8185 (m-80) REVERT: A 348 SER cc_start: 0.8411 (m) cc_final: 0.8208 (m) REVERT: A 439 LYS cc_start: 0.8491 (mttt) cc_final: 0.8103 (mtpm) REVERT: A 585 TRP cc_start: 0.6791 (m100) cc_final: 0.6542 (m-10) REVERT: A 611 LEU cc_start: 0.8222 (tp) cc_final: 0.7839 (tt) REVERT: E 111 TYR cc_start: 0.8222 (t80) cc_final: 0.7846 (t80) REVERT: E 120 ASN cc_start: 0.8206 (m-40) cc_final: 0.7990 (m-40) REVERT: E 133 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.6754 (m-80) REVERT: E 494 TRP cc_start: 0.7747 (m100) cc_final: 0.7422 (m100) outliers start: 49 outliers final: 9 residues processed: 279 average time/residue: 0.7852 time to fit residues: 240.6935 Evaluate side-chains 160 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 180 TRP Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 205 TYR Chi-restraints excluded: chain E residue 359 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.0870 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 overall best weight: 1.2960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN A 234 GLN A 280 HIS A 350 ASN A 507 GLN E 120 ASN E 153 ASN E 337 ASN ** E 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9349 Z= 0.243 Angle : 0.597 8.967 12757 Z= 0.303 Chirality : 0.040 0.143 1418 Planarity : 0.004 0.030 1554 Dihedral : 8.168 141.265 1242 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 5.36 % Allowed : 16.81 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.24), residues: 1126 helix: 0.22 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -1.40 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 128 HIS 0.005 0.001 HIS E 372 PHE 0.022 0.002 PHE A 362 TYR 0.024 0.002 TYR E 151 ARG 0.009 0.001 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 153 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7332 (mm-30) REVERT: A 189 LYS cc_start: 0.7665 (pptt) cc_final: 0.7106 (tttt) REVERT: A 271 TYR cc_start: 0.8505 (m-80) cc_final: 0.8302 (m-80) REVERT: A 297 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7934 (pt) REVERT: A 348 SER cc_start: 0.8545 (m) cc_final: 0.8278 (m) REVERT: A 425 GLU cc_start: 0.7775 (tp30) cc_final: 0.7560 (mm-30) REVERT: A 439 LYS cc_start: 0.8622 (mttt) cc_final: 0.8209 (mttm) REVERT: A 581 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7208 (tm-30) REVERT: A 585 TRP cc_start: 0.7049 (m100) cc_final: 0.6740 (m-10) REVERT: A 595 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: A 611 LEU cc_start: 0.8389 (tp) cc_final: 0.8068 (tm) REVERT: E 100 LEU cc_start: 0.8257 (tt) cc_final: 0.7373 (mm) REVERT: E 111 TYR cc_start: 0.8602 (t80) cc_final: 0.8392 (t80) REVERT: E 119 TYR cc_start: 0.6635 (t80) cc_final: 0.6384 (t80) REVERT: E 120 ASN cc_start: 0.8189 (m110) cc_final: 0.7976 (m110) REVERT: E 133 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7694 (m-10) REVERT: E 242 MET cc_start: 0.7067 (mtm) cc_final: 0.6807 (mtt) REVERT: E 254 LYS cc_start: 0.7478 (tptm) cc_final: 0.7160 (tppp) REVERT: E 350 ASN cc_start: 0.6036 (m110) cc_final: 0.5724 (m110) REVERT: E 595 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7159 (mp0) outliers start: 51 outliers final: 20 residues processed: 189 average time/residue: 0.7540 time to fit residues: 157.6481 Evaluate side-chains 147 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 581 GLN Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 612 GLN Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 595 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 81 optimal weight: 0.3980 chunk 100 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9349 Z= 0.235 Angle : 0.577 11.695 12757 Z= 0.288 Chirality : 0.040 0.141 1418 Planarity : 0.004 0.031 1554 Dihedral : 7.810 140.976 1234 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.09 % Allowed : 17.86 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1126 helix: 0.43 (0.20), residues: 725 sheet: None (None), residues: 0 loop : -0.96 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 80 HIS 0.007 0.001 HIS E 370 PHE 0.021 0.002 PHE A 362 TYR 0.019 0.001 TYR E 340 ARG 0.006 0.001 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 129 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7685 (pptt) cc_final: 0.7107 (tttt) REVERT: A 297 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7939 (pt) REVERT: A 410 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8597 (m) REVERT: A 425 GLU cc_start: 0.7971 (tp30) cc_final: 0.7681 (mm-30) REVERT: A 439 LYS cc_start: 0.8620 (mttt) cc_final: 0.8202 (mttm) REVERT: A 502 SER cc_start: 0.8165 (m) cc_final: 0.7869 (p) REVERT: A 585 TRP cc_start: 0.7039 (m100) cc_final: 0.6753 (m-10) REVERT: A 595 GLU cc_start: 0.7931 (mp0) cc_final: 0.7452 (mp0) REVERT: A 612 GLN cc_start: 0.8101 (tp40) cc_final: 0.7879 (tp40) REVERT: E 100 LEU cc_start: 0.8350 (tt) cc_final: 0.7254 (mm) REVERT: E 119 TYR cc_start: 0.6671 (t80) cc_final: 0.6216 (t80) REVERT: E 120 ASN cc_start: 0.8017 (m110) cc_final: 0.7778 (m110) REVERT: E 242 MET cc_start: 0.7005 (mtm) cc_final: 0.6768 (mtt) REVERT: E 254 LYS cc_start: 0.7559 (tptm) cc_final: 0.7080 (tppt) REVERT: E 350 ASN cc_start: 0.6128 (m110) cc_final: 0.5912 (m110) REVERT: E 436 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8376 (mp10) outliers start: 58 outliers final: 28 residues processed: 172 average time/residue: 0.7052 time to fit residues: 135.2260 Evaluate side-chains 150 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 486 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9349 Z= 0.215 Angle : 0.556 10.993 12757 Z= 0.276 Chirality : 0.039 0.132 1418 Planarity : 0.004 0.028 1554 Dihedral : 7.643 140.803 1232 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.46 % Allowed : 18.59 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1126 helix: 0.57 (0.20), residues: 725 sheet: None (None), residues: 0 loop : -0.69 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 80 HIS 0.006 0.001 HIS E 370 PHE 0.023 0.001 PHE E 275 TYR 0.015 0.001 TYR E 151 ARG 0.003 0.000 ARG E 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 119 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7422 (mm-30) REVERT: A 189 LYS cc_start: 0.7755 (pptt) cc_final: 0.7473 (pptt) REVERT: A 297 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7976 (pt) REVERT: A 410 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8606 (m) REVERT: A 425 GLU cc_start: 0.7999 (tp30) cc_final: 0.7705 (mm-30) REVERT: A 439 LYS cc_start: 0.8619 (mttt) cc_final: 0.8222 (mtpm) REVERT: A 502 SER cc_start: 0.8100 (m) cc_final: 0.7811 (p) REVERT: A 581 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: A 585 TRP cc_start: 0.7033 (m100) cc_final: 0.6780 (m-10) REVERT: A 595 GLU cc_start: 0.7988 (mp0) cc_final: 0.7446 (mp0) REVERT: A 597 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7737 (mt-10) REVERT: A 612 GLN cc_start: 0.8225 (tp40) cc_final: 0.8024 (tp40) REVERT: E 100 LEU cc_start: 0.8376 (tt) cc_final: 0.7281 (mm) REVERT: E 119 TYR cc_start: 0.6691 (t80) cc_final: 0.6178 (t80) REVERT: E 120 ASN cc_start: 0.7947 (m110) cc_final: 0.7566 (m110) REVERT: E 242 MET cc_start: 0.7020 (mtm) cc_final: 0.6758 (mtt) REVERT: E 254 LYS cc_start: 0.7565 (tptm) cc_final: 0.7158 (tppt) REVERT: E 257 LYS cc_start: 0.5371 (OUTLIER) cc_final: 0.4988 (mtpm) outliers start: 52 outliers final: 30 residues processed: 158 average time/residue: 0.7997 time to fit residues: 140.0034 Evaluate side-chains 148 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 581 GLN Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 566 MET Chi-restraints excluded: chain E residue 598 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9349 Z= 0.178 Angle : 0.545 12.367 12757 Z= 0.266 Chirality : 0.037 0.142 1418 Planarity : 0.004 0.051 1554 Dihedral : 7.623 140.890 1232 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.62 % Allowed : 20.06 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1126 helix: 0.75 (0.20), residues: 726 sheet: None (None), residues: 0 loop : -0.62 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 80 HIS 0.004 0.001 HIS E 370 PHE 0.019 0.001 PHE A 362 TYR 0.018 0.001 TYR E 340 ARG 0.002 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 120 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: A 189 LYS cc_start: 0.7621 (pptt) cc_final: 0.7317 (pptt) REVERT: A 297 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8002 (pt) REVERT: A 410 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8602 (m) REVERT: A 425 GLU cc_start: 0.8015 (tp30) cc_final: 0.7708 (mm-30) REVERT: A 439 LYS cc_start: 0.8635 (mttt) cc_final: 0.8237 (mtpm) REVERT: A 502 SER cc_start: 0.8095 (m) cc_final: 0.7807 (p) REVERT: A 581 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7614 (tm-30) REVERT: A 585 TRP cc_start: 0.7020 (m100) cc_final: 0.6759 (m-10) REVERT: A 595 GLU cc_start: 0.7987 (mp0) cc_final: 0.7452 (mp0) REVERT: A 612 GLN cc_start: 0.8185 (tp40) cc_final: 0.7965 (tp40) REVERT: E 112 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7952 (ttp) REVERT: E 119 TYR cc_start: 0.6695 (t80) cc_final: 0.6153 (t80) REVERT: E 120 ASN cc_start: 0.7854 (m110) cc_final: 0.7457 (m110) REVERT: E 242 MET cc_start: 0.7015 (mtm) cc_final: 0.6762 (mtt) REVERT: E 254 LYS cc_start: 0.7550 (tptm) cc_final: 0.7137 (tppt) REVERT: E 257 LYS cc_start: 0.5511 (OUTLIER) cc_final: 0.5163 (mmmt) REVERT: E 528 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6577 (t80) outliers start: 44 outliers final: 27 residues processed: 152 average time/residue: 0.7449 time to fit residues: 125.6571 Evaluate side-chains 146 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 112 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 581 GLN Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 528 PHE Chi-restraints excluded: chain E residue 598 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 HIS ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 HIS ** E 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9349 Z= 0.226 Angle : 0.579 13.113 12757 Z= 0.282 Chirality : 0.039 0.145 1418 Planarity : 0.004 0.036 1554 Dihedral : 7.694 140.755 1232 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.15 % Allowed : 19.85 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1126 helix: 0.76 (0.20), residues: 724 sheet: None (None), residues: 0 loop : -0.51 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 80 HIS 0.005 0.001 HIS A 599 PHE 0.021 0.001 PHE A 362 TYR 0.015 0.001 TYR E 151 ARG 0.003 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 110 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7427 (mm-30) REVERT: A 189 LYS cc_start: 0.7608 (pptt) cc_final: 0.7340 (pptt) REVERT: A 297 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8036 (pt) REVERT: A 410 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8605 (m) REVERT: A 425 GLU cc_start: 0.8028 (tp30) cc_final: 0.7628 (mm-30) REVERT: A 439 LYS cc_start: 0.8628 (mttt) cc_final: 0.8225 (mtpm) REVERT: A 502 SER cc_start: 0.8110 (m) cc_final: 0.7824 (p) REVERT: A 581 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: A 585 TRP cc_start: 0.7025 (m100) cc_final: 0.6773 (m-10) REVERT: A 595 GLU cc_start: 0.8003 (mp0) cc_final: 0.7445 (mp0) REVERT: A 612 GLN cc_start: 0.8254 (tp40) cc_final: 0.8048 (tp40) REVERT: E 119 TYR cc_start: 0.6760 (t80) cc_final: 0.6236 (t80) REVERT: E 120 ASN cc_start: 0.7878 (m110) cc_final: 0.7489 (m110) REVERT: E 242 MET cc_start: 0.7063 (mtm) cc_final: 0.6785 (mtt) REVERT: E 254 LYS cc_start: 0.7555 (tptm) cc_final: 0.7136 (tppt) REVERT: E 257 LYS cc_start: 0.5595 (OUTLIER) cc_final: 0.5157 (mmmt) outliers start: 49 outliers final: 29 residues processed: 149 average time/residue: 0.7386 time to fit residues: 122.2273 Evaluate side-chains 139 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 105 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 581 GLN Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 598 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9349 Z= 0.168 Angle : 0.563 14.324 12757 Z= 0.270 Chirality : 0.037 0.132 1418 Planarity : 0.004 0.032 1554 Dihedral : 7.651 140.592 1232 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.52 % Allowed : 20.90 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.26), residues: 1126 helix: 0.90 (0.20), residues: 724 sheet: None (None), residues: 0 loop : -0.46 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 80 HIS 0.004 0.001 HIS E 370 PHE 0.031 0.001 PHE E 408 TYR 0.019 0.001 TYR E 340 ARG 0.002 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 115 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7607 (pptt) cc_final: 0.7317 (pptt) REVERT: A 297 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8048 (pt) REVERT: A 410 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8603 (m) REVERT: A 425 GLU cc_start: 0.8013 (tp30) cc_final: 0.7613 (mm-30) REVERT: A 439 LYS cc_start: 0.8643 (mttt) cc_final: 0.8240 (mtpm) REVERT: A 502 SER cc_start: 0.8111 (m) cc_final: 0.7826 (p) REVERT: A 585 TRP cc_start: 0.7047 (m100) cc_final: 0.6841 (m-10) REVERT: A 595 GLU cc_start: 0.7994 (mp0) cc_final: 0.7713 (mp0) REVERT: A 612 GLN cc_start: 0.8206 (tp40) cc_final: 0.7980 (tp40) REVERT: E 112 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7955 (ttp) REVERT: E 119 TYR cc_start: 0.6722 (t80) cc_final: 0.6183 (t80) REVERT: E 120 ASN cc_start: 0.7833 (m110) cc_final: 0.7434 (m110) REVERT: E 242 MET cc_start: 0.7076 (mtm) cc_final: 0.6773 (mtt) REVERT: E 254 LYS cc_start: 0.7571 (tptm) cc_final: 0.7136 (tppt) REVERT: E 257 LYS cc_start: 0.5623 (OUTLIER) cc_final: 0.5173 (mmmt) REVERT: E 350 ASN cc_start: 0.5916 (m110) cc_final: 0.5637 (m110) REVERT: E 479 THR cc_start: 0.6442 (m) cc_final: 0.5586 (t) REVERT: E 528 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6666 (t80) outliers start: 43 outliers final: 25 residues processed: 149 average time/residue: 0.7560 time to fit residues: 125.0510 Evaluate side-chains 135 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 105 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 528 PHE Chi-restraints excluded: chain E residue 598 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.0040 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 73 optimal weight: 0.6980 chunk 53 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 98 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9349 Z= 0.148 Angle : 0.556 14.486 12757 Z= 0.264 Chirality : 0.037 0.164 1418 Planarity : 0.003 0.029 1554 Dihedral : 7.609 140.600 1232 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.26 % Allowed : 22.48 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1126 helix: 0.97 (0.20), residues: 726 sheet: None (None), residues: 0 loop : -0.37 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 80 HIS 0.003 0.001 HIS E 370 PHE 0.027 0.001 PHE E 408 TYR 0.011 0.001 TYR E 391 ARG 0.002 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7501 (pptt) cc_final: 0.7188 (pptt) REVERT: A 297 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8073 (pt) REVERT: A 410 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8598 (m) REVERT: A 425 GLU cc_start: 0.7969 (tp30) cc_final: 0.7590 (mm-30) REVERT: A 439 LYS cc_start: 0.8612 (mttt) cc_final: 0.8196 (mtpm) REVERT: A 502 SER cc_start: 0.8111 (m) cc_final: 0.7833 (p) REVERT: A 585 TRP cc_start: 0.7010 (m100) cc_final: 0.6803 (m-10) REVERT: A 595 GLU cc_start: 0.8033 (mp0) cc_final: 0.7737 (mp0) REVERT: A 612 GLN cc_start: 0.8172 (tp40) cc_final: 0.7956 (tp40) REVERT: E 112 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7978 (ttp) REVERT: E 119 TYR cc_start: 0.6752 (t80) cc_final: 0.6233 (t80) REVERT: E 120 ASN cc_start: 0.7794 (m110) cc_final: 0.7429 (m110) REVERT: E 242 MET cc_start: 0.7090 (mtm) cc_final: 0.6777 (mtt) REVERT: E 254 LYS cc_start: 0.7560 (tptm) cc_final: 0.7124 (tppt) REVERT: E 257 LYS cc_start: 0.5548 (OUTLIER) cc_final: 0.5119 (mmmt) REVERT: E 350 ASN cc_start: 0.5833 (m110) cc_final: 0.5527 (m110) REVERT: E 479 THR cc_start: 0.6438 (m) cc_final: 0.6060 (t) REVERT: E 528 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6694 (t80) outliers start: 31 outliers final: 23 residues processed: 139 average time/residue: 0.6743 time to fit residues: 104.9994 Evaluate side-chains 136 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 528 PHE Chi-restraints excluded: chain E residue 598 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9349 Z= 0.201 Angle : 0.595 14.568 12757 Z= 0.284 Chirality : 0.038 0.154 1418 Planarity : 0.004 0.029 1554 Dihedral : 7.673 140.578 1231 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.78 % Allowed : 22.69 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.26), residues: 1126 helix: 0.95 (0.20), residues: 723 sheet: None (None), residues: 0 loop : -0.37 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 80 HIS 0.004 0.001 HIS E 370 PHE 0.025 0.001 PHE E 408 TYR 0.020 0.001 TYR E 340 ARG 0.002 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 110 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7527 (pptt) cc_final: 0.7211 (pptt) REVERT: A 297 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8130 (pt) REVERT: A 410 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8601 (m) REVERT: A 425 GLU cc_start: 0.8029 (tp30) cc_final: 0.7629 (mm-30) REVERT: A 439 LYS cc_start: 0.8597 (mttt) cc_final: 0.8179 (mtpm) REVERT: A 502 SER cc_start: 0.8088 (m) cc_final: 0.7816 (p) REVERT: A 585 TRP cc_start: 0.7061 (m100) cc_final: 0.6855 (m-10) REVERT: A 595 GLU cc_start: 0.8018 (mp0) cc_final: 0.7692 (mp0) REVERT: A 610 GLN cc_start: 0.7657 (mm110) cc_final: 0.7450 (mm-40) REVERT: A 612 GLN cc_start: 0.8215 (tp40) cc_final: 0.8012 (tp40) REVERT: E 119 TYR cc_start: 0.6805 (t80) cc_final: 0.6311 (t80) REVERT: E 120 ASN cc_start: 0.7793 (m110) cc_final: 0.7385 (m110) REVERT: E 242 MET cc_start: 0.7113 (mtm) cc_final: 0.6796 (mtt) REVERT: E 254 LYS cc_start: 0.7556 (tptm) cc_final: 0.7117 (tppt) REVERT: E 350 ASN cc_start: 0.5928 (m110) cc_final: 0.5674 (m110) REVERT: E 479 THR cc_start: 0.6259 (m) cc_final: 0.5608 (t) REVERT: E 528 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.6650 (t80) REVERT: E 584 LEU cc_start: 0.5361 (OUTLIER) cc_final: 0.5093 (tt) outliers start: 36 outliers final: 25 residues processed: 139 average time/residue: 0.7147 time to fit residues: 111.1834 Evaluate side-chains 136 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 528 PHE Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 598 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 111 optimal weight: 0.3980 chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN E 289 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9349 Z= 0.197 Angle : 0.601 13.397 12757 Z= 0.289 Chirality : 0.039 0.355 1418 Planarity : 0.004 0.029 1554 Dihedral : 7.720 140.417 1231 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.78 % Allowed : 22.69 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1126 helix: 0.96 (0.20), residues: 723 sheet: None (None), residues: 0 loop : -0.33 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 80 HIS 0.004 0.001 HIS E 228 PHE 0.042 0.001 PHE E 408 TYR 0.016 0.001 TYR E 391 ARG 0.002 0.000 ARG A 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7548 (pptt) cc_final: 0.6938 (tttt) REVERT: A 410 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8608 (m) REVERT: A 425 GLU cc_start: 0.8025 (tp30) cc_final: 0.7652 (mm-30) REVERT: A 439 LYS cc_start: 0.8606 (mttt) cc_final: 0.8192 (mtpm) REVERT: A 502 SER cc_start: 0.8098 (m) cc_final: 0.7821 (p) REVERT: A 581 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: A 585 TRP cc_start: 0.7050 (m100) cc_final: 0.6843 (m-10) REVERT: A 595 GLU cc_start: 0.7997 (mp0) cc_final: 0.7666 (mp0) REVERT: E 119 TYR cc_start: 0.6820 (t80) cc_final: 0.6335 (t80) REVERT: E 120 ASN cc_start: 0.7828 (m110) cc_final: 0.7418 (m110) REVERT: E 242 MET cc_start: 0.7112 (mtm) cc_final: 0.6794 (mtt) REVERT: E 254 LYS cc_start: 0.7552 (tptm) cc_final: 0.7108 (tppt) REVERT: E 257 LYS cc_start: 0.5487 (OUTLIER) cc_final: 0.5067 (mmmt) REVERT: E 350 ASN cc_start: 0.5928 (m110) cc_final: 0.5674 (m110) REVERT: E 479 THR cc_start: 0.6193 (m) cc_final: 0.5598 (t) REVERT: E 584 LEU cc_start: 0.5363 (OUTLIER) cc_final: 0.5098 (tt) outliers start: 36 outliers final: 28 residues processed: 133 average time/residue: 0.7354 time to fit residues: 108.7720 Evaluate side-chains 138 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 106 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 581 GLN Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 598 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 78 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.171452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.138701 restraints weight = 12250.165| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.17 r_work: 0.3666 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9349 Z= 0.242 Angle : 0.634 15.534 12757 Z= 0.305 Chirality : 0.039 0.171 1418 Planarity : 0.004 0.029 1554 Dihedral : 7.777 140.503 1231 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.89 % Allowed : 22.69 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.26), residues: 1126 helix: 0.88 (0.20), residues: 721 sheet: None (None), residues: 0 loop : -0.36 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 80 HIS 0.004 0.001 HIS E 228 PHE 0.045 0.002 PHE E 408 TYR 0.019 0.001 TYR E 340 ARG 0.002 0.000 ARG A 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3080.15 seconds wall clock time: 54 minutes 47.69 seconds (3287.69 seconds total)