Starting phenix.real_space_refine on Sat Jul 20 17:37:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrg_14913/07_2024/7zrg_14913.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrg_14913/07_2024/7zrg_14913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrg_14913/07_2024/7zrg_14913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrg_14913/07_2024/7zrg_14913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrg_14913/07_2024/7zrg_14913.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrg_14913/07_2024/7zrg_14913.cif" } resolution = 3.5 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= 0.008 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 K 7 8.98 5 P 8 5.49 5 S 62 5.16 5 C 7124 2.51 5 N 1824 2.21 5 O 2007 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 45": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B GLU 560": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11032 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5008 Classifications: {'peptide': 674} Link IDs: {'PTRANS': 26, 'TRANS': 647} Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 207 Unusual residues: {' K': 7, 'CDL': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.92, per 1000 atoms: 0.63 Number of scatterers: 11032 At special positions: 0 Unit cell: (100.188, 111.32, 148.764, 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) K 7 19.00 S 62 16.00 P 8 15.00 O 2007 8.00 N 1824 7.00 C 7124 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: 4.52 Conformation dependent library (CDL) restraints added in 2.1 seconds 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2634 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 10 sheets defined 63.0% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 removed outlier: 3.959A pdb=" N MET A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 39 through 51 Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 131 through 157 Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.963A pdb=" N VAL A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.931A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.388A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.454A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 removed outlier: 4.094A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.748A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 377 through 399 Processing helix chain 'A' and resid 410 through 436 removed outlier: 4.562A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 449 through 465 removed outlier: 4.043A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 495 Processing helix chain 'A' and resid 496 through 509 removed outlier: 3.888A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 550 removed outlier: 3.991A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'C' and resid 3 through 21 removed outlier: 4.124A pdb=" N ALA C 7 " --> pdb=" O GLY C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 34 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 91 through 109 Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.800A pdb=" N VAL C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.646A pdb=" N VAL C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'D' and resid 2 through 25 Processing helix chain 'B' and resid 11 through 24 removed outlier: 4.748A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 54 Processing helix chain 'B' and resid 61 through 97 removed outlier: 4.156A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 209 Processing helix chain 'B' and resid 215 through 238 Processing helix chain 'B' and resid 238 through 246 removed outlier: 4.162A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 264 through 285 removed outlier: 5.434A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.649A pdb=" N GLY B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 397 through 406 Processing helix chain 'B' and resid 413 through 427 removed outlier: 4.155A pdb=" N ASP B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 462 removed outlier: 3.715A pdb=" N LYS B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.658A pdb=" N GLU B 509 " --> pdb=" O GLN B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 522 through 528 Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 557 through 595 removed outlier: 4.123A pdb=" N ASP B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) Proline residue: B 592 - end of helix removed outlier: 3.570A pdb=" N PHE B 595 " --> pdb=" O ILE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 606 removed outlier: 3.751A pdb=" N ASN B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 631 removed outlier: 4.488A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 645 through 680 removed outlier: 4.044A pdb=" N GLY B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLY B 661 " --> pdb=" O TYR B 657 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU B 662 " --> pdb=" O GLY B 658 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 204 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 removed outlier: 3.602A pdb=" N LYS A 407 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 44 removed outlier: 6.336A pdb=" N ILE C 43 " --> pdb=" O ARG C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 134 removed outlier: 3.645A pdb=" N GLU B 145 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain 'B' and resid 287 through 289 Processing sheet with id=AA8, first strand: chain 'B' and resid 303 through 304 removed outlier: 6.549A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N THR B 516 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL B 513 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL B 533 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET B 515 " --> pdb=" O VAL B 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 306 through 307 removed outlier: 6.675A pdb=" N LEU B 306 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N MET B 469 " --> pdb=" O LEU B 491 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 429 through 431 648 hydrogen bonds defined for protein. 1914 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1946 1.33 - 1.45: 2647 1.45 - 1.57: 6503 1.57 - 1.70: 17 1.70 - 1.82: 112 Bond restraints: 11225 Sorted by residual: bond pdb=" OA3 CDL A 609 " pdb=" PA1 CDL A 609 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.44e+00 bond pdb=" OA3 CDL A 608 " pdb=" PA1 CDL A 608 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.11e+00 bond pdb=" OB3 CDL A 608 " pdb=" PB2 CDL A 608 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.08e+00 bond pdb=" OB3 CDL A 609 " pdb=" PB2 CDL A 609 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.08e+00 bond pdb=" C11 CDL A 608 " pdb=" C12 CDL A 608 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.50e-02 4.44e+03 4.48e+00 ... (remaining 11220 not shown) Histogram of bond angle deviations from ideal: 99.13 - 107.28: 407 107.28 - 115.42: 6963 115.42 - 123.57: 7557 123.57 - 131.72: 279 131.72 - 139.86: 32 Bond angle restraints: 15238 Sorted by residual: angle pdb=" CA TYR A 381 " pdb=" CB TYR A 381 " pdb=" CG TYR A 381 " ideal model delta sigma weight residual 113.90 120.97 -7.07 1.80e+00 3.09e-01 1.54e+01 angle pdb=" C ASP B 366 " pdb=" N VAL B 367 " pdb=" CA VAL B 367 " ideal model delta sigma weight residual 121.97 128.98 -7.01 1.80e+00 3.09e-01 1.52e+01 angle pdb=" CB MET B 36 " pdb=" CG MET B 36 " pdb=" SD MET B 36 " ideal model delta sigma weight residual 112.70 123.29 -10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CB MET A 274 " pdb=" CG MET A 274 " pdb=" SD MET A 274 " ideal model delta sigma weight residual 112.70 123.10 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C LEU A 178 " pdb=" N VAL A 179 " pdb=" CA VAL A 179 " ideal model delta sigma weight residual 120.33 123.10 -2.77 8.00e-01 1.56e+00 1.20e+01 ... (remaining 15233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.78: 5978 18.78 - 37.56: 589 37.56 - 56.34: 142 56.34 - 75.12: 38 75.12 - 93.90: 14 Dihedral angle restraints: 6761 sinusoidal: 2661 harmonic: 4100 Sorted by residual: dihedral pdb=" CA ALA A 470 " pdb=" C ALA A 470 " pdb=" N PHE A 471 " pdb=" CA PHE A 471 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA GLY B 658 " pdb=" C GLY B 658 " pdb=" N LEU B 659 " pdb=" CA LEU B 659 " ideal model delta harmonic sigma weight residual 180.00 161.67 18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA5 CDL A 608 " pdb=" CA4 CDL A 608 " pdb=" OA6 CDL A 608 " pdb=" CA6 CDL A 608 " ideal model delta sinusoidal sigma weight residual 168.24 -97.86 -93.90 1 3.00e+01 1.11e-03 1.14e+01 ... (remaining 6758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1405 0.052 - 0.103: 337 0.103 - 0.155: 60 0.155 - 0.206: 5 0.206 - 0.258: 5 Chirality restraints: 1812 Sorted by residual: chirality pdb=" CA4 CDL A 608 " pdb=" CA3 CDL A 608 " pdb=" CA6 CDL A 608 " pdb=" OA6 CDL A 608 " both_signs ideal model delta sigma weight residual False -2.57 -2.32 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB VAL B 664 " pdb=" CA VAL B 664 " pdb=" CG1 VAL B 664 " pdb=" CG2 VAL B 664 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE B 182 " pdb=" CA ILE B 182 " pdb=" CG1 ILE B 182 " pdb=" CG2 ILE B 182 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1809 not shown) Planarity restraints: 1908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 105 " -0.016 2.00e-02 2.50e+03 2.09e-02 7.67e+00 pdb=" CG PHE B 105 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B 105 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 105 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE B 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 105 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 105 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 381 " 0.017 2.00e-02 2.50e+03 1.43e-02 4.08e+00 pdb=" CG TYR A 381 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 381 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 381 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 381 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 381 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 381 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 381 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 361 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO A 362 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " 0.028 5.00e-02 4.00e+02 ... (remaining 1905 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 3790 2.86 - 3.43: 12485 3.43 - 4.00: 21344 4.00 - 4.57: 30580 4.57 - 5.14: 43138 Nonbonded interactions: 111337 Sorted by model distance: nonbonded pdb=" O LEU A 541 " pdb=" OH TYR B 587 " model vdw 2.291 2.440 nonbonded pdb=" OG SER A 325 " pdb=" O ASN C 131 " model vdw 2.295 2.440 nonbonded pdb=" O SER A 119 " pdb=" OG1 THR A 123 " model vdw 2.300 2.440 nonbonded pdb=" OD1 ASN B 474 " pdb=" OG1 THR B 477 " model vdw 2.301 2.440 nonbonded pdb=" OG SER A 343 " pdb=" O ASN A 466 " model vdw 2.304 2.440 ... (remaining 111332 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 33.780 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.004 0.044 11225 Z= 0.256 Angle : 0.782 10.595 15238 Z= 0.396 Chirality : 0.046 0.258 1812 Planarity : 0.005 0.049 1908 Dihedral : 16.908 93.902 4127 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -1.09 (0.21), residues: 1437 helix: 0.09 (0.16), residues: 881 sheet: -1.58 (0.57), residues: 87 loop : -2.02 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 176 HIS 0.003 0.001 HIS A 242 PHE 0.048 0.002 PHE B 105 TYR 0.035 0.002 TYR A 381 ARG 0.008 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8029 (m-10) cc_final: 0.7828 (m-10) REVERT: B 515 MET cc_start: 0.7513 (ptm) cc_final: 0.7248 (ppp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2292 time to fit residues: 54.9870 Evaluate side-chains 136 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 129 optimal weight: 20.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11225 Z= 0.302 Angle : 0.607 8.183 15238 Z= 0.302 Chirality : 0.041 0.189 1812 Planarity : 0.005 0.079 1908 Dihedral : 12.803 88.022 1747 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.71 % Allowed : 9.17 % Favored : 90.12 % 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: -0.39 (0.21), residues: 1437 helix: 0.81 (0.17), residues: 875 sheet: -1.61 (0.62), residues: 73 loop : -1.99 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 PHE 0.021 0.002 PHE A 471 TYR 0.028 0.002 TYR A 381 ARG 0.005 0.000 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 1.066 Fit side-chains REVERT: A 135 VAL cc_start: 0.8781 (m) cc_final: 0.8530 (p) REVERT: B 515 MET cc_start: 0.7573 (ptm) cc_final: 0.7356 (ppp) outliers start: 8 outliers final: 5 residues processed: 149 average time/residue: 0.2287 time to fit residues: 49.2089 Evaluate side-chains 135 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 598 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 35 optimal weight: 0.2980 chunk 130 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 44 optimal weight: 0.0040 chunk 104 optimal weight: 1.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11225 Z= 0.164 Angle : 0.522 7.222 15238 Z= 0.258 Chirality : 0.038 0.171 1812 Planarity : 0.003 0.035 1908 Dihedral : 11.995 87.506 1747 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.88 % Allowed : 10.93 % Favored : 88.18 % 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: 0.09 (0.22), residues: 1437 helix: 1.18 (0.17), residues: 883 sheet: -1.48 (0.64), residues: 73 loop : -1.82 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 176 HIS 0.002 0.000 HIS A 451 PHE 0.014 0.001 PHE A 373 TYR 0.025 0.001 TYR A 381 ARG 0.002 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 1.159 Fit side-chains REVERT: B 13 LEU cc_start: 0.8022 (pt) cc_final: 0.7614 (pp) REVERT: B 515 MET cc_start: 0.7609 (ptm) cc_final: 0.7370 (ppp) REVERT: B 560 GLU cc_start: 0.7025 (pm20) cc_final: 0.6769 (mp0) outliers start: 10 outliers final: 7 residues processed: 145 average time/residue: 0.2135 time to fit residues: 45.6544 Evaluate side-chains 139 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 0.3980 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 138 optimal weight: 0.0070 chunk 68 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11225 Z= 0.162 Angle : 0.510 7.146 15238 Z= 0.252 Chirality : 0.038 0.181 1812 Planarity : 0.003 0.039 1908 Dihedral : 11.443 87.047 1747 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.85 % Allowed : 11.29 % Favored : 86.86 % 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: 0.30 (0.22), residues: 1437 helix: 1.38 (0.17), residues: 885 sheet: -1.52 (0.64), residues: 73 loop : -1.79 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 71 HIS 0.002 0.000 HIS B 404 PHE 0.013 0.001 PHE A 373 TYR 0.024 0.001 TYR A 381 ARG 0.002 0.000 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: B 515 MET cc_start: 0.7633 (ptm) cc_final: 0.7383 (ppp) REVERT: B 560 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6899 (mp0) outliers start: 21 outliers final: 15 residues processed: 157 average time/residue: 0.2111 time to fit residues: 48.5865 Evaluate side-chains 149 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 102 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11225 Z= 0.213 Angle : 0.549 9.206 15238 Z= 0.268 Chirality : 0.039 0.212 1812 Planarity : 0.004 0.044 1908 Dihedral : 11.242 86.066 1747 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.85 % Allowed : 14.02 % Favored : 84.13 % 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: 0.31 (0.22), residues: 1437 helix: 1.37 (0.17), residues: 885 sheet: -1.55 (0.65), residues: 73 loop : -1.76 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 71 HIS 0.002 0.001 HIS A 451 PHE 0.014 0.001 PHE A 373 TYR 0.025 0.001 TYR A 381 ARG 0.002 0.000 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.085 Fit side-chains REVERT: A 327 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8576 (m-80) REVERT: A 489 MET cc_start: 0.8644 (mtm) cc_final: 0.8397 (mtt) REVERT: B 13 LEU cc_start: 0.8034 (pt) cc_final: 0.7765 (pp) REVERT: B 125 GLN cc_start: 0.5406 (pm20) cc_final: 0.5057 (tm-30) REVERT: B 213 ARG cc_start: 0.7353 (tpm170) cc_final: 0.7030 (tpm170) REVERT: B 560 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: B 570 MET cc_start: 0.7753 (mtt) cc_final: 0.7551 (mtt) outliers start: 21 outliers final: 14 residues processed: 150 average time/residue: 0.2102 time to fit residues: 46.5186 Evaluate side-chains 143 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 138 optimal weight: 0.0570 chunk 114 optimal weight: 8.9990 chunk 64 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11225 Z= 0.157 Angle : 0.509 7.727 15238 Z= 0.251 Chirality : 0.038 0.161 1812 Planarity : 0.003 0.036 1908 Dihedral : 10.912 85.242 1747 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.03 % Allowed : 14.46 % Favored : 83.51 % 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: 0.52 (0.22), residues: 1437 helix: 1.54 (0.18), residues: 885 sheet: -1.55 (0.65), residues: 73 loop : -1.65 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 176 HIS 0.002 0.000 HIS B 404 PHE 0.012 0.001 PHE A 373 TYR 0.024 0.001 TYR A 381 ARG 0.001 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 1.513 Fit side-chains REVERT: A 327 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: A 471 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.6060 (m-10) REVERT: A 489 MET cc_start: 0.8595 (mtm) cc_final: 0.8386 (mtt) REVERT: B 13 LEU cc_start: 0.8058 (pt) cc_final: 0.7846 (pp) REVERT: B 125 GLN cc_start: 0.5440 (pm20) cc_final: 0.4979 (tm-30) REVERT: B 213 ARG cc_start: 0.7360 (tpm170) cc_final: 0.7057 (tpm170) REVERT: B 282 MET cc_start: 0.8213 (tpt) cc_final: 0.7993 (tpt) REVERT: B 560 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6855 (mp0) outliers start: 23 outliers final: 17 residues processed: 152 average time/residue: 0.2206 time to fit residues: 50.0354 Evaluate side-chains 149 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 116 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11225 Z= 0.185 Angle : 0.531 12.150 15238 Z= 0.261 Chirality : 0.038 0.149 1812 Planarity : 0.003 0.036 1908 Dihedral : 10.788 87.602 1747 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.94 % Allowed : 15.26 % Favored : 82.80 % 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: 0.56 (0.22), residues: 1437 helix: 1.56 (0.18), residues: 880 sheet: -1.53 (0.65), residues: 73 loop : -1.58 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 71 HIS 0.002 0.000 HIS B 404 PHE 0.013 0.001 PHE A 373 TYR 0.024 0.001 TYR A 381 ARG 0.002 0.000 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.193 Fit side-chains REVERT: A 327 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8531 (m-80) REVERT: A 471 PHE cc_start: 0.6995 (OUTLIER) cc_final: 0.6162 (m-10) REVERT: A 489 MET cc_start: 0.8619 (mtm) cc_final: 0.8353 (mtt) REVERT: B 125 GLN cc_start: 0.5405 (pm20) cc_final: 0.4950 (tm-30) REVERT: B 560 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6850 (mp0) outliers start: 22 outliers final: 18 residues processed: 149 average time/residue: 0.2187 time to fit residues: 48.4707 Evaluate side-chains 148 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 87 optimal weight: 0.0670 chunk 93 optimal weight: 30.0000 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11225 Z= 0.160 Angle : 0.519 8.358 15238 Z= 0.255 Chirality : 0.038 0.148 1812 Planarity : 0.003 0.035 1908 Dihedral : 10.495 89.925 1747 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.12 % Allowed : 15.34 % Favored : 82.54 % 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: 0.65 (0.22), residues: 1437 helix: 1.66 (0.18), residues: 876 sheet: -1.46 (0.60), residues: 83 loop : -1.58 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 71 HIS 0.003 0.000 HIS B 404 PHE 0.012 0.001 PHE A 373 TYR 0.023 0.001 TYR A 381 ARG 0.001 0.000 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.232 Fit side-chains REVERT: A 327 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8505 (m-80) REVERT: A 471 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.6023 (m-10) REVERT: A 489 MET cc_start: 0.8602 (mtm) cc_final: 0.8397 (mtt) REVERT: B 125 GLN cc_start: 0.5659 (pm20) cc_final: 0.5076 (tm-30) REVERT: B 560 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6862 (mp0) outliers start: 24 outliers final: 20 residues processed: 155 average time/residue: 0.2080 time to fit residues: 47.5707 Evaluate side-chains 153 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.9980 chunk 120 optimal weight: 0.0000 chunk 128 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11225 Z= 0.161 Angle : 0.518 9.526 15238 Z= 0.253 Chirality : 0.038 0.145 1812 Planarity : 0.003 0.035 1908 Dihedral : 10.254 86.559 1747 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.20 % Allowed : 15.52 % Favored : 82.28 % 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: 0.65 (0.22), residues: 1437 helix: 1.65 (0.18), residues: 879 sheet: -1.57 (0.62), residues: 78 loop : -1.56 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 71 HIS 0.003 0.000 HIS B 404 PHE 0.012 0.001 PHE A 373 TYR 0.023 0.001 TYR A 381 ARG 0.001 0.000 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 1.157 Fit side-chains REVERT: A 299 MET cc_start: 0.8441 (mtt) cc_final: 0.8100 (mtt) REVERT: A 327 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8530 (m-80) REVERT: A 471 PHE cc_start: 0.6868 (OUTLIER) cc_final: 0.6024 (m-10) REVERT: A 489 MET cc_start: 0.8609 (mtm) cc_final: 0.8404 (mtt) REVERT: B 125 GLN cc_start: 0.5613 (pm20) cc_final: 0.5055 (tm-30) REVERT: B 560 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6839 (mp0) outliers start: 25 outliers final: 19 residues processed: 152 average time/residue: 0.2219 time to fit residues: 49.7399 Evaluate side-chains 149 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 94 optimal weight: 0.4980 chunk 142 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 87 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 90 optimal weight: 30.0000 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 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11225 Z= 0.164 Angle : 0.524 9.565 15238 Z= 0.256 Chirality : 0.038 0.147 1812 Planarity : 0.003 0.036 1908 Dihedral : 10.052 81.684 1747 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.03 % Allowed : 16.14 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.22), residues: 1437 helix: 1.67 (0.18), residues: 879 sheet: -1.58 (0.62), residues: 78 loop : -1.55 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 71 HIS 0.003 0.000 HIS B 404 PHE 0.012 0.001 PHE A 373 TYR 0.024 0.001 TYR A 381 ARG 0.001 0.000 ARG B 394 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 1.199 Fit side-chains REVERT: A 299 MET cc_start: 0.8438 (mtt) cc_final: 0.8101 (mtt) REVERT: A 327 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8588 (m-80) REVERT: A 471 PHE cc_start: 0.6890 (OUTLIER) cc_final: 0.6039 (m-10) REVERT: A 489 MET cc_start: 0.8615 (mtm) cc_final: 0.8329 (mtt) REVERT: B 125 GLN cc_start: 0.5612 (pm20) cc_final: 0.5147 (tm-30) REVERT: B 213 ARG cc_start: 0.7585 (tpm170) cc_final: 0.7212 (tpm170) REVERT: B 560 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6798 (mp0) outliers start: 23 outliers final: 19 residues processed: 151 average time/residue: 0.2099 time to fit residues: 47.3932 Evaluate side-chains 149 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.0060 chunk 34 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 113 optimal weight: 0.0770 chunk 47 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.9758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.144308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107849 restraints weight = 15035.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106958 restraints weight = 10390.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107359 restraints weight = 8770.052| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11225 Z= 0.181 Angle : 0.526 9.501 15238 Z= 0.258 Chirality : 0.038 0.148 1812 Planarity : 0.003 0.041 1908 Dihedral : 9.983 80.286 1747 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.12 % Allowed : 16.23 % Favored : 81.66 % 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: 0.64 (0.22), residues: 1437 helix: 1.64 (0.17), residues: 879 sheet: -1.59 (0.62), residues: 78 loop : -1.56 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 71 HIS 0.002 0.000 HIS B 404 PHE 0.014 0.001 PHE A 373 TYR 0.024 0.001 TYR A 381 ARG 0.001 0.000 ARG B 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2037.94 seconds wall clock time: 37 minutes 53.86 seconds (2273.86 seconds total)