Starting phenix.real_space_refine on Fri Mar 15 15:39:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zri_14915/03_2024/7zri_14915_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zri_14915/03_2024/7zri_14915.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/7zri_14915/03_2024/7zri_14915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zri_14915/03_2024/7zri_14915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zri_14915/03_2024/7zri_14915_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zri_14915/03_2024/7zri_14915_updated.pdb" } 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1040 atoms to isotropic. 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 5 5.49 5 S 62 5.16 5 C 7123 2.51 5 N 1822 2.21 5 O 1995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 370": "OE1" <-> "OE2" Residue "C GLU 74": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11014 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: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5021 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 26, 'TRANS': 649} Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 105 Unusual residues: {' K': 5, 'CDL': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 102 Unusual residues: {' K': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.41, per 1000 atoms: 0.58 Number of scatterers: 11014 At special positions: 0 Unit cell: (104.236, 110.308, 155.848, 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 5 15.00 O 1995 8.00 N 1822 7.00 C 7123 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: 4.50 Conformation dependent library (CDL) restraints added in 2.3 seconds 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 7 sheets defined 55.3% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 2 through 31 Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 40 through 50 removed outlier: 3.586A pdb=" N VAL A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 82 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 133 through 156 removed outlier: 3.788A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 179 through 192 removed outlier: 4.149A pdb=" N LEU A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.932A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 273 removed outlier: 4.527A 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 277 through 304 removed outlier: 4.331A pdb=" N MET A 282 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET A 287 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 289 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 293 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.737A 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 380 through 398 removed outlier: 3.718A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 437 removed outlier: 3.754A pdb=" N LEU A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix removed outlier: 3.726A pdb=" N ALA A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.562A pdb=" N GLY A 452 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 460 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 494 Processing helix chain 'A' and resid 497 through 507 Processing helix chain 'A' and resid 525 through 539 Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'C' and resid 4 through 19 Processing helix chain 'C' and resid 22 through 33 Processing helix chain 'C' and resid 35 through 38 No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 92 through 108 Processing helix chain 'C' and resid 134 through 148 removed outlier: 4.345A pdb=" N TRP C 139 " --> pdb=" O GLN C 135 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Proline residue: C 142 - end of helix Processing helix chain 'C' and resid 152 through 161 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'D' and resid 6 through 24 removed outlier: 3.903A pdb=" N LEU D 10 " --> pdb=" O ILE D 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 25 removed outlier: 3.906A pdb=" N GLN B 16 " --> pdb=" O THR B 12 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 54 Processing helix chain 'B' and resid 62 through 97 Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 216 through 236 Processing helix chain 'B' and resid 240 through 246 removed outlier: 3.972A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 265 through 268 No H-bonds generated for 'chain 'B' and resid 265 through 268' Processing helix chain 'B' and resid 271 through 285 Processing helix chain 'B' and resid 292 through 300 removed outlier: 4.187A pdb=" N ASP B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 398 through 408 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 454 through 463 Processing helix chain 'B' and resid 475 through 485 removed outlier: 3.673A pdb=" N GLU B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 509 Processing helix chain 'B' and resid 523 through 527 Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 555 through 594 removed outlier: 4.278A pdb=" N LEU B 558 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 559 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET B 568 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 575 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 581 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN B 582 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP B 583 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 584 " --> pdb=" O ALA B 581 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 585 " --> pdb=" O ASN B 582 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE B 591 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 605 removed outlier: 4.013A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 637 removed outlier: 4.008A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 649 through 678 removed outlier: 4.370A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 202 through 205 Processing sheet with id= B, first strand: chain 'B' and resid 131 through 134 Processing sheet with id= C, first strand: chain 'B' and resid 138 through 140 removed outlier: 3.522A pdb=" N ASP B 138 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N THR B 180 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.712A pdb=" N VAL B 165 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 287 through 289 Processing sheet with id= F, first strand: chain 'B' and resid 513 through 515 removed outlier: 6.242A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS B 466 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU B 306 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL B 468 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP B 489 " --> pdb=" O MET B 469 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 321 through 323 removed outlier: 3.889A pdb=" N GLU B 321 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 444 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE B 323 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL B 442 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL B 442 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU B 431 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ALA B 444 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR B 429 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B 432 " --> pdb=" O GLY B 396 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY B 396 " --> pdb=" O VAL B 432 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 434 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG B 394 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 393 " --> pdb=" O ILE B 386 " (cutoff:3.500A) 533 hydrogen bonds defined for protein. 1416 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: 2.99 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1774 1.31 - 1.43: 2711 1.43 - 1.56: 6596 1.56 - 1.69: 12 1.69 - 1.81: 112 Bond restraints: 11205 Sorted by residual: bond pdb=" CB7 CDL B 702 " pdb=" OB8 CDL B 702 " ideal model delta sigma weight residual 1.334 1.423 -0.089 1.10e-02 8.26e+03 6.49e+01 bond pdb=" CB7 CDL A 606 " pdb=" OB8 CDL A 606 " ideal model delta sigma weight residual 1.334 1.421 -0.087 1.10e-02 8.26e+03 6.32e+01 bond pdb=" CA7 CDL A 606 " pdb=" OA8 CDL A 606 " ideal model delta sigma weight residual 1.334 1.421 -0.087 1.10e-02 8.26e+03 6.21e+01 bond pdb=" CA7 CDL B 702 " pdb=" OA8 CDL B 702 " ideal model delta sigma weight residual 1.334 1.417 -0.083 1.10e-02 8.26e+03 5.66e+01 bond pdb=" OB2 CDL A 606 " pdb=" PB2 CDL A 606 " ideal model delta sigma weight residual 1.579 1.668 -0.089 1.50e-02 4.44e+03 3.49e+01 ... (remaining 11200 not shown) Histogram of bond angle deviations from ideal: 94.86 - 102.69: 63 102.69 - 110.51: 3174 110.51 - 118.34: 5675 118.34 - 126.17: 6131 126.17 - 134.00: 161 Bond angle restraints: 15204 Sorted by residual: angle pdb=" C11 CDL B 702 " pdb=" CA5 CDL B 702 " pdb=" OA6 CDL B 702 " ideal model delta sigma weight residual 111.33 121.01 -9.68 1.32e+00 5.72e-01 5.36e+01 angle pdb=" C51 CDL B 702 " pdb=" CB5 CDL B 702 " pdb=" OB6 CDL B 702 " ideal model delta sigma weight residual 111.33 120.39 -9.06 1.32e+00 5.72e-01 4.69e+01 angle pdb=" C11 CDL A 606 " pdb=" CA5 CDL A 606 " pdb=" OA6 CDL A 606 " ideal model delta sigma weight residual 111.33 120.17 -8.84 1.32e+00 5.72e-01 4.47e+01 angle pdb=" C51 CDL A 606 " pdb=" CB5 CDL A 606 " pdb=" OB6 CDL A 606 " ideal model delta sigma weight residual 111.33 119.99 -8.66 1.32e+00 5.72e-01 4.29e+01 angle pdb=" C31 CDL A 606 " pdb=" CA7 CDL A 606 " pdb=" OA8 CDL A 606 " ideal model delta sigma weight residual 111.64 121.44 -9.80 1.65e+00 3.69e-01 3.54e+01 ... (remaining 15199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 5834 16.81 - 33.63: 661 33.63 - 50.44: 170 50.44 - 67.25: 58 67.25 - 84.06: 12 Dihedral angle restraints: 6735 sinusoidal: 2629 harmonic: 4106 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 180.00 153.10 26.90 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA THR B 236 " pdb=" C THR B 236 " pdb=" N ALA B 237 " pdb=" CA ALA B 237 " ideal model delta harmonic sigma weight residual 180.00 156.96 23.04 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ALA B 106 " pdb=" C ALA B 106 " pdb=" N ARG B 107 " pdb=" CA ARG B 107 " ideal model delta harmonic sigma weight residual -180.00 -160.34 -19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 6732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1231 0.042 - 0.084: 418 0.084 - 0.127: 143 0.127 - 0.169: 14 0.169 - 0.211: 5 Chirality restraints: 1811 Sorted by residual: chirality pdb=" CB THR B 516 " pdb=" CA THR B 516 " pdb=" OG1 THR B 516 " pdb=" CG2 THR B 516 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB ILE A 34 " pdb=" CA ILE A 34 " pdb=" CG1 ILE A 34 " pdb=" CG2 ILE A 34 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 1808 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 215 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO B 216 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 216 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 216 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 586 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C LYS B 586 " 0.043 2.00e-02 2.50e+03 pdb=" O LYS B 586 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR B 587 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 126 " 0.009 2.00e-02 2.50e+03 1.59e-02 5.07e+00 pdb=" CG TYR A 126 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 126 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR A 126 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 126 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 126 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 126 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 126 " -0.001 2.00e-02 2.50e+03 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.78: 2434 2.78 - 3.37: 12491 3.37 - 3.96: 21586 3.96 - 4.55: 30007 4.55 - 5.14: 44619 Nonbonded interactions: 111137 Sorted by model distance: nonbonded pdb=" O VAL A 107 " pdb=" OG1 THR A 111 " model vdw 2.196 2.440 nonbonded pdb=" OG1 THR C 72 " pdb=" O MET C 75 " model vdw 2.228 2.440 nonbonded pdb=" O SER A 119 " pdb=" OG1 THR A 123 " model vdw 2.274 2.440 nonbonded pdb=" O THR A 248 " pdb=" OG1 THR A 251 " model vdw 2.287 2.440 nonbonded pdb=" O LEU C 14 " pdb=" OG1 THR C 18 " model vdw 2.302 2.440 ... (remaining 111132 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: 0.010 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 3.640 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.390 Find NCS groups from input model: 0.300 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 : 0.006 0.089 11205 Z= 0.385 Angle : 0.919 9.799 15204 Z= 0.465 Chirality : 0.047 0.211 1811 Planarity : 0.006 0.064 1909 Dihedral : 16.165 84.064 4097 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.22 (0.21), residues: 1439 helix: -0.00 (0.17), residues: 857 sheet: -1.69 (0.59), residues: 77 loop : -1.98 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 32 HIS 0.002 0.000 HIS A 242 PHE 0.029 0.002 PHE A 260 TYR 0.033 0.002 TYR A 126 ARG 0.005 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.176 Fit side-chains REVERT: A 363 MET cc_start: 0.9147 (ttm) cc_final: 0.8814 (ttp) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2144 time to fit residues: 46.0054 Evaluate side-chains 116 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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: 0.0050 chunk 108 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 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: 0.8153 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11205 Z= 0.341 Angle : 0.601 6.379 15204 Z= 0.308 Chirality : 0.042 0.215 1811 Planarity : 0.005 0.054 1909 Dihedral : 11.479 76.023 1715 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.88 % Allowed : 9.96 % Favored : 89.16 % 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: -0.73 (0.22), residues: 1439 helix: 0.42 (0.17), residues: 868 sheet: -1.59 (0.55), residues: 87 loop : -1.86 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 32 HIS 0.005 0.001 HIS A 242 PHE 0.015 0.002 PHE A 354 TYR 0.024 0.002 TYR A 381 ARG 0.002 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.223 Fit side-chains REVERT: A 176 TRP cc_start: 0.7281 (m-10) cc_final: 0.6959 (m-10) REVERT: A 397 MET cc_start: 0.8563 (mmt) cc_final: 0.8277 (mmt) outliers start: 10 outliers final: 9 residues processed: 125 average time/residue: 0.2061 time to fit residues: 38.5697 Evaluate side-chains 121 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 614 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 115 optimal weight: 0.0570 chunk 129 optimal weight: 4.9990 chunk 44 optimal weight: 0.1980 chunk 104 optimal weight: 1.9990 overall best weight: 1.4504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11205 Z= 0.224 Angle : 0.529 6.202 15204 Z= 0.267 Chirality : 0.040 0.195 1811 Planarity : 0.004 0.052 1909 Dihedral : 10.594 75.079 1715 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.23 % Allowed : 12.86 % Favored : 85.90 % 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: -0.44 (0.22), residues: 1439 helix: 0.68 (0.18), residues: 863 sheet: -1.60 (0.54), residues: 87 loop : -1.75 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 71 HIS 0.004 0.001 HIS A 242 PHE 0.010 0.001 PHE A 527 TYR 0.020 0.001 TYR A 381 ARG 0.001 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 1.303 Fit side-chains REVERT: A 176 TRP cc_start: 0.7260 (m-10) cc_final: 0.6842 (m-10) REVERT: A 363 MET cc_start: 0.9190 (ttm) cc_final: 0.8877 (ttp) outliers start: 14 outliers final: 11 residues processed: 132 average time/residue: 0.2028 time to fit residues: 40.2778 Evaluate side-chains 128 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 614 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 0.2980 chunk 87 optimal weight: 30.0000 chunk 130 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 ASN C 154 GLN B 30 GLN B 80 ASN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11205 Z= 0.199 Angle : 0.514 7.413 15204 Z= 0.258 Chirality : 0.039 0.141 1811 Planarity : 0.004 0.051 1909 Dihedral : 9.989 75.334 1715 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.23 % Allowed : 14.80 % Favored : 83.96 % 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: -0.26 (0.22), residues: 1439 helix: 0.82 (0.18), residues: 861 sheet: -1.58 (0.54), residues: 86 loop : -1.66 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 71 HIS 0.002 0.000 HIS A 451 PHE 0.009 0.001 PHE A 527 TYR 0.019 0.001 TYR A 381 ARG 0.002 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 1.236 Fit side-chains REVERT: A 176 TRP cc_start: 0.7247 (m-10) cc_final: 0.6986 (m-90) outliers start: 14 outliers final: 11 residues processed: 135 average time/residue: 0.2005 time to fit residues: 41.0451 Evaluate side-chains 130 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 614 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11205 Z= 0.205 Angle : 0.506 6.048 15204 Z= 0.256 Chirality : 0.039 0.133 1811 Planarity : 0.004 0.052 1909 Dihedral : 9.587 75.982 1715 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.50 % Allowed : 16.21 % Favored : 82.29 % 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: -0.17 (0.22), residues: 1439 helix: 0.90 (0.18), residues: 861 sheet: -1.56 (0.55), residues: 86 loop : -1.63 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 71 HIS 0.002 0.000 HIS A 451 PHE 0.009 0.001 PHE A 527 TYR 0.020 0.001 TYR A 381 ARG 0.002 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.341 Fit side-chains REVERT: C 89 VAL cc_start: 0.8807 (p) cc_final: 0.8574 (t) outliers start: 17 outliers final: 12 residues processed: 130 average time/residue: 0.2075 time to fit residues: 40.9333 Evaluate side-chains 125 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 614 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11205 Z= 0.262 Angle : 0.532 7.599 15204 Z= 0.268 Chirality : 0.040 0.139 1811 Planarity : 0.004 0.053 1909 Dihedral : 9.465 76.780 1715 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.03 % Allowed : 16.92 % Favored : 81.06 % 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: -0.17 (0.22), residues: 1439 helix: 0.88 (0.18), residues: 863 sheet: -1.59 (0.56), residues: 86 loop : -1.59 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 186 HIS 0.002 0.000 HIS A 451 PHE 0.010 0.001 PHE A 373 TYR 0.021 0.002 TYR A 381 ARG 0.002 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: C 89 VAL cc_start: 0.8846 (p) cc_final: 0.8617 (t) REVERT: B 203 MET cc_start: 0.7723 (tpp) cc_final: 0.7304 (tpt) outliers start: 23 outliers final: 19 residues processed: 133 average time/residue: 0.2186 time to fit residues: 43.2869 Evaluate side-chains 131 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 63 optimal weight: 0.0370 chunk 85 optimal weight: 10.0000 overall best weight: 1.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 154 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11205 Z= 0.179 Angle : 0.503 6.124 15204 Z= 0.254 Chirality : 0.038 0.141 1811 Planarity : 0.004 0.053 1909 Dihedral : 9.164 76.435 1715 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.67 % Allowed : 17.80 % Favored : 80.53 % 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: 0.04 (0.23), residues: 1439 helix: 1.05 (0.18), residues: 850 sheet: -1.63 (0.56), residues: 86 loop : -1.41 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 364 HIS 0.001 0.000 HIS A 451 PHE 0.009 0.001 PHE A 527 TYR 0.018 0.001 TYR A 381 ARG 0.002 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 1.363 Fit side-chains REVERT: C 89 VAL cc_start: 0.8792 (p) cc_final: 0.8564 (t) REVERT: B 203 MET cc_start: 0.7642 (tpp) cc_final: 0.7254 (tpt) outliers start: 19 outliers final: 14 residues processed: 127 average time/residue: 0.2041 time to fit residues: 39.6621 Evaluate side-chains 126 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 93 optimal weight: 30.0000 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11205 Z= 0.165 Angle : 0.493 6.420 15204 Z= 0.249 Chirality : 0.038 0.131 1811 Planarity : 0.004 0.052 1909 Dihedral : 8.895 76.381 1715 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.85 % Allowed : 17.80 % Favored : 80.35 % 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: 0.13 (0.23), residues: 1439 helix: 1.15 (0.18), residues: 840 sheet: -1.45 (0.56), residues: 86 loop : -1.41 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 364 HIS 0.001 0.000 HIS B 563 PHE 0.009 0.001 PHE A 527 TYR 0.025 0.001 TYR A 126 ARG 0.002 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: C 89 VAL cc_start: 0.8757 (p) cc_final: 0.8544 (t) REVERT: B 109 LEU cc_start: 0.0637 (OUTLIER) cc_final: 0.0367 (pp) REVERT: B 203 MET cc_start: 0.7804 (tpp) cc_final: 0.7399 (tpt) REVERT: B 282 MET cc_start: 0.8794 (mmp) cc_final: 0.8585 (tpp) outliers start: 21 outliers final: 19 residues processed: 134 average time/residue: 0.2155 time to fit residues: 44.9249 Evaluate side-chains 130 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.0181 > 50: distance: 9 - 34: 27.363 distance: 15 - 20: 8.664 distance: 16 - 42: 10.645 distance: 20 - 21: 13.318 distance: 21 - 22: 10.467 distance: 21 - 24: 9.068 distance: 22 - 23: 24.849 distance: 22 - 29: 20.804 distance: 23 - 51: 37.697 distance: 24 - 25: 10.057 distance: 25 - 26: 4.630 distance: 26 - 27: 10.986 distance: 26 - 28: 22.018 distance: 29 - 30: 12.711 distance: 30 - 31: 36.393 distance: 30 - 33: 12.853 distance: 31 - 32: 7.975 distance: 31 - 34: 13.227 distance: 34 - 35: 13.194 distance: 35 - 36: 24.027 distance: 35 - 38: 33.896 distance: 36 - 37: 20.706 distance: 36 - 42: 6.502 distance: 37 - 65: 35.115 distance: 38 - 39: 12.834 distance: 39 - 40: 4.163 distance: 39 - 41: 4.948 distance: 42 - 43: 16.354 distance: 43 - 44: 21.515 distance: 43 - 46: 40.676 distance: 44 - 45: 6.858 distance: 44 - 51: 19.313 distance: 46 - 47: 16.962 distance: 47 - 48: 20.768 distance: 48 - 49: 12.921 distance: 49 - 50: 33.279 distance: 52 - 53: 12.549 distance: 52 - 55: 26.565 distance: 53 - 54: 17.880 distance: 53 - 60: 13.641 distance: 55 - 56: 41.348 distance: 60 - 61: 4.290 distance: 61 - 62: 37.230 distance: 61 - 64: 26.821 distance: 62 - 63: 14.079 distance: 62 - 65: 32.924 distance: 65 - 66: 6.656 distance: 66 - 67: 3.548 distance: 66 - 69: 25.625 distance: 67 - 68: 34.859 distance: 67 - 72: 20.352 distance: 69 - 70: 30.920 distance: 69 - 71: 16.759 distance: 72 - 73: 9.372 distance: 73 - 74: 17.122 distance: 73 - 76: 21.274 distance: 74 - 75: 10.308 distance: 74 - 81: 22.043 distance: 76 - 77: 32.920 distance: 77 - 78: 18.717 distance: 78 - 79: 32.505 distance: 79 - 80: 17.326 distance: 81 - 82: 7.920 distance: 82 - 83: 6.845 distance: 82 - 85: 5.046 distance: 83 - 84: 26.420 distance: 83 - 90: 15.961 distance: 85 - 86: 28.486 distance: 86 - 87: 10.272 distance: 90 - 91: 29.186 distance: 91 - 92: 28.467 distance: 91 - 94: 25.802 distance: 92 - 93: 31.254 distance: 92 - 98: 19.387 distance: 94 - 95: 42.258 distance: 95 - 96: 38.287 distance: 95 - 97: 38.800