Starting phenix.real_space_refine on Wed Feb 12 23:14:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a8z_11680/02_2025/7a8z_11680.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a8z_11680/02_2025/7a8z_11680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7a8z_11680/02_2025/7a8z_11680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a8z_11680/02_2025/7a8z_11680.map" model { file = "/net/cci-nas-00/data/ceres_data/7a8z_11680/02_2025/7a8z_11680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a8z_11680/02_2025/7a8z_11680.cif" } resolution = 3.35 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= 0.036 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 5352 2.51 5 N 1447 2.21 5 O 1575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8402 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4211 Classifications: {'peptide': 553} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 29, 'TRANS': 523} Chain breaks: 4 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 4191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4191 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 28, 'TRANS': 521} Chain breaks: 4 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 62 Time building chain proxies: 5.48, per 1000 atoms: 0.65 Number of scatterers: 8402 At special positions: 0 Unit cell: (99.75, 126, 82.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1575 8.00 N 1447 7.00 C 5352 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2006 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 55.0% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 72 through 85 removed outlier: 4.650A pdb=" N ARG A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 148 through 156 removed outlier: 4.614A pdb=" N LYS A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 240 through 254 Processing helix chain 'A' and resid 259 through 271 removed outlier: 3.877A pdb=" N ALA A 263 " --> pdb=" O ASP A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 381 through 387 removed outlier: 4.164A pdb=" N ARG A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.540A pdb=" N ARG A 392 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 400 through 418 removed outlier: 3.675A pdb=" N LEU A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 440 removed outlier: 3.732A pdb=" N ASP A 440 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 463 removed outlier: 3.693A pdb=" N ARG A 463 " --> pdb=" O LYS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 481 removed outlier: 3.713A pdb=" N SER A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 504 removed outlier: 3.521A pdb=" N GLY A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 531 removed outlier: 3.542A pdb=" N ALA A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 559 Processing helix chain 'A' and resid 575 through 579 removed outlier: 3.536A pdb=" N THR A 579 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 617 Processing helix chain 'A' and resid 620 through 635 Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 655 through 663 Processing helix chain 'A' and resid 692 through 701 Processing helix chain 'A' and resid 702 through 712 Processing helix chain 'A' and resid 716 through 733 Processing helix chain 'A' and resid 733 through 738 removed outlier: 3.759A pdb=" N PHE A 737 " --> pdb=" O ASN A 733 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 733 through 738' Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 63 through 69 removed outlier: 3.849A pdb=" N GLU B 67 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 85 removed outlier: 3.525A pdb=" N THR B 77 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 removed outlier: 4.212A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 156 removed outlier: 4.564A pdb=" N LYS B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 260 through 272 Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.942A pdb=" N ILE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 381 through 387 removed outlier: 4.017A pdb=" N ARG B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 removed outlier: 4.146A pdb=" N ILE B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 417 removed outlier: 3.773A pdb=" N LEU B 404 " --> pdb=" O HIS B 400 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 405 " --> pdb=" O PRO B 401 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 removed outlier: 3.520A pdb=" N TYR B 426 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.683A pdb=" N ASP B 440 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 464 Processing helix chain 'B' and resid 468 through 481 removed outlier: 3.679A pdb=" N SER B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 509 through 514 removed outlier: 3.990A pdb=" N ASP B 513 " --> pdb=" O ASP B 509 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU B 514 " --> pdb=" O PRO B 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 509 through 514' Processing helix chain 'B' and resid 515 through 531 removed outlier: 3.744A pdb=" N SER B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 531 " --> pdb=" O SER B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 560 Processing helix chain 'B' and resid 575 through 579 Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 605 through 617 removed outlier: 3.824A pdb=" N LEU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 635 Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 694 through 698 removed outlier: 3.959A pdb=" N VAL B 697 " --> pdb=" O VAL B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 733 Processing helix chain 'B' and resid 734 through 736 No H-bonds generated for 'chain 'B' and resid 734 through 736' Processing sheet with id=AA1, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AA2, first strand: chain 'A' and resid 666 through 668 removed outlier: 6.918A pdb=" N GLY A 680 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 591 through 592 Processing sheet with id=AA4, first strand: chain 'B' and resid 666 through 668 removed outlier: 6.509A pdb=" N ASP B 682 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL B 687 " --> pdb=" O ASP B 682 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 1005 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: 2.22 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2795 1.34 - 1.46: 1444 1.46 - 1.58: 4310 1.58 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 8601 Sorted by residual: bond pdb=" CG PRO A 92 " pdb=" CD PRO A 92 " ideal model delta sigma weight residual 1.503 1.561 -0.058 3.40e-02 8.65e+02 2.95e+00 bond pdb=" CB PRO A 92 " pdb=" CG PRO A 92 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.45e+00 bond pdb=" N VAL A 423 " pdb=" CA VAL A 423 " ideal model delta sigma weight residual 1.474 1.456 0.018 1.57e-02 4.06e+03 1.37e+00 bond pdb=" CB VAL B 166 " pdb=" CG1 VAL B 166 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" CA ASP B 513 " pdb=" CB ASP B 513 " ideal model delta sigma weight residual 1.528 1.544 -0.016 1.67e-02 3.59e+03 9.16e-01 ... (remaining 8596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 11446 1.61 - 3.22: 217 3.22 - 4.83: 32 4.83 - 6.44: 12 6.44 - 8.06: 1 Bond angle restraints: 11708 Sorted by residual: angle pdb=" N ARG A 515 " pdb=" CA ARG A 515 " pdb=" C ARG A 515 " ideal model delta sigma weight residual 113.12 108.62 4.50 1.25e+00 6.40e-01 1.30e+01 angle pdb=" C PRO A 422 " pdb=" N VAL A 423 " pdb=" CA VAL A 423 " ideal model delta sigma weight residual 121.65 118.27 3.38 9.40e-01 1.13e+00 1.29e+01 angle pdb=" N VAL B 710 " pdb=" CA VAL B 710 " pdb=" C VAL B 710 " ideal model delta sigma weight residual 111.81 108.81 3.00 8.60e-01 1.35e+00 1.21e+01 angle pdb=" CA PRO A 92 " pdb=" N PRO A 92 " pdb=" CD PRO A 92 " ideal model delta sigma weight residual 112.00 107.81 4.19 1.40e+00 5.10e-01 8.97e+00 angle pdb=" N VAL A 423 " pdb=" CA VAL A 423 " pdb=" C VAL A 423 " ideal model delta sigma weight residual 106.21 109.33 -3.12 1.07e+00 8.73e-01 8.51e+00 ... (remaining 11703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 4480 17.14 - 34.27: 442 34.27 - 51.40: 89 51.40 - 68.54: 22 68.54 - 85.67: 6 Dihedral angle restraints: 5039 sinusoidal: 1912 harmonic: 3127 Sorted by residual: dihedral pdb=" CA VAL A 423 " pdb=" C VAL A 423 " pdb=" N ALA A 424 " pdb=" CA ALA A 424 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASP A 513 " pdb=" C ASP A 513 " pdb=" N LEU A 514 " pdb=" CA LEU A 514 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA LEU A 604 " pdb=" C LEU A 604 " pdb=" N PRO A 605 " pdb=" CA PRO A 605 " ideal model delta harmonic sigma weight residual -180.00 -157.91 -22.09 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 5036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 667 0.027 - 0.055: 398 0.055 - 0.082: 158 0.082 - 0.110: 55 0.110 - 0.137: 11 Chirality restraints: 1289 Sorted by residual: chirality pdb=" CA PRO A 605 " pdb=" N PRO A 605 " pdb=" C PRO A 605 " pdb=" CB PRO A 605 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ASN B 330 " pdb=" N ASN B 330 " pdb=" C ASN B 330 " pdb=" CB ASN B 330 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA PRO A 92 " pdb=" N PRO A 92 " pdb=" C PRO A 92 " pdb=" CB PRO A 92 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1286 not shown) Planarity restraints: 1531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 91 " 0.075 5.00e-02 4.00e+02 1.12e-01 2.02e+01 pdb=" N PRO A 92 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO A 92 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 92 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 99 " 0.027 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO A 100 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 100 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 100 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 604 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO B 605 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 605 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 605 " 0.021 5.00e-02 4.00e+02 ... (remaining 1528 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2003 2.78 - 3.31: 7835 3.31 - 3.84: 13189 3.84 - 4.37: 15440 4.37 - 4.90: 27330 Nonbonded interactions: 65797 Sorted by model distance: nonbonded pdb=" O GLU B 67 " pdb=" OG1 THR B 70 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP A 580 " pdb=" OG SER A 583 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLN B 88 " pdb=" NE1 TRP B 90 " model vdw 2.284 3.120 nonbonded pdb=" OD1 ASP A 592 " pdb=" NZ LYS A 613 " model vdw 2.305 3.120 nonbonded pdb=" O GLU A 67 " pdb=" OG1 THR A 70 " model vdw 2.314 3.040 ... (remaining 65792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 42 through 124 or resid 141 through 190 or resid 238 throu \ gh 249 or (resid 250 and (name N or name CA or name C or name O or name CB )) or \ resid 251 through 384 or (resid 385 and (name N or name CA or name C or name O \ or name CB )) or resid 386 through 390 or (resid 391 through 392 and (name N or \ name CA or name C or name O or name CB )) or resid 393 through 406 or (resid 407 \ and (name N or name CA or name C or name O or name CB )) or resid 408 through 4 \ 62 or (resid 463 through 464 and (name N or name CA or name C or name O or name \ CB )) or resid 465 through 525 or (resid 526 and (name N or name CA or name C or \ name O or name CB )) or resid 527 through 639 or (resid 640 and (name N or name \ CA or name C or name O or name CB )) or resid 641 through 739 or (resid 740 and \ (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 42 through 142 or (resid 143 through 144 and (name N or na \ me CA or name C or name O or name CB )) or resid 145 through 152 or (resid 153 a \ nd (name N or name CA or name C or name O or name CB )) or resid 154 through 271 \ or resid 329 through 344 or (resid 345 and (name N or name CA or name C or name \ O or name CB )) or resid 378 through 391 or (resid 392 and (name N or name CA o \ r name C or name O or name CB )) or resid 393 through 398 or (resid 399 and (nam \ e N or name CA or name C or name O or name CB )) or resid 400 through 486 or (re \ sid 487 and (name N or name CA or name C or name O or name CB )) or resid 488 th \ rough 512 or (resid 513 and (name N or name CA or name C or name O or name CB )) \ or resid 514 or (resid 515 and (name N or name CA or name C or name O or name C \ B )) or resid 516 through 556 or (resid 557 through 559 and (name N or name CA o \ r name C or name O or name CB )) or resid 560 through 647 or (resid 648 through \ 649 and (name N or name CA or name C or name O or name CB )) or resid 650 throug \ h 685 or (resid 686 and (name N or name CA or name C or name O or name CB )) or \ resid 687 through 740)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.440 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 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 0.060 8601 Z= 0.258 Angle : 0.588 8.055 11708 Z= 0.326 Chirality : 0.041 0.137 1289 Planarity : 0.005 0.112 1531 Dihedral : 14.415 85.674 3033 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.57 % Favored : 92.34 % 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: -1.49 (0.25), residues: 1083 helix: -0.10 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -1.90 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 191 HIS 0.003 0.001 HIS B 97 PHE 0.011 0.001 PHE A 332 TYR 0.009 0.001 TYR A 597 ARG 0.002 0.000 ARG B 395 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.890 Fit side-chains REVERT: B 557 LYS cc_start: 0.7456 (ttmt) cc_final: 0.7242 (ttmt) REVERT: B 723 ASP cc_start: 0.7724 (t70) cc_final: 0.7418 (t0) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2707 time to fit residues: 30.4317 Evaluate side-chains 70 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 0.0270 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.145507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.109843 restraints weight = 10692.045| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.14 r_work: 0.3165 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8601 Z= 0.180 Angle : 0.527 5.605 11708 Z= 0.271 Chirality : 0.040 0.147 1289 Planarity : 0.005 0.071 1531 Dihedral : 4.322 23.396 1178 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.11 % Favored : 92.80 % Rotamer: Outliers : 0.24 % Allowed : 6.62 % Favored : 93.14 % 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: -1.07 (0.25), residues: 1083 helix: 0.37 (0.23), residues: 535 sheet: None (None), residues: 0 loop : -1.88 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 191 HIS 0.003 0.001 HIS B 116 PHE 0.011 0.001 PHE A 332 TYR 0.010 0.001 TYR B 337 ARG 0.004 0.000 ARG B 484 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.918 Fit side-chains REVERT: A 514 LEU cc_start: 0.7655 (tp) cc_final: 0.7326 (tp) REVERT: B 155 TYR cc_start: 0.8757 (m-80) cc_final: 0.8140 (m-80) REVERT: B 626 VAL cc_start: 0.7976 (t) cc_final: 0.7743 (p) outliers start: 2 outliers final: 2 residues processed: 83 average time/residue: 0.2322 time to fit residues: 26.5140 Evaluate side-chains 72 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain B residue 337 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.4139 > 50: distance: 35 - 59: 23.865 distance: 42 - 67: 10.654 distance: 50 - 75: 14.533 distance: 54 - 59: 20.100 distance: 55 - 83: 10.659 distance: 59 - 60: 20.111 distance: 60 - 61: 9.749 distance: 60 - 63: 18.082 distance: 61 - 62: 10.021 distance: 61 - 67: 10.806 distance: 63 - 64: 18.720 distance: 64 - 65: 24.119 distance: 64 - 66: 27.532 distance: 67 - 68: 7.179 distance: 68 - 69: 17.045 distance: 68 - 71: 7.380 distance: 69 - 70: 6.649 distance: 69 - 75: 24.619 distance: 71 - 72: 16.597 distance: 72 - 73: 18.683 distance: 72 - 74: 16.266 distance: 75 - 76: 11.673 distance: 76 - 77: 7.871 distance: 76 - 79: 13.285 distance: 77 - 78: 22.704 distance: 77 - 83: 7.343 distance: 79 - 80: 26.049 distance: 80 - 81: 9.681 distance: 80 - 82: 11.575 distance: 83 - 84: 16.847 distance: 84 - 85: 25.820 distance: 84 - 87: 27.486 distance: 85 - 86: 15.404 distance: 85 - 91: 7.195 distance: 87 - 88: 51.089 distance: 88 - 89: 10.381 distance: 88 - 90: 5.486 distance: 91 - 92: 21.392 distance: 92 - 93: 32.393 distance: 92 - 95: 36.054 distance: 93 - 94: 11.922 distance: 93 - 99: 23.105 distance: 95 - 96: 15.191 distance: 96 - 97: 27.840 distance: 97 - 98: 42.276 distance: 99 - 100: 37.886 distance: 100 - 101: 5.900 distance: 101 - 102: 14.615 distance: 101 - 103: 16.158 distance: 103 - 104: 27.378 distance: 104 - 105: 10.691 distance: 104 - 107: 19.853 distance: 105 - 106: 26.216 distance: 105 - 111: 16.768 distance: 107 - 108: 10.919 distance: 107 - 109: 33.112 distance: 108 - 110: 17.086 distance: 111 - 112: 14.759 distance: 111 - 164: 7.305 distance: 112 - 113: 9.266 distance: 112 - 115: 18.380 distance: 113 - 114: 19.562 distance: 113 - 118: 23.322 distance: 114 - 161: 11.733 distance: 115 - 116: 8.429 distance: 115 - 117: 9.819 distance: 118 - 119: 20.347 distance: 119 - 120: 16.572 distance: 119 - 122: 4.582 distance: 120 - 121: 17.544 distance: 120 - 132: 18.139 distance: 122 - 123: 14.988 distance: 123 - 124: 5.677 distance: 123 - 125: 8.438 distance: 124 - 126: 8.614 distance: 125 - 127: 4.354 distance: 125 - 128: 9.788 distance: 126 - 127: 4.395 distance: 127 - 129: 9.347 distance: 128 - 130: 9.016 distance: 129 - 131: 11.202 distance: 130 - 131: 8.508 distance: 132 - 133: 21.606 distance: 133 - 134: 8.137 distance: 133 - 136: 21.255 distance: 134 - 135: 14.707 distance: 134 - 141: 12.282 distance: 136 - 137: 19.126 distance: 138 - 139: 10.975 distance: 138 - 140: 23.633