Starting phenix.real_space_refine on Fri Jul 3 00:05:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x1s_38000/07_2026/8x1s_38000_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x1s_38000/07_2026/8x1s_38000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x1s_38000/07_2026/8x1s_38000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x1s_38000/07_2026/8x1s_38000.map" model { file = "/net/cci-nas-00/data/ceres_data/8x1s_38000/07_2026/8x1s_38000_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x1s_38000/07_2026/8x1s_38000_neut.cif" } resolution = 2.37 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.133 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 42 5.16 5 Cl 4 4.86 5 C 7233 2.51 5 N 1790 2.21 5 O 1944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 130 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11015 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5460 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 670} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5463 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 670} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'I2U': 1, 'LPE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'I2U': 1, 'LPE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 2.34, per 1000 atoms: 0.21 Number of scatterers: 11015 At special positions: 0 Unit cell: (88.54, 127.684, 102.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 42 16.00 P 2 15.00 O 1944 8.00 N 1790 7.00 C 7233 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: 0.97 Conformation dependent library (CDL) restraints added in 337.6 milliseconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2628 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 5 sheets defined 69.7% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 68 through 99 removed outlier: 5.665A pdb=" N LEU A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N SER A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.713A pdb=" N LEU A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Proline residue: A 112 - end of helix removed outlier: 3.730A pdb=" N PHE A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 147 Processing helix chain 'A' and resid 169 through 196 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.503A pdb=" N VAL A 201 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL A 202 " --> pdb=" O GLY A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 241 through 253 removed outlier: 3.764A pdb=" N GLN A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 258 through 282 Processing helix chain 'A' and resid 291 through 307 Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 332 through 366 removed outlier: 5.824A pdb=" N GLY A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 428 through 433 Processing helix chain 'A' and resid 436 through 447 removed outlier: 3.530A pdb=" N ASN A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 453 removed outlier: 4.728A pdb=" N MET A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 465 Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 483 through 504 removed outlier: 3.697A pdb=" N ILE A 499 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 563 through 585 Processing helix chain 'A' and resid 612 through 618 Processing helix chain 'A' and resid 635 through 639 removed outlier: 3.767A pdb=" N ASN A 638 " --> pdb=" O LEU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 677 Processing helix chain 'A' and resid 687 through 697 removed outlier: 3.573A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 712 through 725 Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 59 through 64 Processing helix chain 'B' and resid 68 through 99 removed outlier: 5.842A pdb=" N LEU B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N SER B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 120 removed outlier: 3.713A pdb=" N LEU B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Proline residue: B 112 - end of helix removed outlier: 3.915A pdb=" N PHE B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 148 Processing helix chain 'B' and resid 169 through 196 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.588A pdb=" N VAL B 201 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL B 202 " --> pdb=" O GLY B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 241 through 253 removed outlier: 3.619A pdb=" N GLN B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 258 through 282 Processing helix chain 'B' and resid 291 through 307 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 332 through 366 removed outlier: 6.018A pdb=" N GLY B 341 " --> pdb=" O GLN B 337 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP B 342 " --> pdb=" O ASN B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 396 through 406 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 436 through 447 removed outlier: 3.626A pdb=" N LEU B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 456 through 465 Processing helix chain 'B' and resid 465 through 482 Processing helix chain 'B' and resid 483 through 504 removed outlier: 3.697A pdb=" N ILE B 499 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 563 through 585 Processing helix chain 'B' and resid 612 through 618 Processing helix chain 'B' and resid 621 through 625 removed outlier: 4.341A pdb=" N ASP B 624 " --> pdb=" O ASN B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 639 removed outlier: 3.855A pdb=" N ASN B 638 " --> pdb=" O LEU B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 677 Processing helix chain 'B' and resid 687 through 697 removed outlier: 3.572A pdb=" N ILE B 691 " --> pdb=" O ASP B 687 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR B 697 " --> pdb=" O LYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 707 No H-bonds generated for 'chain 'B' and resid 705 through 707' Processing helix chain 'B' and resid 712 through 725 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.596A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N ASN A 513 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 12.876A pdb=" N VAL A 535 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS A 536 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP A 652 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE A 538 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE A 710 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE A 683 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 589 Processing sheet with id=AA4, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.508A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N ASN B 513 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 12.852A pdb=" N VAL B 535 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS B 536 " --> pdb=" O ILE B 650 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP B 652 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE B 538 " --> pdb=" O ASP B 652 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N PHE B 710 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE B 683 " --> pdb=" O PHE B 710 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 588 through 590 703 hydrogen bonds defined for protein. 2016 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: 1.85 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1766 1.32 - 1.44: 2911 1.44 - 1.56: 6506 1.56 - 1.69: 5 1.69 - 1.81: 65 Bond restraints: 11253 Sorted by residual: bond pdb=" CD GLN B 672 " pdb=" OE1 GLN B 672 " ideal model delta sigma weight residual 1.231 1.327 -0.096 1.90e-02 2.77e+03 2.53e+01 bond pdb=" CD GLN B 672 " pdb=" NE2 GLN B 672 " ideal model delta sigma weight residual 1.328 1.229 0.099 2.10e-02 2.27e+03 2.24e+01 bond pdb=" C SER B 663 " pdb=" O SER B 663 " ideal model delta sigma weight residual 1.237 1.191 0.046 1.19e-02 7.06e+03 1.50e+01 bond pdb=" C THR A 517 " pdb=" O THR A 517 " ideal model delta sigma weight residual 1.236 1.202 0.034 9.90e-03 1.02e+04 1.15e+01 bond pdb=" O33 LPE B 802 " pdb=" P LPE B 802 " ideal model delta sigma weight residual 1.673 1.609 0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 11248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 14841 2.91 - 5.83: 383 5.83 - 8.74: 46 8.74 - 11.65: 12 11.65 - 14.56: 2 Bond angle restraints: 15284 Sorted by residual: angle pdb=" N ILE A 480 " pdb=" CA ILE A 480 " pdb=" C ILE A 480 " ideal model delta sigma weight residual 110.72 118.48 -7.76 1.01e+00 9.80e-01 5.90e+01 angle pdb=" N LYS A 464 " pdb=" CA LYS A 464 " pdb=" C LYS A 464 " ideal model delta sigma weight residual 111.14 119.40 -8.26 1.08e+00 8.57e-01 5.84e+01 angle pdb=" N LEU B 482 " pdb=" CA LEU B 482 " pdb=" C LEU B 482 " ideal model delta sigma weight residual 110.35 100.32 10.03 1.38e+00 5.25e-01 5.29e+01 angle pdb=" N SER B 17 " pdb=" CA SER B 17 " pdb=" C SER B 17 " ideal model delta sigma weight residual 110.52 100.39 10.13 1.48e+00 4.57e-01 4.68e+01 angle pdb=" C VAL B 288 " pdb=" N PRO B 289 " pdb=" CA PRO B 289 " ideal model delta sigma weight residual 119.76 126.75 -6.99 1.03e+00 9.43e-01 4.60e+01 ... (remaining 15279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.45: 6505 29.45 - 58.89: 178 58.89 - 88.34: 17 88.34 - 117.78: 0 117.78 - 147.23: 6 Dihedral angle restraints: 6706 sinusoidal: 2638 harmonic: 4068 Sorted by residual: dihedral pdb=" C THR B 517 " pdb=" N THR B 517 " pdb=" CA THR B 517 " pdb=" CB THR B 517 " ideal model delta harmonic sigma weight residual -122.00 -104.47 -17.53 0 2.50e+00 1.60e-01 4.91e+01 dihedral pdb=" N ARG A 389 " pdb=" C ARG A 389 " pdb=" CA ARG A 389 " pdb=" CB ARG A 389 " ideal model delta harmonic sigma weight residual 122.80 137.06 -14.26 0 2.50e+00 1.60e-01 3.25e+01 dihedral pdb=" C ARG A 389 " pdb=" N ARG A 389 " pdb=" CA ARG A 389 " pdb=" CB ARG A 389 " ideal model delta harmonic sigma weight residual -122.60 -136.78 14.18 0 2.50e+00 1.60e-01 3.22e+01 ... (remaining 6703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1683 0.133 - 0.266: 106 0.266 - 0.399: 19 0.399 - 0.532: 1 0.532 - 0.664: 2 Chirality restraints: 1811 Sorted by residual: chirality pdb=" CA ARG A 389 " pdb=" N ARG A 389 " pdb=" C ARG A 389 " pdb=" CB ARG A 389 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA PHE A 251 " pdb=" N PHE A 251 " pdb=" C PHE A 251 " pdb=" CB PHE A 251 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.68e+00 chirality pdb=" CA THR B 517 " pdb=" N THR B 517 " pdb=" C THR B 517 " pdb=" CB THR B 517 " both_signs ideal model delta sigma weight residual False 2.53 2.97 -0.44 2.00e-01 2.50e+01 4.83e+00 ... (remaining 1808 not shown) Planarity restraints: 1896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 479 " -0.023 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C THR A 479 " 0.080 2.00e-02 2.50e+03 pdb=" O THR A 479 " -0.030 2.00e-02 2.50e+03 pdb=" N ILE A 480 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 540 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.71e+00 pdb=" C CYS A 540 " 0.048 2.00e-02 2.50e+03 pdb=" O CYS A 540 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO A 541 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 110 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.68e+00 pdb=" C PHE A 110 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE A 110 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE A 111 " -0.014 2.00e-02 2.50e+03 ... (remaining 1893 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2266 2.76 - 3.29: 11007 3.29 - 3.83: 18942 3.83 - 4.36: 24007 4.36 - 4.90: 38433 Nonbonded interactions: 94655 Sorted by model distance: nonbonded pdb=" NE ARG B 569 " pdb=" OD1 ASP B 617 " model vdw 2.224 3.120 nonbonded pdb=" O THR B 335 " pdb=" OG1 THR B 339 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR B 712 " pdb=" OD2 ASP B 715 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR A 712 " pdb=" OD2 ASP A 715 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR B 503 " pdb=" OH TYR B 545 " model vdw 2.344 3.040 ... (remaining 94650 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' selection = (chain 'B' and (resid 7 through 600 or (resid 601 and (name N or name CA or name \ C or name O or name CB )) or resid 602 through 803)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.200 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 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:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.100 11253 Z= 0.601 Angle : 1.118 14.565 15284 Z= 0.728 Chirality : 0.076 0.664 1811 Planarity : 0.006 0.047 1896 Dihedral : 14.309 147.230 4078 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.92 % Allowed : 7.83 % Favored : 91.26 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.21), residues: 1396 helix: 0.86 (0.16), residues: 894 sheet: 2.59 (0.72), residues: 34 loop : -1.30 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 389 TYR 0.021 0.003 TYR B 9 PHE 0.026 0.002 PHE A 251 TRP 0.012 0.002 TRP A 63 HIS 0.005 0.002 HIS A 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00986 / 0.60 (11253) covalent geometry : angle 1.11787 / 0.73 (15284) hydrogen bonds : bond 0.16920 / 11.36 ( 703) hydrogen bonds : angle 6.05351 / 4.35 ( 2016) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.260 Fit side-chains REVERT: A 26 LYS cc_start: 0.7606 (tttp) cc_final: 0.7055 (mmmt) REVERT: A 58 PHE cc_start: 0.8160 (t80) cc_final: 0.7897 (t80) REVERT: A 70 LYS cc_start: 0.7275 (mmtt) cc_final: 0.6874 (pmtt) REVERT: A 296 MET cc_start: 0.8403 (mmp) cc_final: 0.8147 (mmm) REVERT: A 312 ARG cc_start: 0.7578 (ttm170) cc_final: 0.7303 (ttm110) REVERT: A 332 ASP cc_start: 0.7603 (m-30) cc_final: 0.7065 (t0) REVERT: A 474 MET cc_start: 0.8440 (mmm) cc_final: 0.7962 (mmm) REVERT: A 609 ASP cc_start: 0.7477 (p0) cc_final: 0.7160 (p0) REVERT: A 629 ILE cc_start: 0.7541 (mt) cc_final: 0.7301 (mt) REVERT: A 643 LYS cc_start: 0.8332 (mttt) cc_final: 0.7995 (mttt) REVERT: A 687 ASP cc_start: 0.7094 (p0) cc_final: 0.6578 (p0) REVERT: A 707 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.8210 (p) REVERT: B 26 LYS cc_start: 0.7486 (tttp) cc_final: 0.6913 (mmmt) REVERT: B 58 PHE cc_start: 0.7071 (m-80) cc_final: 0.6710 (t80) REVERT: B 332 ASP cc_start: 0.7336 (m-30) cc_final: 0.7019 (t0) REVERT: B 348 MET cc_start: 0.6834 (mmp) cc_final: 0.6610 (tpp) REVERT: B 405 SER cc_start: 0.7964 (t) cc_final: 0.7694 (m) REVERT: B 621 ASN cc_start: 0.8050 (t0) cc_final: 0.7683 (t0) REVERT: B 687 ASP cc_start: 0.7227 (p0) cc_final: 0.6871 (p0) REVERT: B 688 ASP cc_start: 0.7834 (m-30) cc_final: 0.7514 (m-30) REVERT: B 692 GLU cc_start: 0.6910 (tt0) cc_final: 0.6649 (mt-10) outliers start: 11 outliers final: 4 residues processed: 158 average time/residue: 0.5608 time to fit residues: 94.8994 Evaluate side-chains 112 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain B residue 707 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 ASN A 8 GLN A 32 HIS A 38 HIS A 48 GLN A 253 GLN A 279 ASN A 311 ASN A 322 ASN A 326 GLN A 495 GLN A 584 GLN A 611 ASN A 714 HIS B 8 GLN B 38 HIS B 48 GLN B 279 ASN B 311 ASN B 322 ASN B 326 GLN B 495 GLN B 513 ASN B 584 GLN B 714 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.136153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.094935 restraints weight = 10601.941| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.76 r_work: 0.2923 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11253 Z= 0.137 Angle : 0.558 10.003 15284 Z= 0.291 Chirality : 0.042 0.162 1811 Planarity : 0.005 0.049 1896 Dihedral : 10.527 129.848 1564 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.50 % Allowed : 10.16 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.23), residues: 1396 helix: 1.67 (0.17), residues: 896 sheet: 2.89 (0.79), residues: 34 loop : -0.54 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 13 TYR 0.020 0.002 TYR A 9 PHE 0.016 0.001 PHE A 130 TRP 0.016 0.002 TRP B 72 HIS 0.004 0.001 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (11253) covalent geometry : angle 0.55759 / 0.29 (15284) hydrogen bonds : bond 0.05001 / 3.40 ( 703) hydrogen bonds : angle 4.63981 / 3.36 ( 2016) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.403 Fit side-chains REVERT: A 26 LYS cc_start: 0.7899 (tttp) cc_final: 0.7262 (mmmt) REVERT: A 56 SER cc_start: 0.8035 (t) cc_final: 0.7762 (p) REVERT: A 70 LYS cc_start: 0.7583 (mmtt) cc_final: 0.7119 (pmmt) REVERT: A 322 ASN cc_start: 0.7561 (OUTLIER) cc_final: 0.7360 (m110) REVERT: A 332 ASP cc_start: 0.7522 (m-30) cc_final: 0.6847 (t0) REVERT: A 342 ASP cc_start: 0.8283 (m-30) cc_final: 0.8039 (m-30) REVERT: A 495 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8695 (tt0) REVERT: A 618 GLN cc_start: 0.8154 (mm110) cc_final: 0.7727 (mm-40) REVERT: A 630 ASP cc_start: 0.7926 (t70) cc_final: 0.7593 (t0) REVERT: A 643 LYS cc_start: 0.8668 (mttt) cc_final: 0.8417 (mttt) REVERT: A 692 GLU cc_start: 0.7596 (tt0) cc_final: 0.6855 (tm-30) REVERT: B 22 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7589 (mm-30) REVERT: B 26 LYS cc_start: 0.7915 (tttp) cc_final: 0.7267 (mmmt) REVERT: B 56 SER cc_start: 0.8110 (OUTLIER) cc_final: 0.7779 (p) REVERT: B 58 PHE cc_start: 0.7465 (m-80) cc_final: 0.7130 (t80) REVERT: B 277 GLU cc_start: 0.6315 (mt-10) cc_final: 0.5802 (mm-30) REVERT: B 312 ARG cc_start: 0.7865 (ttm110) cc_final: 0.7612 (ttm-80) REVERT: B 322 ASN cc_start: 0.7526 (OUTLIER) cc_final: 0.7224 (m110) REVERT: B 332 ASP cc_start: 0.7538 (m-30) cc_final: 0.6908 (t0) REVERT: B 348 MET cc_start: 0.8004 (mmp) cc_final: 0.7768 (tpp) REVERT: B 495 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8745 (tt0) REVERT: B 621 ASN cc_start: 0.8320 (t0) cc_final: 0.7947 (t0) REVERT: B 692 GLU cc_start: 0.7633 (tt0) cc_final: 0.7259 (tp30) outliers start: 18 outliers final: 5 residues processed: 132 average time/residue: 0.5496 time to fit residues: 78.5039 Evaluate side-chains 113 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 495 GLN Chi-restraints excluded: chain B residue 514 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 99 optimal weight: 0.0040 chunk 133 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 ASN A 495 GLN B 322 ASN B 495 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.092430 restraints weight = 10625.319| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.76 r_work: 0.2883 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11253 Z= 0.162 Angle : 0.568 10.040 15284 Z= 0.295 Chirality : 0.043 0.168 1811 Planarity : 0.004 0.052 1896 Dihedral : 10.276 130.813 1557 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.42 % Allowed : 10.24 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.23), residues: 1396 helix: 1.75 (0.17), residues: 896 sheet: 2.87 (0.81), residues: 34 loop : -0.37 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 312 TYR 0.026 0.002 TYR A 9 PHE 0.015 0.002 PHE A 130 TRP 0.013 0.002 TRP A 63 HIS 0.005 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (11253) covalent geometry : angle 0.56808 / 0.30 (15284) hydrogen bonds : bond 0.05279 / 3.57 ( 703) hydrogen bonds : angle 4.59453 / 3.33 ( 2016) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.427 Fit side-chains REVERT: A 26 LYS cc_start: 0.7898 (tttp) cc_final: 0.7289 (mmmt) REVERT: A 56 SER cc_start: 0.8204 (t) cc_final: 0.7819 (p) REVERT: A 70 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7323 (ptmm) REVERT: A 332 ASP cc_start: 0.7559 (m-30) cc_final: 0.6881 (t0) REVERT: A 495 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8701 (tt0) REVERT: A 528 ASP cc_start: 0.8508 (m-30) cc_final: 0.8226 (m-30) REVERT: A 692 GLU cc_start: 0.7864 (tt0) cc_final: 0.7112 (tm-30) REVERT: B 22 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7666 (mm-30) REVERT: B 26 LYS cc_start: 0.7948 (tttp) cc_final: 0.7303 (mmmt) REVERT: B 56 SER cc_start: 0.8197 (OUTLIER) cc_final: 0.7762 (p) REVERT: B 58 PHE cc_start: 0.7568 (m-80) cc_final: 0.7223 (t80) REVERT: B 68 ARG cc_start: 0.8338 (mtp180) cc_final: 0.8072 (mtp180) REVERT: B 270 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7226 (tp) REVERT: B 277 GLU cc_start: 0.6412 (mt-10) cc_final: 0.5690 (mm-30) REVERT: B 312 ARG cc_start: 0.7927 (ttm110) cc_final: 0.7706 (ttm-80) REVERT: B 332 ASP cc_start: 0.7580 (m-30) cc_final: 0.6863 (t0) REVERT: B 495 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8719 (tt0) REVERT: B 528 ASP cc_start: 0.8478 (m-30) cc_final: 0.8139 (m-30) REVERT: B 579 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7585 (mtt180) REVERT: B 621 ASN cc_start: 0.8401 (t0) cc_final: 0.8051 (t0) REVERT: B 640 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7301 (tm-30) REVERT: B 692 GLU cc_start: 0.7740 (tt0) cc_final: 0.7145 (tm-30) outliers start: 17 outliers final: 7 residues processed: 129 average time/residue: 0.5632 time to fit residues: 78.2886 Evaluate side-chains 122 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 495 GLN Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 579 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 30 optimal weight: 0.0470 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 103 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 26 optimal weight: 0.0980 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 GLN A 495 GLN B 495 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.097361 restraints weight = 10667.607| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.75 r_work: 0.2957 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 11253 Z= 0.106 Angle : 0.493 8.627 15284 Z= 0.256 Chirality : 0.040 0.168 1811 Planarity : 0.004 0.051 1896 Dihedral : 9.299 112.866 1557 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.83 % Allowed : 10.91 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.23), residues: 1396 helix: 1.99 (0.17), residues: 896 sheet: 3.00 (0.82), residues: 34 loop : -0.26 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 312 TYR 0.017 0.001 TYR B 9 PHE 0.013 0.001 PHE B 130 TRP 0.013 0.001 TRP A 63 HIS 0.002 0.001 HIS B 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (11253) covalent geometry : angle 0.49332 / 0.26 (15284) hydrogen bonds : bond 0.04240 / 2.87 ( 703) hydrogen bonds : angle 4.31033 / 3.11 ( 2016) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.420 Fit side-chains REVERT: A 26 LYS cc_start: 0.7924 (tttp) cc_final: 0.7280 (mmmt) REVERT: A 56 SER cc_start: 0.8024 (t) cc_final: 0.7820 (p) REVERT: A 70 LYS cc_start: 0.7571 (mmtt) cc_final: 0.7235 (ptmm) REVERT: A 528 ASP cc_start: 0.8432 (m-30) cc_final: 0.8202 (m-30) REVERT: A 614 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6776 (pm20) REVERT: A 629 ILE cc_start: 0.7875 (mt) cc_final: 0.7517 (mt) REVERT: A 630 ASP cc_start: 0.7875 (t70) cc_final: 0.7562 (t0) REVERT: A 692 GLU cc_start: 0.7767 (tt0) cc_final: 0.7032 (tm-30) REVERT: B 22 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7604 (mm-30) REVERT: B 26 LYS cc_start: 0.7952 (tttp) cc_final: 0.7238 (mmmt) REVERT: B 56 SER cc_start: 0.8083 (t) cc_final: 0.7757 (p) REVERT: B 58 PHE cc_start: 0.7379 (m-80) cc_final: 0.6987 (t80) REVERT: B 68 ARG cc_start: 0.8244 (mtp180) cc_final: 0.7979 (mtp180) REVERT: B 70 LYS cc_start: 0.8116 (tttm) cc_final: 0.7509 (pmmt) REVERT: B 277 GLU cc_start: 0.6317 (mt-10) cc_final: 0.5588 (mm-30) REVERT: B 332 ASP cc_start: 0.7459 (m-30) cc_final: 0.6770 (t0) REVERT: B 495 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8654 (tt0) REVERT: B 528 ASP cc_start: 0.8408 (m-30) cc_final: 0.8146 (m-30) REVERT: B 640 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7331 (tm-30) REVERT: B 692 GLU cc_start: 0.7655 (tt0) cc_final: 0.7108 (tm-30) REVERT: B 701 ASP cc_start: 0.8102 (p0) cc_final: 0.7856 (p0) outliers start: 10 outliers final: 1 residues processed: 120 average time/residue: 0.5994 time to fit residues: 77.7718 Evaluate side-chains 113 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain B residue 495 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 121 optimal weight: 0.2980 chunk 95 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 124 optimal weight: 0.5980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 612 GLN B 454 GLN B 495 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.133772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.091942 restraints weight = 10553.448| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.75 r_work: 0.2876 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11253 Z= 0.171 Angle : 0.569 10.218 15284 Z= 0.295 Chirality : 0.043 0.178 1811 Planarity : 0.004 0.051 1896 Dihedral : 10.190 130.093 1557 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.08 % Allowed : 10.82 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.23), residues: 1396 helix: 1.84 (0.17), residues: 898 sheet: 3.03 (0.84), residues: 34 loop : -0.24 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 312 TYR 0.027 0.002 TYR A 9 PHE 0.016 0.002 PHE B 130 TRP 0.014 0.002 TRP B 63 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (11253) covalent geometry : angle 0.56939 / 0.29 (15284) hydrogen bonds : bond 0.05312 / 3.58 ( 703) hydrogen bonds : angle 4.52450 / 3.27 ( 2016) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.383 Fit side-chains REVERT: A 26 LYS cc_start: 0.7883 (tttp) cc_final: 0.7231 (mmmt) REVERT: A 56 SER cc_start: 0.8160 (t) cc_final: 0.7776 (p) REVERT: A 68 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7817 (mtp180) REVERT: A 70 LYS cc_start: 0.7739 (mmtt) cc_final: 0.7331 (ptmm) REVERT: A 332 ASP cc_start: 0.7511 (m-30) cc_final: 0.6831 (t0) REVERT: A 528 ASP cc_start: 0.8547 (m-30) cc_final: 0.8282 (m-30) REVERT: A 630 ASP cc_start: 0.7916 (t70) cc_final: 0.7608 (t0) REVERT: A 687 ASP cc_start: 0.7623 (p0) cc_final: 0.7144 (p0) REVERT: A 692 GLU cc_start: 0.7876 (tt0) cc_final: 0.7144 (tm-30) REVERT: A 698 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: A 701 ASP cc_start: 0.7958 (p0) cc_final: 0.7561 (p0) REVERT: B 22 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7594 (mm-30) REVERT: B 26 LYS cc_start: 0.8035 (tttp) cc_final: 0.7261 (mmmt) REVERT: B 58 PHE cc_start: 0.7527 (m-80) cc_final: 0.7124 (t80) REVERT: B 312 ARG cc_start: 0.8047 (ttm-80) cc_final: 0.7838 (ttm-80) REVERT: B 332 ASP cc_start: 0.7543 (m-30) cc_final: 0.6799 (t0) REVERT: B 495 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8676 (tt0) REVERT: B 528 ASP cc_start: 0.8526 (m-30) cc_final: 0.8271 (m-30) REVERT: B 640 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7366 (tm-30) REVERT: B 692 GLU cc_start: 0.7805 (tt0) cc_final: 0.7283 (tm-30) outliers start: 13 outliers final: 3 residues processed: 126 average time/residue: 0.5808 time to fit residues: 78.8581 Evaluate side-chains 118 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 495 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 7 ASN B 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.136049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.094204 restraints weight = 10584.668| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.77 r_work: 0.2891 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11253 Z= 0.127 Angle : 0.525 9.340 15284 Z= 0.271 Chirality : 0.041 0.193 1811 Planarity : 0.004 0.052 1896 Dihedral : 9.701 121.818 1556 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.92 % Allowed : 11.49 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.23), residues: 1396 helix: 1.94 (0.17), residues: 896 sheet: 3.03 (0.85), residues: 34 loop : -0.16 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 312 TYR 0.022 0.001 TYR A 9 PHE 0.015 0.001 PHE B 130 TRP 0.014 0.001 TRP B 63 HIS 0.004 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (11253) covalent geometry : angle 0.52505 / 0.27 (15284) hydrogen bonds : bond 0.04696 / 3.17 ( 703) hydrogen bonds : angle 4.38037 / 3.16 ( 2016) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.440 Fit side-chains REVERT: A 26 LYS cc_start: 0.7899 (tttp) cc_final: 0.7229 (mmmt) REVERT: A 70 LYS cc_start: 0.7602 (mmtt) cc_final: 0.7183 (ptmm) REVERT: A 270 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7147 (tp) REVERT: A 528 ASP cc_start: 0.8520 (m-30) cc_final: 0.8277 (m-30) REVERT: A 614 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6807 (pm20) REVERT: A 630 ASP cc_start: 0.7904 (t70) cc_final: 0.7594 (t0) REVERT: A 692 GLU cc_start: 0.7880 (tt0) cc_final: 0.7156 (tm-30) REVERT: A 698 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: A 701 ASP cc_start: 0.7978 (p0) cc_final: 0.7772 (p0) REVERT: B 22 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7622 (mm-30) REVERT: B 26 LYS cc_start: 0.8033 (tttp) cc_final: 0.7258 (mmmt) REVERT: B 58 PHE cc_start: 0.7453 (m-80) cc_final: 0.7009 (t80) REVERT: B 70 LYS cc_start: 0.8192 (tttm) cc_final: 0.7617 (mptt) REVERT: B 236 SER cc_start: 0.8670 (m) cc_final: 0.8279 (p) REVERT: B 312 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7834 (ttm-80) REVERT: B 332 ASP cc_start: 0.7503 (m-30) cc_final: 0.6757 (t0) REVERT: B 495 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8691 (tt0) REVERT: B 528 ASP cc_start: 0.8530 (m-30) cc_final: 0.8289 (m-30) REVERT: B 640 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7368 (tm-30) REVERT: B 692 GLU cc_start: 0.7813 (tt0) cc_final: 0.7281 (tm-30) outliers start: 11 outliers final: 2 residues processed: 118 average time/residue: 0.4770 time to fit residues: 61.0567 Evaluate side-chains 117 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain B residue 495 GLN Chi-restraints excluded: chain B residue 514 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.132813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.091002 restraints weight = 10489.214| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.74 r_work: 0.2863 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 11253 Z= 0.207 Angle : 0.603 10.572 15284 Z= 0.312 Chirality : 0.045 0.196 1811 Planarity : 0.005 0.052 1896 Dihedral : 10.463 135.414 1556 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.33 % Allowed : 11.41 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.23), residues: 1396 helix: 1.71 (0.17), residues: 896 sheet: 3.09 (0.85), residues: 34 loop : -0.25 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 312 TYR 0.028 0.002 TYR A 9 PHE 0.017 0.002 PHE B 130 TRP 0.015 0.002 TRP B 63 HIS 0.003 0.001 HIS B 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (11253) covalent geometry : angle 0.60276 / 0.31 (15284) hydrogen bonds : bond 0.05639 / 3.81 ( 703) hydrogen bonds : angle 4.60194 / 3.32 ( 2016) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.428 Fit side-chains REVERT: A 26 LYS cc_start: 0.7975 (tttp) cc_final: 0.7222 (mmmt) REVERT: A 70 LYS cc_start: 0.7818 (mmtt) cc_final: 0.7365 (ptmm) REVERT: A 495 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8693 (tt0) REVERT: A 528 ASP cc_start: 0.8567 (m-30) cc_final: 0.8307 (m-30) REVERT: A 630 ASP cc_start: 0.7905 (t70) cc_final: 0.7617 (t0) REVERT: A 687 ASP cc_start: 0.7715 (p0) cc_final: 0.7443 (p0) REVERT: A 692 GLU cc_start: 0.7885 (tt0) cc_final: 0.7176 (tm-30) REVERT: A 698 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: B 22 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7616 (mm-30) REVERT: B 26 LYS cc_start: 0.8038 (tttp) cc_final: 0.7261 (mmmt) REVERT: B 58 PHE cc_start: 0.7537 (m-80) cc_final: 0.7324 (m-80) REVERT: B 236 SER cc_start: 0.8676 (m) cc_final: 0.8260 (p) REVERT: B 332 ASP cc_start: 0.7551 (m-30) cc_final: 0.6784 (t0) REVERT: B 495 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8868 (tt0) REVERT: B 528 ASP cc_start: 0.8570 (m-30) cc_final: 0.8338 (m-30) REVERT: B 579 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7568 (mtt180) REVERT: B 640 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7416 (tm-30) REVERT: B 687 ASP cc_start: 0.7679 (p0) cc_final: 0.7408 (p0) REVERT: B 692 GLU cc_start: 0.7805 (tt0) cc_final: 0.7292 (tm-30) outliers start: 16 outliers final: 4 residues processed: 121 average time/residue: 0.5947 time to fit residues: 77.6567 Evaluate side-chains 119 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 495 GLN Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 495 GLN Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 579 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.0519 > 50: distance: 118 - 135: 3.359 distance: 122 - 144: 6.898 distance: 130 - 135: 4.636 distance: 131 - 159: 3.775 distance: 135 - 136: 5.458 distance: 136 - 137: 6.707 distance: 136 - 139: 8.863 distance: 137 - 138: 16.404 distance: 137 - 144: 5.313 distance: 139 - 140: 8.607 distance: 140 - 141: 6.758 distance: 141 - 143: 6.113 distance: 144 - 145: 3.080 distance: 145 - 146: 3.410 distance: 145 - 148: 7.541 distance: 146 - 147: 4.726 distance: 148 - 149: 4.248 distance: 149 - 150: 3.827 distance: 150 - 151: 5.622 distance: 150 - 152: 9.519 distance: 154 - 157: 3.614 distance: 155 - 156: 4.529 distance: 155 - 159: 6.335 distance: 157 - 158: 8.559 distance: 159 - 160: 15.593 distance: 160 - 161: 18.547 distance: 160 - 163: 11.310 distance: 161 - 162: 13.218 distance: 161 - 166: 26.496 distance: 163 - 164: 9.323 distance: 163 - 165: 12.238 distance: 166 - 167: 18.279 distance: 167 - 168: 22.054 distance: 168 - 169: 15.623 distance: 168 - 170: 14.711 distance: 170 - 171: 3.280 distance: 171 - 172: 11.352 distance: 172 - 173: 9.998 distance: 172 - 174: 4.143 distance: 175 - 176: 6.081 distance: 176 - 177: 8.372 distance: 179 - 180: 5.635 distance: 180 - 181: 4.095 distance: 181 - 182: 12.821 distance: 183 - 184: 4.240 distance: 184 - 185: 3.656 distance: 184 - 187: 7.041 distance: 185 - 186: 9.400 distance: 185 - 190: 8.193 distance: 187 - 188: 4.822 distance: 187 - 189: 5.651 distance: 190 - 191: 3.917 distance: 191 - 194: 6.421 distance: 192 - 193: 3.724 distance: 192 - 199: 4.272 distance: 193 - 216: 8.281 distance: 195 - 196: 5.538 distance: 196 - 197: 4.005 distance: 199 - 200: 4.392 distance: 200 - 203: 7.067 distance: 201 - 202: 5.473 distance: 202 - 223: 7.753 distance: 203 - 204: 5.470