Starting phenix.real_space_refine on Sun May 3 10:44:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ce0_45489/05_2026/9ce0_45489_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ce0_45489/05_2026/9ce0_45489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ce0_45489/05_2026/9ce0_45489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ce0_45489/05_2026/9ce0_45489.map" model { file = "/net/cci-nas-00/data/ceres_data/9ce0_45489/05_2026/9ce0_45489_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ce0_45489/05_2026/9ce0_45489_neut.cif" } resolution = 3.97 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= -0.001 sd= 0.018 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: 5 Type Number sf(0) Gaussians Fe 2 7.16 5 S 66 5.16 5 C 7957 2.51 5 N 2188 2.21 5 O 2338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12551 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6257 Classifications: {'peptide': 787} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 33, 'TRANS': 750} Chain: "B" Number of atoms: 6204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6204 Classifications: {'peptide': 781} Link IDs: {'PTRANS': 35, 'TRANS': 745} Chain breaks: 1 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.90, per 1000 atoms: 0.23 Number of scatterers: 12551 At special positions: 0 Unit cell: (93.6383, 103.325, 195.349, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 2 26.01 S 66 16.00 O 2338 8.00 N 2188 7.00 C 7957 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 631.0 milliseconds 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2956 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 13 sheets defined 51.0% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 removed outlier: 3.802A pdb=" N ALA A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.810A pdb=" N VAL A 60 " --> pdb=" O LYS A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.929A pdb=" N MET A 67 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.647A pdb=" N TYR A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY A 87 " --> pdb=" O HIS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 133 through 152 Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 200 through 212 removed outlier: 4.202A pdb=" N ILE A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 275 Processing helix chain 'A' and resid 278 through 294 Processing helix chain 'A' and resid 352 through 383 Processing helix chain 'A' and resid 394 through 409 Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 430 through 449 removed outlier: 4.219A pdb=" N GLN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 485 Processing helix chain 'A' and resid 512 through 531 Processing helix chain 'A' and resid 542 through 563 removed outlier: 3.627A pdb=" N ARG A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 609 Proline residue: A 604 - end of helix Processing helix chain 'A' and resid 611 through 634 Processing helix chain 'A' and resid 645 through 648 Processing helix chain 'A' and resid 650 through 652 No H-bonds generated for 'chain 'A' and resid 650 through 652' Processing helix chain 'A' and resid 653 through 665 removed outlier: 4.265A pdb=" N ALA A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 699 Processing helix chain 'A' and resid 710 through 720 removed outlier: 3.758A pdb=" N LEU A 720 " --> pdb=" O ARG A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.813A pdb=" N ARG A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU A 736 " --> pdb=" O VAL A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 756 removed outlier: 3.615A pdb=" N LEU A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 777 Processing helix chain 'A' and resid 794 through 803 removed outlier: 3.859A pdb=" N SER A 800 " --> pdb=" O PRO A 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 28 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 76 through 88 removed outlier: 3.621A pdb=" N GLY B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 Processing helix chain 'B' and resid 134 through 153 Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 201 through 210 removed outlier: 4.054A pdb=" N ARG B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 276 Processing helix chain 'B' and resid 278 through 294 Processing helix chain 'B' and resid 352 through 377 Processing helix chain 'B' and resid 394 through 408 removed outlier: 3.686A pdb=" N LYS B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 447 removed outlier: 4.142A pdb=" N VAL B 425 " --> pdb=" O HIS B 421 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N TYR B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N ALA B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 486 removed outlier: 3.755A pdb=" N VAL B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 531 Processing helix chain 'B' and resid 539 through 562 Processing helix chain 'B' and resid 598 through 610 Proline residue: B 604 - end of helix Processing helix chain 'B' and resid 611 through 632 Processing helix chain 'B' and resid 643 through 648 Processing helix chain 'B' and resid 650 through 654 removed outlier: 3.921A pdb=" N GLN B 653 " --> pdb=" O ARG B 650 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU B 654 " --> pdb=" O SER B 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 650 through 654' Processing helix chain 'B' and resid 655 through 665 removed outlier: 4.914A pdb=" N ALA B 661 " --> pdb=" O GLN B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 683 Processing helix chain 'B' and resid 686 through 699 removed outlier: 3.706A pdb=" N LYS B 690 " --> pdb=" O THR B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 720 Processing helix chain 'B' and resid 728 through 733 Processing helix chain 'B' and resid 738 through 755 Processing helix chain 'B' and resid 766 through 776 Processing helix chain 'B' and resid 794 through 802 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 removed outlier: 3.764A pdb=" N GLN A 168 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 314 removed outlier: 6.615A pdb=" N LEU A 301 " --> pdb=" O TRP A 312 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER A 314 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL A 299 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN A 343 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 339 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 331 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE A 341 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA A 329 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN A 343 " --> pdb=" O TRP A 327 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP A 327 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS A 345 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLN A 325 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 454 through 459 removed outlier: 5.507A pdb=" N LEU A 455 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL A 466 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG A 457 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL A 464 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 459 " --> pdb=" O GLN A 462 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 490 through 492 Processing sheet with id=AA6, first strand: chain 'A' and resid 566 through 573 removed outlier: 4.453A pdb=" N TRP A 589 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 566 through 573 removed outlier: 4.652A pdb=" N ASN A 643 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA A 587 " --> pdb=" O ASN A 643 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 675 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 701 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU A 702 " --> pdb=" O GLU A 724 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LYS A 726 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 704 " --> pdb=" O LYS A 726 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE A 725 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLU A 762 " --> pdb=" O ILE A 725 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE A 727 " --> pdb=" O GLU A 762 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL A 764 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLN A 782 " --> pdb=" O VAL A 759 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA A 761 " --> pdb=" O GLN A 782 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 42 through 45 removed outlier: 6.673A pdb=" N LEU B 35 " --> pdb=" O MET B 43 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE B 45 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA B 33 " --> pdb=" O PHE B 45 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 32 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 166 through 168 removed outlier: 6.055A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 308 through 314 removed outlier: 6.714A pdb=" N LEU B 301 " --> pdb=" O TRP B 312 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER B 314 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 299 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA B 339 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE B 331 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE B 341 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA B 329 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN B 343 " --> pdb=" O TRP B 327 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP B 327 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS B 345 " --> pdb=" O GLN B 325 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN B 325 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 454 through 459 removed outlier: 7.109A pdb=" N GLN B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 672 through 674 removed outlier: 6.344A pdb=" N LEU B 640 " --> pdb=" O THR B 673 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N SER B 641 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE B 583 " --> pdb=" O SER B 641 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLN B 572 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE B 583 " --> pdb=" O GLN B 570 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLN B 570 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA B 585 " --> pdb=" O VAL B 568 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 568 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA B 587 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LYS B 566 " --> pdb=" O ALA B 587 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL B 759 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 725 " --> pdb=" O VAL B 760 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 590 through 591 696 hydrogen bonds defined for protein. 1998 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: 2.30 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 4943 1.38 - 1.56: 7750 1.56 - 1.73: 0 1.73 - 1.91: 116 1.91 - 2.08: 8 Bond restraints: 12817 Sorted by residual: bond pdb=" O1 OXY B 902 " pdb=" O2 OXY B 902 " ideal model delta sigma weight residual 1.109 1.206 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" O1 OXY A 902 " pdb=" O2 OXY A 902 " ideal model delta sigma weight residual 1.109 1.206 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" CA SER A 600 " pdb=" C SER A 600 " ideal model delta sigma weight residual 1.522 1.475 0.047 1.45e-02 4.76e+03 1.03e+01 bond pdb=" N PHE B 386 " pdb=" CA PHE B 386 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.13e-02 7.83e+03 6.19e+00 bond pdb=" N ILE B 384 " pdb=" CA ILE B 384 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.60e+00 ... (remaining 12812 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 16472 1.45 - 2.90: 803 2.90 - 4.36: 102 4.36 - 5.81: 8 5.81 - 7.26: 3 Bond angle restraints: 17388 Sorted by residual: angle pdb=" N ILE A 148 " pdb=" CA ILE A 148 " pdb=" C ILE A 148 " ideal model delta sigma weight residual 110.72 106.18 4.54 1.01e+00 9.80e-01 2.02e+01 angle pdb=" N ARG A 779 " pdb=" CA ARG A 779 " pdb=" CB ARG A 779 " ideal model delta sigma weight residual 114.17 109.61 4.56 1.14e+00 7.69e-01 1.60e+01 angle pdb=" C GLU B 793 " pdb=" N GLU B 794 " pdb=" CA GLU B 794 " ideal model delta sigma weight residual 121.54 128.65 -7.11 1.91e+00 2.74e-01 1.39e+01 angle pdb=" N GLN B 385 " pdb=" CA GLN B 385 " pdb=" C GLN B 385 " ideal model delta sigma weight residual 113.40 108.14 5.26 1.47e+00 4.63e-01 1.28e+01 angle pdb=" N ASP A 151 " pdb=" CA ASP A 151 " pdb=" C ASP A 151 " ideal model delta sigma weight residual 111.28 107.61 3.67 1.09e+00 8.42e-01 1.13e+01 ... (remaining 17383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 6911 17.75 - 35.50: 648 35.50 - 53.25: 127 53.25 - 71.00: 41 71.00 - 88.75: 17 Dihedral angle restraints: 7744 sinusoidal: 3191 harmonic: 4553 Sorted by residual: dihedral pdb=" CA GLN B 657 " pdb=" C GLN B 657 " pdb=" N VAL B 658 " pdb=" CA VAL B 658 " ideal model delta harmonic sigma weight residual 180.00 151.15 28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLY A 227 " pdb=" C GLY A 227 " pdb=" N GLU A 228 " pdb=" CA GLU A 228 " ideal model delta harmonic sigma weight residual -180.00 -151.83 -28.17 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA LEU A 720 " pdb=" C LEU A 720 " pdb=" N PRO A 721 " pdb=" CA PRO A 721 " ideal model delta harmonic sigma weight residual 180.00 -154.42 -25.58 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 7741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1405 0.040 - 0.080: 363 0.080 - 0.120: 137 0.120 - 0.160: 16 0.160 - 0.200: 1 Chirality restraints: 1922 Sorted by residual: chirality pdb=" CA ILE B 384 " pdb=" N ILE B 384 " pdb=" C ILE B 384 " pdb=" CB ILE B 384 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE A 331 " pdb=" N ILE A 331 " pdb=" C ILE A 331 " pdb=" CB ILE A 331 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE A 69 " pdb=" N ILE A 69 " pdb=" C ILE A 69 " pdb=" CB ILE A 69 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1919 not shown) Planarity restraints: 2261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 155 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 156 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 266 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C GLU B 266 " -0.038 2.00e-02 2.50e+03 pdb=" O GLU B 266 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY B 267 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 144 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C ARG B 144 " 0.037 2.00e-02 2.50e+03 pdb=" O ARG B 144 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN B 145 " -0.012 2.00e-02 2.50e+03 ... (remaining 2258 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 184 2.52 - 3.12: 10812 3.12 - 3.71: 20858 3.71 - 4.31: 27856 4.31 - 4.90: 45103 Nonbonded interactions: 104813 Sorted by model distance: nonbonded pdb=" O LYS A 140 " pdb=" OG1 THR A 143 " model vdw 1.931 3.040 nonbonded pdb=" O ALA A 272 " pdb=" OG SER A 275 " model vdw 1.963 3.040 nonbonded pdb=" O ASN A 84 " pdb=" OH TYR A 126 " model vdw 1.979 3.040 nonbonded pdb=" OG SER B 632 " pdb=" OE1 GLN B 633 " model vdw 1.997 3.040 nonbonded pdb=" O GLY B 708 " pdb=" OG1 THR B 709 " model vdw 2.048 3.040 ... (remaining 104808 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 20 through 377 or resid 384 through 902)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 13.230 Find NCS groups from input model: 0.220 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 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 0.714 12819 Z= 0.240 Angle : 0.693 7.261 17388 Z= 0.460 Chirality : 0.042 0.200 1922 Planarity : 0.006 0.069 2261 Dihedral : 15.095 88.749 4788 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.27 % Favored : 93.60 % Rotamer: Outliers : 0.15 % Allowed : 9.12 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.07 % 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: -1.00 (0.21), residues: 1562 helix: 0.30 (0.20), residues: 713 sheet: -0.96 (0.29), residues: 322 loop : -1.66 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 164 TYR 0.018 0.001 TYR B 454 PHE 0.022 0.002 PHE A 602 TRP 0.013 0.001 TRP A 665 HIS 0.005 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00430 (12817) covalent geometry : angle 0.69275 (17388) hydrogen bonds : bond 0.10649 ( 688) hydrogen bonds : angle 6.47419 ( 1998) Misc. bond : bond 0.70627 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: -0.0135 (ptm) cc_final: -0.0388 (ptt) REVERT: A 43 MET cc_start: 0.2565 (mpp) cc_final: 0.2218 (mpp) REVERT: B 416 LEU cc_start: 0.9075 (tp) cc_final: 0.8350 (tp) outliers start: 2 outliers final: 0 residues processed: 140 average time/residue: 0.1216 time to fit residues: 23.8121 Evaluate side-chains 87 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 HIS B 139 GLN B 217 GLN B 248 ASN ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.070088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.046494 restraints weight = 93172.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.046145 restraints weight = 72323.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.046661 restraints weight = 56909.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.046907 restraints weight = 49678.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.047121 restraints weight = 44334.425| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.247 12819 Z= 0.168 Angle : 0.743 9.181 17388 Z= 0.376 Chirality : 0.047 0.181 1922 Planarity : 0.006 0.054 2261 Dihedral : 6.411 76.460 1707 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.74 % Favored : 95.13 % Rotamer: Outliers : 1.54 % Allowed : 13.09 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.07 % 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: -0.71 (0.22), residues: 1562 helix: 0.40 (0.19), residues: 708 sheet: -0.77 (0.28), residues: 345 loop : -1.32 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 112 TYR 0.018 0.001 TYR B 179 PHE 0.024 0.002 PHE B 602 TRP 0.013 0.001 TRP A 589 HIS 0.007 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00349 (12817) covalent geometry : angle 0.74270 (17388) hydrogen bonds : bond 0.04466 ( 688) hydrogen bonds : angle 5.59137 ( 1998) Misc. bond : bond 0.22228 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLN cc_start: 0.9418 (OUTLIER) cc_final: 0.9172 (tm-30) REVERT: B 253 PHE cc_start: 0.8713 (m-80) cc_final: 0.8298 (m-10) REVERT: B 772 MET cc_start: 0.9365 (mtm) cc_final: 0.9026 (ptp) outliers start: 21 outliers final: 4 residues processed: 107 average time/residue: 0.1239 time to fit residues: 19.4297 Evaluate side-chains 83 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 685 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2828 > 50: distance: 50 - 56: 33.460 distance: 51 - 78: 37.328 distance: 56 - 57: 40.089 distance: 56 - 62: 39.543 distance: 57 - 58: 50.736 distance: 57 - 60: 5.943 distance: 58 - 59: 27.485 distance: 58 - 63: 20.344 distance: 59 - 86: 52.394 distance: 60 - 61: 38.914 distance: 61 - 62: 39.132 distance: 63 - 64: 19.335 distance: 64 - 65: 47.694 distance: 64 - 67: 31.945 distance: 65 - 66: 39.898 distance: 65 - 71: 3.518 distance: 68 - 69: 38.785 distance: 68 - 70: 56.181 distance: 71 - 72: 41.741 distance: 72 - 73: 34.356 distance: 72 - 75: 41.820 distance: 75 - 76: 32.928 distance: 75 - 77: 7.471 distance: 78 - 79: 50.743 distance: 79 - 80: 46.549 distance: 79 - 82: 24.940 distance: 80 - 81: 35.214 distance: 80 - 86: 8.152 distance: 82 - 83: 40.426 distance: 83 - 84: 11.177 distance: 83 - 85: 30.908 distance: 86 - 87: 6.893 distance: 87 - 88: 30.551 distance: 87 - 90: 53.573 distance: 88 - 89: 49.293 distance: 88 - 94: 35.372 distance: 90 - 91: 38.432 distance: 91 - 92: 25.324 distance: 91 - 93: 13.011 distance: 94 - 95: 25.411 distance: 95 - 96: 29.492 distance: 95 - 98: 25.652 distance: 98 - 99: 17.298 distance: 99 - 100: 9.635 distance: 99 - 101: 11.957 distance: 102 - 103: 19.816 distance: 103 - 104: 19.810 distance: 103 - 106: 19.451 distance: 104 - 105: 39.397 distance: 104 - 109: 46.403 distance: 106 - 107: 39.715 distance: 109 - 110: 24.051 distance: 109 - 115: 45.265 distance: 110 - 111: 8.733 distance: 110 - 113: 22.744 distance: 111 - 112: 54.624 distance: 111 - 116: 8.272 distance: 113 - 114: 43.444 distance: 114 - 115: 25.360 distance: 116 - 117: 43.220 distance: 117 - 118: 19.076 distance: 117 - 120: 19.490 distance: 118 - 119: 16.860 distance: 118 - 125: 15.930 distance: 120 - 121: 15.335 distance: 122 - 123: 39.525 distance: 122 - 124: 39.433 distance: 125 - 126: 32.855 distance: 126 - 127: 31.747 distance: 126 - 129: 9.922 distance: 127 - 128: 31.290 distance: 127 - 136: 21.015 distance: 129 - 130: 38.387 distance: 130 - 131: 12.285 distance: 130 - 132: 28.323 distance: 131 - 133: 15.415 distance: 132 - 134: 13.780 distance: 133 - 135: 9.589 distance: 134 - 135: 28.022