Starting phenix.real_space_refine on Thu Jun 27 01:41:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpo_36485/06_2024/8jpo_36485_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpo_36485/06_2024/8jpo_36485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpo_36485/06_2024/8jpo_36485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpo_36485/06_2024/8jpo_36485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpo_36485/06_2024/8jpo_36485_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpo_36485/06_2024/8jpo_36485_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 70 5.16 5 Cl 4 4.86 5 C 7430 2.51 5 N 1922 2.21 5 O 2042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A GLU 856": "OE1" <-> "OE2" Residue "A PHE 857": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B GLU 161": "OE1" <-> "OE2" Residue "B GLU 398": "OE1" <-> "OE2" Residue "B TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 670": "OE1" <-> "OE2" Residue "B GLU 762": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 11476 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5704 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 701} Chain breaks: 4 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 5704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5704 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 701} Chain breaks: 4 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CL': 2, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CL': 2, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.48, per 1000 atoms: 0.56 Number of scatterers: 11476 At special positions: 0 Unit cell: (92.9514, 96.301, 113.886, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 4 17.00 S 70 16.00 P 6 15.00 Mg 2 11.99 O 2042 8.00 N 1922 7.00 C 7430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 125 " distance=2.02 Simple disulfide: pdb=" SG CYS A 319 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 399 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 125 " distance=2.02 Simple disulfide: pdb=" SG CYS B 319 " - pdb=" SG CYS B 326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 430 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.51 Conformation dependent library (CDL) restraints added in 1.8 seconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 6 sheets defined 58.5% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 59 through 67 Processing helix chain 'A' and resid 70 through 122 removed outlier: 3.554A pdb=" N LEU A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 150 removed outlier: 3.605A pdb=" N VAL A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 159 through 167 removed outlier: 3.966A pdb=" N LYS A 163 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N CYS A 164 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 165 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A 166 " --> pdb=" O LYS A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.618A pdb=" N GLY A 186 " --> pdb=" O CYS A 182 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 235 through 254 removed outlier: 4.087A pdb=" N ASP A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 277 through 298 removed outlier: 3.681A pdb=" N PHE A 282 " --> pdb=" O TRP A 278 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 297 " --> pdb=" O PHE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 365 removed outlier: 3.814A pdb=" N GLY A 345 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A 363 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 394 Processing helix chain 'A' and resid 437 through 442 Processing helix chain 'A' and resid 446 through 455 Processing helix chain 'A' and resid 462 through 479 Processing helix chain 'A' and resid 489 through 510 removed outlier: 3.760A pdb=" N CYS A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 533 Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 551 through 568 removed outlier: 4.480A pdb=" N LEU A 555 " --> pdb=" O THR A 552 " (cutoff:3.500A) Proline residue: A 556 - end of helix removed outlier: 3.745A pdb=" N VAL A 559 " --> pdb=" O PRO A 556 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET A 562 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 563 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA A 564 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS A 565 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR A 567 " --> pdb=" O ALA A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 581 Processing helix chain 'A' and resid 594 through 597 No H-bonds generated for 'chain 'A' and resid 594 through 597' Processing helix chain 'A' and resid 601 through 604 No H-bonds generated for 'chain 'A' and resid 601 through 604' Processing helix chain 'A' and resid 618 through 627 Processing helix chain 'A' and resid 650 through 663 Processing helix chain 'A' and resid 667 through 676 Processing helix chain 'A' and resid 732 through 735 No H-bonds generated for 'chain 'A' and resid 732 through 735' Processing helix chain 'A' and resid 747 through 755 Processing helix chain 'A' and resid 774 through 778 Processing helix chain 'A' and resid 820 through 829 Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 855 through 868 Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 70 through 122 removed outlier: 3.648A pdb=" N VAL B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 150 removed outlier: 3.600A pdb=" N VAL B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 159 through 167 removed outlier: 4.022A pdb=" N LYS B 163 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N CYS B 164 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 165 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU B 166 " --> pdb=" O LYS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 193 removed outlier: 3.623A pdb=" N GLY B 186 " --> pdb=" O CYS B 182 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY B 193 " --> pdb=" O PHE B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 214 removed outlier: 4.172A pdb=" N ILE B 204 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N HIS B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 235 through 254 removed outlier: 4.067A pdb=" N ASP B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 265 Processing helix chain 'B' and resid 277 through 298 removed outlier: 3.668A pdb=" N PHE B 282 " --> pdb=" O TRP B 278 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 365 removed outlier: 3.799A pdb=" N GLY B 345 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET B 363 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 394 removed outlier: 3.636A pdb=" N VAL B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 442 Processing helix chain 'B' and resid 446 through 455 Processing helix chain 'B' and resid 462 through 479 Processing helix chain 'B' and resid 489 through 510 removed outlier: 3.751A pdb=" N CYS B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 496 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 533 Processing helix chain 'B' and resid 539 through 548 Processing helix chain 'B' and resid 551 through 570 removed outlier: 4.546A pdb=" N LEU B 555 " --> pdb=" O THR B 552 " (cutoff:3.500A) Proline residue: B 556 - end of helix removed outlier: 3.815A pdb=" N VAL B 559 " --> pdb=" O PRO B 556 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N MET B 562 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL B 563 " --> pdb=" O THR B 560 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA B 564 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS B 565 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR B 567 " --> pdb=" O ALA B 564 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP B 569 " --> pdb=" O TRP B 566 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE B 570 " --> pdb=" O THR B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 581 Processing helix chain 'B' and resid 594 through 597 No H-bonds generated for 'chain 'B' and resid 594 through 597' Processing helix chain 'B' and resid 601 through 604 No H-bonds generated for 'chain 'B' and resid 601 through 604' Processing helix chain 'B' and resid 618 through 627 Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'B' and resid 667 through 676 Processing helix chain 'B' and resid 732 through 735 No H-bonds generated for 'chain 'B' and resid 732 through 735' Processing helix chain 'B' and resid 747 through 755 Processing helix chain 'B' and resid 774 through 778 Processing helix chain 'B' and resid 820 through 829 Processing helix chain 'B' and resid 855 through 868 Processing sheet with id= A, first strand: chain 'A' and resid 399 through 401 Processing sheet with id= B, first strand: chain 'A' and resid 632 through 638 removed outlier: 6.546A pdb=" N THR A 637 " --> pdb=" O PHE A 741 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE A 741 " --> pdb=" O THR A 637 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 835 through 838 Processing sheet with id= D, first strand: chain 'B' and resid 399 through 401 Processing sheet with id= E, first strand: chain 'B' and resid 632 through 638 removed outlier: 6.546A pdb=" N THR B 637 " --> pdb=" O PHE B 741 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE B 741 " --> pdb=" O THR B 637 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 835 through 838 565 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3614 1.34 - 1.47: 2886 1.47 - 1.59: 5122 1.59 - 1.71: 2 1.71 - 1.83: 110 Bond restraints: 11734 Sorted by residual: bond pdb=" C HIS B 367 " pdb=" N PRO B 368 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.54e+00 bond pdb=" C HIS A 367 " pdb=" N PRO A 368 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.42e+00 bond pdb=" CA GLY B 397 " pdb=" C GLY B 397 " ideal model delta sigma weight residual 1.520 1.512 0.008 7.30e-03 1.88e+04 1.29e+00 bond pdb=" C VAL A 175 " pdb=" O VAL A 175 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.16e+00 bond pdb=" CA GLY A 397 " pdb=" C GLY A 397 " ideal model delta sigma weight residual 1.520 1.512 0.008 7.30e-03 1.88e+04 1.13e+00 ... (remaining 11729 not shown) Histogram of bond angle deviations from ideal: 99.95 - 107.90: 435 107.90 - 115.85: 7176 115.85 - 123.80: 8058 123.80 - 131.76: 239 131.76 - 139.71: 20 Bond angle restraints: 15928 Sorted by residual: angle pdb=" N VAL A 162 " pdb=" CA VAL A 162 " pdb=" C VAL A 162 " ideal model delta sigma weight residual 112.96 107.99 4.97 1.00e+00 1.00e+00 2.47e+01 angle pdb=" N VAL B 162 " pdb=" CA VAL B 162 " pdb=" C VAL B 162 " ideal model delta sigma weight residual 112.96 108.09 4.87 1.00e+00 1.00e+00 2.37e+01 angle pdb=" C GLY A 158 " pdb=" N ILE A 159 " pdb=" CA ILE A 159 " ideal model delta sigma weight residual 120.24 122.96 -2.72 6.30e-01 2.52e+00 1.86e+01 angle pdb=" C GLY B 158 " pdb=" N ILE B 159 " pdb=" CA ILE B 159 " ideal model delta sigma weight residual 120.24 122.94 -2.70 6.30e-01 2.52e+00 1.83e+01 angle pdb=" C ILE A 159 " pdb=" CA ILE A 159 " pdb=" CB ILE A 159 " ideal model delta sigma weight residual 114.35 110.96 3.39 1.06e+00 8.90e-01 1.02e+01 ... (remaining 15923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.64: 6212 14.64 - 29.27: 527 29.27 - 43.91: 140 43.91 - 58.55: 46 58.55 - 73.19: 21 Dihedral angle restraints: 6946 sinusoidal: 2748 harmonic: 4198 Sorted by residual: dihedral pdb=" CB CYS A 120 " pdb=" SG CYS A 120 " pdb=" SG CYS A 125 " pdb=" CB CYS A 125 " ideal model delta sinusoidal sigma weight residual -86.00 -148.19 62.19 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS B 120 " pdb=" SG CYS B 120 " pdb=" SG CYS B 125 " pdb=" CB CYS B 125 " ideal model delta sinusoidal sigma weight residual -86.00 -147.05 61.05 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CA VAL A 171 " pdb=" C VAL A 171 " pdb=" N PRO A 172 " pdb=" CA PRO A 172 " ideal model delta harmonic sigma weight residual 180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 6943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1173 0.032 - 0.064: 466 0.064 - 0.096: 132 0.096 - 0.128: 64 0.128 - 0.160: 7 Chirality restraints: 1842 Sorted by residual: chirality pdb=" CA VAL A 171 " pdb=" N VAL A 171 " pdb=" C VAL A 171 " pdb=" CB VAL A 171 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CA VAL B 171 " pdb=" N VAL B 171 " pdb=" C VAL B 171 " pdb=" CB VAL B 171 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CB VAL B 242 " pdb=" CA VAL B 242 " pdb=" CG1 VAL B 242 " pdb=" CG2 VAL B 242 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 1839 not shown) Planarity restraints: 1990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 769 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 770 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 770 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 770 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 769 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO B 770 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 770 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 770 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 484 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO B 485 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " 0.022 5.00e-02 4.00e+02 ... (remaining 1987 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2832 2.79 - 3.32: 11307 3.32 - 3.85: 18917 3.85 - 4.37: 22521 4.37 - 4.90: 39213 Nonbonded interactions: 94790 Sorted by model distance: nonbonded pdb=" O THR B 440 " pdb=" ND2 ASN B 444 " model vdw 2.267 2.520 nonbonded pdb=" O ASP A 603 " pdb=" NH1 ARG A 861 " model vdw 2.272 2.520 nonbonded pdb=" O ASP B 603 " pdb=" NH1 ARG B 861 " model vdw 2.284 2.520 nonbonded pdb=" O THR A 440 " pdb=" ND2 ASN A 444 " model vdw 2.302 2.520 nonbonded pdb=" O PRO B 431 " pdb=" OG1 THR B 434 " model vdw 2.308 2.440 ... (remaining 94785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 869 or resid 902 or resid 904)) selection = (chain 'B' and (resid 46 through 869 or resid 902 or resid 904)) } 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: 0.670 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: 2.960 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.940 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11734 Z= 0.240 Angle : 0.628 6.396 15928 Z= 0.372 Chirality : 0.041 0.160 1842 Planarity : 0.005 0.040 1990 Dihedral : 12.938 73.186 4232 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.23), residues: 1446 helix: 1.12 (0.18), residues: 896 sheet: -2.55 (0.85), residues: 24 loop : -0.96 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 478 HIS 0.002 0.001 HIS A 851 PHE 0.014 0.001 PHE A 390 TYR 0.013 0.001 TYR A 781 ARG 0.005 0.000 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.234 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1910 time to fit residues: 32.3011 Evaluate side-chains 92 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 114 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN B 764 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11734 Z= 0.320 Angle : 0.586 7.878 15928 Z= 0.304 Chirality : 0.042 0.155 1842 Planarity : 0.005 0.040 1990 Dihedral : 7.585 52.052 1642 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.64 % Allowed : 6.00 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1446 helix: 1.26 (0.18), residues: 892 sheet: -2.74 (0.81), residues: 24 loop : -1.05 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 303 HIS 0.003 0.001 HIS A 851 PHE 0.015 0.001 PHE B 351 TYR 0.025 0.002 TYR A 510 ARG 0.004 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 1.444 Fit side-chains REVERT: A 360 LYS cc_start: 0.8887 (mttt) cc_final: 0.8597 (mtmm) REVERT: B 325 LYS cc_start: 0.7737 (mmtt) cc_final: 0.7158 (pttt) outliers start: 8 outliers final: 5 residues processed: 99 average time/residue: 0.2175 time to fit residues: 32.3751 Evaluate side-chains 96 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 117 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11734 Z= 0.212 Angle : 0.513 7.006 15928 Z= 0.263 Chirality : 0.039 0.158 1842 Planarity : 0.005 0.037 1990 Dihedral : 6.959 53.194 1642 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.04 % Allowed : 8.48 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.23), residues: 1446 helix: 1.37 (0.18), residues: 882 sheet: -2.85 (0.82), residues: 24 loop : -0.99 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 278 HIS 0.004 0.001 HIS A 851 PHE 0.010 0.001 PHE B 351 TYR 0.013 0.001 TYR A 781 ARG 0.002 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 1.482 Fit side-chains REVERT: A 360 LYS cc_start: 0.8822 (mttt) cc_final: 0.8543 (mtmm) REVERT: A 673 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8305 (tttm) outliers start: 13 outliers final: 9 residues processed: 108 average time/residue: 0.1885 time to fit residues: 32.0610 Evaluate side-chains 98 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11734 Z= 0.416 Angle : 0.606 6.520 15928 Z= 0.312 Chirality : 0.044 0.157 1842 Planarity : 0.005 0.042 1990 Dihedral : 7.177 53.902 1642 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.92 % Allowed : 9.60 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1446 helix: 1.09 (0.18), residues: 894 sheet: -2.67 (0.86), residues: 24 loop : -1.08 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 303 HIS 0.004 0.001 HIS B 615 PHE 0.016 0.002 PHE A 351 TYR 0.016 0.002 TYR A 781 ARG 0.003 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 1.270 Fit side-chains outliers start: 24 outliers final: 13 residues processed: 111 average time/residue: 0.1948 time to fit residues: 33.8282 Evaluate side-chains 99 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11734 Z= 0.234 Angle : 0.526 7.394 15928 Z= 0.268 Chirality : 0.039 0.158 1842 Planarity : 0.005 0.039 1990 Dihedral : 6.722 47.920 1642 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.52 % Allowed : 11.20 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.23), residues: 1446 helix: 1.29 (0.18), residues: 890 sheet: -2.86 (0.87), residues: 24 loop : -1.08 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 278 HIS 0.002 0.001 HIS B 515 PHE 0.012 0.001 PHE A 101 TYR 0.014 0.001 TYR A 781 ARG 0.002 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.333 Fit side-chains REVERT: A 360 LYS cc_start: 0.8852 (mttt) cc_final: 0.8591 (mtmm) outliers start: 19 outliers final: 12 residues processed: 114 average time/residue: 0.1912 time to fit residues: 34.0525 Evaluate side-chains 107 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.5980 chunk 127 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11734 Z= 0.228 Angle : 0.517 8.088 15928 Z= 0.264 Chirality : 0.039 0.158 1842 Planarity : 0.005 0.038 1990 Dihedral : 6.609 52.749 1642 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.68 % Allowed : 12.16 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1446 helix: 1.40 (0.18), residues: 886 sheet: -2.97 (0.88), residues: 24 loop : -1.13 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 278 HIS 0.003 0.001 HIS B 515 PHE 0.013 0.001 PHE A 101 TYR 0.014 0.001 TYR A 781 ARG 0.002 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 1.252 Fit side-chains REVERT: A 360 LYS cc_start: 0.8794 (mttt) cc_final: 0.8539 (mtmm) outliers start: 21 outliers final: 13 residues processed: 114 average time/residue: 0.1836 time to fit residues: 32.9327 Evaluate side-chains 108 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.4406 > 50: distance: 68 - 94: 11.223 distance: 74 - 77: 4.070 distance: 77 - 78: 7.418 distance: 78 - 79: 10.265 distance: 78 - 81: 10.541 distance: 79 - 80: 8.356 distance: 79 - 86: 14.784 distance: 81 - 82: 6.582 distance: 82 - 83: 5.610 distance: 86 - 87: 10.903 distance: 87 - 88: 15.031 distance: 87 - 90: 23.216 distance: 88 - 89: 8.587 distance: 88 - 94: 9.368 distance: 90 - 91: 20.048 distance: 91 - 92: 17.547 distance: 92 - 93: 14.622 distance: 94 - 95: 32.376 distance: 95 - 96: 23.284 distance: 95 - 98: 30.143 distance: 96 - 97: 33.247 distance: 96 - 99: 25.174 distance: 99 - 100: 33.315 distance: 100 - 101: 11.831 distance: 100 - 103: 29.464 distance: 101 - 102: 51.646 distance: 101 - 108: 40.068 distance: 103 - 104: 27.355 distance: 104 - 105: 15.757 distance: 105 - 106: 23.886 distance: 105 - 107: 26.828 distance: 108 - 109: 50.855 distance: 109 - 110: 26.833 distance: 109 - 112: 49.214 distance: 110 - 111: 43.077 distance: 110 - 116: 58.874 distance: 112 - 113: 42.982 distance: 113 - 114: 44.471 distance: 113 - 115: 40.208 distance: 116 - 117: 39.704 distance: 117 - 118: 47.877 distance: 117 - 120: 51.000 distance: 118 - 119: 35.372 distance: 118 - 128: 37.183 distance: 120 - 121: 16.441 distance: 121 - 122: 33.546 distance: 121 - 123: 13.854 distance: 122 - 124: 20.772 distance: 123 - 125: 25.949 distance: 124 - 126: 9.972 distance: 125 - 126: 14.475 distance: 126 - 127: 7.774 distance: 128 - 134: 56.491 distance: 129 - 130: 15.058 distance: 129 - 132: 67.503 distance: 130 - 131: 61.552 distance: 130 - 135: 61.010 distance: 132 - 133: 55.804 distance: 133 - 134: 69.590 distance: 135 - 136: 18.704 distance: 136 - 137: 43.134 distance: 136 - 139: 47.922 distance: 137 - 138: 46.857 distance: 137 - 146: 43.148 distance: 139 - 140: 36.135 distance: 140 - 141: 27.729 distance: 141 - 142: 14.681 distance: 142 - 143: 5.220 distance: 143 - 144: 4.584 distance: 143 - 145: 10.246 distance: 146 - 147: 28.635 distance: 147 - 148: 35.819 distance: 147 - 150: 56.514 distance: 148 - 149: 22.530 distance: 148 - 158: 56.784 distance: 150 - 151: 56.837 distance: 151 - 152: 26.020 distance: 151 - 153: 13.477 distance: 152 - 154: 51.489 distance: 153 - 155: 46.758 distance: 154 - 156: 27.825 distance: 155 - 156: 26.165 distance: 156 - 157: 14.074 distance: 158 - 159: 48.019 distance: 158 - 164: 36.022 distance: 159 - 160: 4.787 distance: 159 - 162: 43.433 distance: 160 - 161: 41.697 distance: 160 - 165: 35.264 distance: 162 - 163: 46.660 distance: 163 - 164: 57.898