Starting phenix.real_space_refine on Fri Jan 17 12:20:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u54_41912/01_2025/8u54_41912.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u54_41912/01_2025/8u54_41912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u54_41912/01_2025/8u54_41912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u54_41912/01_2025/8u54_41912.map" model { file = "/net/cci-nas-00/data/ceres_data/8u54_41912/01_2025/8u54_41912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u54_41912/01_2025/8u54_41912.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 7130 2.51 5 N 1690 2.21 5 O 1859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10745 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5353 Classifications: {'peptide': 679} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 655} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5364 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 656} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.39, per 1000 atoms: 0.59 Number of scatterers: 10745 At special positions: 0 Unit cell: (94.18, 120.772, 93.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1859 8.00 N 1690 7.00 C 7130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 309 " " NAG B 901 " - " ASN B 309 " Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.5 seconds 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 2 sheets defined 84.6% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 62 Processing helix chain 'A' and resid 66 through 80 removed outlier: 4.033A pdb=" N GLY A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 99 through 125 removed outlier: 3.556A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 143 Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.570A pdb=" N ILE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 197 removed outlier: 3.921A pdb=" N TYR A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 169 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Proline residue: A 174 - end of helix Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.539A pdb=" N ILE A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 241 through 264 removed outlier: 3.619A pdb=" N SER A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLY A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 288 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 326 through 337 removed outlier: 4.085A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.702A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 404 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 411 through 436 removed outlier: 3.699A pdb=" N PHE A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 473 Processing helix chain 'A' and resid 480 through 503 Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 516 through 549 Processing helix chain 'A' and resid 644 through 682 Processing helix chain 'A' and resid 686 through 712 removed outlier: 5.649A pdb=" N GLY A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 720 Processing helix chain 'A' and resid 744 through 757 removed outlier: 3.555A pdb=" N TYR A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 767 removed outlier: 4.770A pdb=" N LEU A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 798 through 812 Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 41 through 62 Processing helix chain 'B' and resid 66 through 80 removed outlier: 4.031A pdb=" N GLY B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 93 Processing helix chain 'B' and resid 99 through 125 removed outlier: 3.568A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 143 Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 149 through 159 removed outlier: 3.578A pdb=" N ILE B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 197 removed outlier: 3.917A pdb=" N TYR B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE B 169 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Proline residue: B 174 - end of helix Proline residue: B 182 - end of helix Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.544A pdb=" N ILE B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 241 through 264 removed outlier: 3.585A pdb=" N SER B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLY B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 288 Processing helix chain 'B' and resid 288 through 302 Processing helix chain 'B' and resid 306 through 322 Processing helix chain 'B' and resid 326 through 337 removed outlier: 4.081A pdb=" N ALA B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 367 removed outlier: 3.689A pdb=" N ALA B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 371 through 404 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 411 through 436 removed outlier: 3.698A pdb=" N PHE B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 473 Processing helix chain 'B' and resid 480 through 503 Proline residue: B 492 - end of helix Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 516 through 549 Processing helix chain 'B' and resid 644 through 682 Processing helix chain 'B' and resid 686 through 712 removed outlier: 5.664A pdb=" N GLY B 704 " --> pdb=" O ASN B 700 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N PHE B 705 " --> pdb=" O PHE B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 720 Processing helix chain 'B' and resid 744 through 757 removed outlier: 3.534A pdb=" N TYR B 757 " --> pdb=" O GLN B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 removed outlier: 4.768A pdb=" N LEU B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 793 Processing helix chain 'B' and resid 798 through 812 Processing sheet with id=AA1, first strand: chain 'A' and resid 780 through 782 Processing sheet with id=AA2, first strand: chain 'B' and resid 780 through 782 852 hydrogen bonds defined for protein. 2532 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: 3.12 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1643 1.30 - 1.43: 2943 1.43 - 1.56: 6307 1.56 - 1.68: 0 1.68 - 1.81: 102 Bond restraints: 10995 Sorted by residual: bond pdb=" C ASN B 309 " pdb=" O ASN B 309 " ideal model delta sigma weight residual 1.236 1.176 0.059 1.29e-02 6.01e+03 2.12e+01 bond pdb=" CA SER B 306 " pdb=" CB SER B 306 " ideal model delta sigma weight residual 1.528 1.466 0.062 1.58e-02 4.01e+03 1.53e+01 bond pdb=" C ASN B 309 " pdb=" N HIS B 310 " ideal model delta sigma weight residual 1.335 1.304 0.031 1.36e-02 5.41e+03 5.06e+00 bond pdb=" C VAL B 308 " pdb=" N ASN B 309 " ideal model delta sigma weight residual 1.335 1.306 0.029 1.38e-02 5.25e+03 4.51e+00 bond pdb=" CB CYS B 696 " pdb=" SG CYS B 696 " ideal model delta sigma weight residual 1.808 1.740 0.068 3.30e-02 9.18e+02 4.24e+00 ... (remaining 10990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 14046 1.47 - 2.94: 703 2.94 - 4.41: 130 4.41 - 5.88: 39 5.88 - 7.36: 8 Bond angle restraints: 14926 Sorted by residual: angle pdb=" CA ASN B 309 " pdb=" CB ASN B 309 " pdb=" CG ASN B 309 " ideal model delta sigma weight residual 112.60 117.54 -4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" C ILE B 388 " pdb=" N VAL B 389 " pdb=" CA VAL B 389 " ideal model delta sigma weight residual 120.29 114.54 5.75 1.72e+00 3.38e-01 1.12e+01 angle pdb=" C ILE A 388 " pdb=" N VAL A 389 " pdb=" CA VAL A 389 " ideal model delta sigma weight residual 120.29 114.57 5.72 1.72e+00 3.38e-01 1.11e+01 angle pdb=" CA TYR B 451 " pdb=" CB TYR B 451 " pdb=" CG TYR B 451 " ideal model delta sigma weight residual 113.90 108.07 5.83 1.80e+00 3.09e-01 1.05e+01 angle pdb=" CA ASN B 309 " pdb=" C ASN B 309 " pdb=" N HIS B 310 " ideal model delta sigma weight residual 118.14 122.35 -4.21 1.31e+00 5.83e-01 1.03e+01 ... (remaining 14921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 5906 16.28 - 32.55: 458 32.55 - 48.83: 76 48.83 - 65.10: 17 65.10 - 81.38: 3 Dihedral angle restraints: 6460 sinusoidal: 2523 harmonic: 3937 Sorted by residual: dihedral pdb=" CA GLY B 266 " pdb=" C GLY B 266 " pdb=" N LYS B 267 " pdb=" CA LYS B 267 " ideal model delta harmonic sigma weight residual -180.00 -154.79 -25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA GLY A 266 " pdb=" C GLY A 266 " pdb=" N LYS A 267 " pdb=" CA LYS A 267 " ideal model delta harmonic sigma weight residual -180.00 -155.41 -24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA SER B 36 " pdb=" C SER B 36 " pdb=" N MET B 37 " pdb=" CA MET B 37 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 6457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1101 0.038 - 0.076: 484 0.076 - 0.114: 149 0.114 - 0.152: 30 0.152 - 0.191: 5 Chirality restraints: 1769 Sorted by residual: chirality pdb=" CA TYR B 451 " pdb=" N TYR B 451 " pdb=" C TYR B 451 " pdb=" CB TYR B 451 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.08e-01 chirality pdb=" CA TYR A 451 " pdb=" N TYR A 451 " pdb=" C TYR A 451 " pdb=" CB TYR A 451 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA PHE B 50 " pdb=" N PHE B 50 " pdb=" C PHE B 50 " pdb=" CB PHE B 50 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.20e-01 ... (remaining 1766 not shown) Planarity restraints: 1824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 309 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C ASN B 309 " -0.042 2.00e-02 2.50e+03 pdb=" O ASN B 309 " 0.015 2.00e-02 2.50e+03 pdb=" N HIS B 310 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 320 " 0.033 2.00e-02 2.50e+03 1.70e-02 5.75e+00 pdb=" CG TYR B 320 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 320 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 320 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 320 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 320 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 320 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 320 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 320 " -0.032 2.00e-02 2.50e+03 1.65e-02 5.42e+00 pdb=" CG TYR A 320 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 320 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 320 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 320 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 320 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 320 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 320 " -0.015 2.00e-02 2.50e+03 ... (remaining 1821 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1796 2.76 - 3.29: 11297 3.29 - 3.83: 18792 3.83 - 4.36: 23026 4.36 - 4.90: 37963 Nonbonded interactions: 92874 Sorted by model distance: nonbonded pdb=" OG SER B 306 " pdb=" C8 NAG B 901 " model vdw 2.221 3.460 nonbonded pdb=" OD1 ASP A 99 " pdb=" OG SER A 101 " model vdw 2.321 3.040 nonbonded pdb=" OD1 ASP B 99 " pdb=" OG SER B 101 " model vdw 2.348 3.040 nonbonded pdb=" O PRO A 238 " pdb=" N TYR A 240 " model vdw 2.374 3.120 nonbonded pdb=" O PRO B 238 " pdb=" N TYR B 240 " model vdw 2.425 3.120 ... (remaining 92869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 34 through 769 or resid 779 through 834 or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.170 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 10995 Z= 0.405 Angle : 0.789 7.356 14926 Z= 0.446 Chirality : 0.047 0.191 1769 Planarity : 0.006 0.054 1822 Dihedral : 12.072 81.377 3926 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.17 % Allowed : 3.55 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1343 helix: -0.75 (0.14), residues: 1058 sheet: None (None), residues: 0 loop : -0.70 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 396 HIS 0.011 0.002 HIS B 310 PHE 0.031 0.004 PHE A 711 TYR 0.033 0.003 TYR B 320 ARG 0.003 0.001 ARG B 808 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 386 time to evaluate : 1.132 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: symmetry clash outliers start: 2 outliers final: 5 residues processed: 388 average time/residue: 0.7121 time to fit residues: 311.6537 Evaluate side-chains 200 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 195 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 807 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 310 HIS ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.126006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.084652 restraints weight = 25620.402| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.00 r_work: 0.3333 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10995 Z= 0.309 Angle : 0.817 14.247 14926 Z= 0.402 Chirality : 0.047 0.222 1769 Planarity : 0.005 0.052 1822 Dihedral : 5.311 46.551 1492 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.94 % Favored : 97.92 % Rotamer: Outliers : 5.83 % Allowed : 15.72 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.76 (0.23), residues: 1343 helix: 0.81 (0.15), residues: 1054 sheet: None (None), residues: 0 loop : -0.28 (0.42), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 489 HIS 0.009 0.002 HIS B 505 PHE 0.021 0.002 PHE A 50 TYR 0.025 0.002 TYR A 689 ARG 0.008 0.001 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 1.240 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: A 41 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7777 (mmm-85) REVERT: A 198 ASN cc_start: 0.9022 (m110) cc_final: 0.8812 (p0) REVERT: A 278 VAL cc_start: 0.8699 (t) cc_final: 0.8391 (p) REVERT: A 297 MET cc_start: 0.9076 (mmm) cc_final: 0.8789 (mmm) REVERT: A 301 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8574 (tp) REVERT: A 316 TYR cc_start: 0.8589 (t80) cc_final: 0.8347 (t80) REVERT: A 667 ILE cc_start: 0.9165 (mt) cc_final: 0.8920 (mm) REVERT: A 752 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8714 (tp-100) REVERT: B 41 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7814 (mmm-85) REVERT: B 278 VAL cc_start: 0.8741 (t) cc_final: 0.8457 (p) REVERT: B 288 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8575 (tp) REVERT: B 293 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8621 (tp) REVERT: B 301 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8557 (tp) REVERT: B 316 TYR cc_start: 0.8706 (t80) cc_final: 0.8403 (t80) REVERT: B 460 TRP cc_start: 0.8930 (m100) cc_final: 0.8710 (m100) REVERT: B 512 SER cc_start: 0.9133 (p) cc_final: 0.8885 (p) REVERT: B 521 MET cc_start: 0.9481 (OUTLIER) cc_final: 0.9252 (tpp) REVERT: B 667 ILE cc_start: 0.9140 (mt) cc_final: 0.8883 (mm) REVERT: B 752 GLN cc_start: 0.9133 (tp-100) cc_final: 0.8750 (tp-100) outliers start: 69 outliers final: 19 residues processed: 250 average time/residue: 0.7258 time to fit residues: 205.4440 Evaluate side-chains 192 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 489 TRP Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 665 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.5678 > 50: distance: 3 - 24: 11.995 distance: 8 - 32: 24.930 distance: 19 - 24: 10.479 distance: 24 - 25: 13.548 distance: 25 - 26: 25.795 distance: 25 - 28: 29.205 distance: 26 - 27: 22.276 distance: 26 - 32: 3.166 distance: 28 - 29: 3.180 distance: 29 - 30: 22.770 distance: 29 - 31: 17.154 distance: 32 - 33: 28.231 distance: 33 - 34: 20.680 distance: 33 - 36: 41.202 distance: 34 - 35: 23.536 distance: 34 - 38: 8.605 distance: 36 - 37: 35.294 distance: 38 - 39: 9.456 distance: 39 - 40: 38.912 distance: 39 - 42: 53.049 distance: 40 - 41: 18.692 distance: 40 - 47: 12.942 distance: 41 - 68: 34.323 distance: 42 - 43: 19.159 distance: 43 - 44: 22.099 distance: 44 - 45: 40.505 distance: 45 - 46: 11.114 distance: 47 - 48: 19.929 distance: 48 - 49: 17.050 distance: 48 - 51: 12.932 distance: 49 - 50: 17.837 distance: 49 - 56: 10.794 distance: 50 - 77: 25.174 distance: 51 - 52: 14.846 distance: 52 - 53: 8.165 distance: 53 - 54: 12.666 distance: 54 - 55: 11.271 distance: 56 - 57: 9.937 distance: 57 - 58: 33.208 distance: 57 - 60: 19.885 distance: 58 - 59: 21.269 distance: 58 - 68: 13.052 distance: 60 - 61: 24.549 distance: 61 - 62: 12.981 distance: 61 - 63: 8.622 distance: 62 - 64: 5.857 distance: 63 - 65: 5.052 distance: 64 - 66: 8.340 distance: 65 - 66: 8.680 distance: 66 - 67: 9.817 distance: 68 - 69: 34.160 distance: 69 - 70: 10.762 distance: 69 - 72: 10.096 distance: 70 - 71: 36.342 distance: 70 - 77: 17.610 distance: 72 - 73: 13.931 distance: 73 - 74: 8.443 distance: 74 - 75: 30.638 distance: 75 - 76: 27.150 distance: 77 - 78: 44.801 distance: 78 - 79: 42.946 distance: 78 - 81: 7.126 distance: 79 - 80: 16.879 distance: 79 - 86: 24.127 distance: 81 - 82: 35.386 distance: 82 - 83: 9.614 distance: 83 - 84: 20.892 distance: 83 - 85: 22.316 distance: 86 - 87: 18.020 distance: 87 - 88: 50.110 distance: 87 - 90: 40.036 distance: 88 - 89: 50.567 distance: 88 - 94: 31.873 distance: 90 - 91: 13.294 distance: 91 - 92: 9.263 distance: 91 - 93: 38.802 distance: 94 - 95: 26.428 distance: 94 - 100: 28.469 distance: 95 - 96: 14.693 distance: 96 - 97: 21.207 distance: 96 - 101: 21.157 distance: 97 - 127: 13.377 distance: 98 - 99: 35.856 distance: 99 - 100: 35.622 distance: 101 - 102: 8.297 distance: 102 - 103: 17.326 distance: 102 - 105: 16.213 distance: 103 - 104: 21.998 distance: 103 - 111: 3.924 distance: 104 - 133: 24.064 distance: 105 - 106: 19.041 distance: 106 - 107: 25.313 distance: 106 - 108: 26.252 distance: 107 - 109: 7.644 distance: 108 - 110: 16.163 distance: 109 - 110: 30.586