Starting phenix.real_space_refine on Fri Aug 22 19:32:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9inf_60705/08_2025/9inf_60705.cif Found real_map, /net/cci-nas-00/data/ceres_data/9inf_60705/08_2025/9inf_60705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9inf_60705/08_2025/9inf_60705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9inf_60705/08_2025/9inf_60705.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9inf_60705/08_2025/9inf_60705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9inf_60705/08_2025/9inf_60705.map" } resolution = 3.36 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= -0.000 sd= 0.013 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 P 6 5.49 5 S 32 5.16 5 C 5000 2.51 5 N 1076 2.21 5 O 1168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7282 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3333 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 385} Chain: "B" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3333 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 385} Chain: "A" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 333 Unusual residues: {'3PE': 3, 'ACD': 1, 'CLR': 5, 'PLM': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 277 Unusual residues: {'3PE': 3, 'ACD': 1, 'CLR': 3, 'PLM': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.11, per 1000 atoms: 0.29 Number of scatterers: 7282 At special positions: 0 Unit cell: (107.551, 96.057, 75.532, 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) S 32 16.00 P 6 15.00 O 1168 8.00 N 1076 7.00 C 5000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 320.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1524 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 0 sheets defined 77.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 230 through 258 Processing helix chain 'A' and resid 265 through 296 removed outlier: 4.207A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 312 through 336 removed outlier: 3.531A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 361 removed outlier: 4.240A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 384 through 387 removed outlier: 3.583A pdb=" N HIS A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 387' Processing helix chain 'A' and resid 390 through 402 Processing helix chain 'A' and resid 403 through 420 removed outlier: 3.851A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 471 Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 472 through 503 removed outlier: 4.135A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 Processing helix chain 'A' and resid 538 through 542 removed outlier: 4.383A pdb=" N GLY A 542 " --> pdb=" O LYS A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 580 removed outlier: 3.862A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 618 removed outlier: 4.247A pdb=" N ASP A 590 " --> pdb=" O PRO A 586 " (cutoff:3.500A) Proline residue: A 598 - end of helix Processing helix chain 'B' and resid 230 through 258 Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.133A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 312 through 336 Processing helix chain 'B' and resid 346 through 361 Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 384 through 387 removed outlier: 3.853A pdb=" N HIS B 387 " --> pdb=" O ALA B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 387' Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.753A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 471 Proline residue: B 455 - end of helix removed outlier: 3.622A pdb=" N ARG B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 502 removed outlier: 4.202A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 506 through 532 Processing helix chain 'B' and resid 538 through 542 removed outlier: 4.408A pdb=" N GLY B 542 " --> pdb=" O LYS B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 581 removed outlier: 3.888A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 618 removed outlier: 4.103A pdb=" N ASP B 590 " --> pdb=" O PRO B 586 " (cutoff:3.500A) Proline residue: B 598 - end of helix removed outlier: 3.654A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1377 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1099 1.33 - 1.45: 2156 1.45 - 1.57: 4201 1.57 - 1.69: 12 1.69 - 1.82: 44 Bond restraints: 7512 Sorted by residual: bond pdb=" CA THR A 491 " pdb=" C THR A 491 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.24e-02 6.50e+03 5.02e+00 bond pdb=" C1 PLM B 807 " pdb=" C2 PLM B 807 " ideal model delta sigma weight residual 1.542 1.569 -0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" CG LEU B 421 " pdb=" CD1 LEU B 421 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.76e+00 bond pdb=" CA LEU A 419 " pdb=" C LEU A 419 " ideal model delta sigma weight residual 1.519 1.533 -0.013 1.01e-02 9.80e+03 1.71e+00 bond pdb=" C1 PLM A 809 " pdb=" C2 PLM A 809 " ideal model delta sigma weight residual 1.542 1.568 -0.026 2.00e-02 2.50e+03 1.67e+00 ... (remaining 7507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 9942 1.87 - 3.73: 169 3.73 - 5.60: 38 5.60 - 7.46: 12 7.46 - 9.33: 5 Bond angle restraints: 10166 Sorted by residual: angle pdb=" C THR A 491 " pdb=" CA THR A 491 " pdb=" CB THR A 491 " ideal model delta sigma weight residual 110.96 105.38 5.58 1.54e+00 4.22e-01 1.31e+01 angle pdb=" C THR A 383 " pdb=" N ALA A 384 " pdb=" CA ALA A 384 " ideal model delta sigma weight residual 120.26 124.36 -4.10 1.34e+00 5.57e-01 9.35e+00 angle pdb=" N THR A 491 " pdb=" CA THR A 491 " pdb=" C THR A 491 " ideal model delta sigma weight residual 110.97 107.84 3.13 1.09e+00 8.42e-01 8.26e+00 angle pdb=" N THR A 491 " pdb=" CA THR A 491 " pdb=" CB THR A 491 " ideal model delta sigma weight residual 109.91 114.05 -4.14 1.46e+00 4.69e-01 8.03e+00 angle pdb=" C SER B 418 " pdb=" N LEU B 419 " pdb=" CA LEU B 419 " ideal model delta sigma weight residual 122.46 117.50 4.96 1.80e+00 3.09e-01 7.61e+00 ... (remaining 10161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.87: 4226 22.87 - 45.75: 457 45.75 - 68.62: 88 68.62 - 91.50: 5 91.50 - 114.37: 8 Dihedral angle restraints: 4784 sinusoidal: 2418 harmonic: 2366 Sorted by residual: dihedral pdb=" CB CYS B 415 " pdb=" SG CYS B 415 " pdb=" SG CYS B 440 " pdb=" CB CYS B 440 " ideal model delta sinusoidal sigma weight residual 93.00 172.38 -79.38 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS A 415 " pdb=" SG CYS A 415 " pdb=" SG CYS A 440 " pdb=" CB CYS A 440 " ideal model delta sinusoidal sigma weight residual 93.00 164.66 -71.66 1 1.00e+01 1.00e-02 6.58e+01 dihedral pdb=" CA LEU B 419 " pdb=" C LEU B 419 " pdb=" N GLU B 420 " pdb=" CA GLU B 420 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 4781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1015 0.076 - 0.153: 73 0.153 - 0.229: 4 0.229 - 0.306: 1 0.306 - 0.382: 1 Chirality restraints: 1094 Sorted by residual: chirality pdb=" C17 CLR A 807 " pdb=" C13 CLR A 807 " pdb=" C16 CLR A 807 " pdb=" C20 CLR A 807 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" C20 CLR A 807 " pdb=" C17 CLR A 807 " pdb=" C21 CLR A 807 " pdb=" C22 CLR A 807 " both_signs ideal model delta sigma weight residual False 2.59 2.35 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CG LEU A 396 " pdb=" CB LEU A 396 " pdb=" CD1 LEU A 396 " pdb=" CD2 LEU A 396 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1091 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 573 " 0.013 2.00e-02 2.50e+03 1.64e-02 6.70e+00 pdb=" CG TRP A 573 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 573 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 573 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 573 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 573 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 573 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 573 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 573 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 573 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 514 " -0.017 2.00e-02 2.50e+03 1.54e-02 5.93e+00 pdb=" CG TRP B 514 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 514 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 514 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 514 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 514 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 514 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 514 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 514 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 514 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 528 " 0.018 2.00e-02 2.50e+03 1.42e-02 5.05e+00 pdb=" CG TRP A 528 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 528 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 528 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 528 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 528 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 528 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 528 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 528 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 528 " 0.006 2.00e-02 2.50e+03 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 777 2.75 - 3.29: 7498 3.29 - 3.82: 12803 3.82 - 4.36: 14733 4.36 - 4.90: 24980 Nonbonded interactions: 60791 Sorted by model distance: nonbonded pdb=" OH TYR A 559 " pdb=" OE2 GLU A 613 " model vdw 2.212 3.040 nonbonded pdb=" OD2 ASP A 529 " pdb=" NH2 ARG A 570 " model vdw 2.215 3.120 nonbonded pdb=" O SER B 578 " pdb=" OG1 THR B 583 " model vdw 2.220 3.040 nonbonded pdb=" O ILE B 271 " pdb=" OH TYR B 352 " model vdw 2.246 3.040 nonbonded pdb=" O ILE A 271 " pdb=" OH TYR A 352 " model vdw 2.258 3.040 ... (remaining 60786 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 226 through 804) selection = (chain 'B' and resid 226 through 804) } 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: 7.720 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.730 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.003 0.045 7514 Z= 0.148 Angle : 0.675 9.330 10170 Z= 0.348 Chirality : 0.043 0.382 1094 Planarity : 0.004 0.053 1172 Dihedral : 17.898 114.372 3254 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.56 % Allowed : 28.45 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.30), residues: 798 helix: 1.75 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -1.32 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 263 TYR 0.022 0.001 TYR A 518 PHE 0.016 0.001 PHE B 511 TRP 0.043 0.003 TRP A 573 HIS 0.003 0.001 HIS B 587 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7512) covalent geometry : angle 0.67500 (10166) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.62336 ( 4) hydrogen bonds : bond 0.10976 ( 461) hydrogen bonds : angle 4.48969 ( 1377) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 152 time to evaluate : 0.221 Fit side-chains REVERT: A 508 MET cc_start: 0.6575 (tpp) cc_final: 0.6269 (tpp) REVERT: B 452 GLN cc_start: 0.8102 (tt0) cc_final: 0.7884 (tt0) REVERT: B 504 HIS cc_start: 0.6191 (t-90) cc_final: 0.5898 (t-90) outliers start: 4 outliers final: 3 residues processed: 155 average time/residue: 0.0850 time to fit residues: 17.8836 Evaluate side-chains 139 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain B residue 394 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS A 614 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.177966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.137088 restraints weight = 8738.826| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.39 r_work: 0.3545 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7514 Z= 0.199 Angle : 0.669 10.417 10170 Z= 0.329 Chirality : 0.044 0.353 1094 Planarity : 0.005 0.056 1172 Dihedral : 12.999 99.175 1761 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 5.63 % Allowed : 23.10 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.29), residues: 798 helix: 1.74 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -1.32 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 611 TYR 0.021 0.002 TYR A 518 PHE 0.023 0.002 PHE A 487 TRP 0.027 0.003 TRP B 514 HIS 0.006 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 7512) covalent geometry : angle 0.66909 (10166) SS BOND : bond 0.00463 ( 2) SS BOND : angle 0.70000 ( 4) hydrogen bonds : bond 0.04995 ( 461) hydrogen bonds : angle 4.24288 ( 1377) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.190 Fit side-chains REVERT: A 298 ASN cc_start: 0.8327 (t0) cc_final: 0.8120 (t0) REVERT: A 489 MET cc_start: 0.7661 (tpt) cc_final: 0.7367 (tpt) REVERT: A 516 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8397 (p) REVERT: A 548 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7554 (mpp80) REVERT: B 284 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8496 (mt) REVERT: B 345 TYR cc_start: 0.8188 (p90) cc_final: 0.7673 (p90) REVERT: B 429 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.6937 (tt) REVERT: B 453 CYS cc_start: 0.8042 (m) cc_final: 0.7809 (m) REVERT: B 489 MET cc_start: 0.7851 (tpt) cc_final: 0.7457 (tpt) REVERT: B 504 HIS cc_start: 0.6332 (t-90) cc_final: 0.5386 (t-90) REVERT: B 516 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8527 (p) REVERT: B 525 THR cc_start: 0.7529 (p) cc_final: 0.7223 (p) REVERT: B 530 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9026 (mp) outliers start: 40 outliers final: 19 residues processed: 176 average time/residue: 0.0709 time to fit residues: 17.6622 Evaluate side-chains 162 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 573 TRP Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 605 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 26 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 HIS B 387 HIS ** B 476 HIS ** 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 = 0.4165 r_free = 0.4165 target = 0.177919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.136745 restraints weight = 8748.971| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.43 r_work: 0.3539 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7514 Z= 0.173 Angle : 0.636 8.926 10170 Z= 0.314 Chirality : 0.044 0.352 1094 Planarity : 0.004 0.055 1172 Dihedral : 12.799 98.929 1757 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.63 % Allowed : 24.93 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.30), residues: 798 helix: 1.83 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -1.28 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 263 TYR 0.023 0.002 TYR A 518 PHE 0.028 0.002 PHE A 487 TRP 0.025 0.002 TRP B 514 HIS 0.004 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 7512) covalent geometry : angle 0.63597 (10166) SS BOND : bond 0.00273 ( 2) SS BOND : angle 0.58395 ( 4) hydrogen bonds : bond 0.04864 ( 461) hydrogen bonds : angle 4.21932 ( 1377) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.290 Fit side-chains REVERT: A 282 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8082 (mt) REVERT: A 298 ASN cc_start: 0.8357 (t0) cc_final: 0.8071 (t0) REVERT: A 489 MET cc_start: 0.7735 (tpt) cc_final: 0.7372 (tpt) REVERT: A 516 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8387 (p) REVERT: B 236 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7060 (mtm180) REVERT: B 284 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8515 (mt) REVERT: B 345 TYR cc_start: 0.8279 (p90) cc_final: 0.7704 (p90) REVERT: B 373 TRP cc_start: 0.8314 (t60) cc_final: 0.8097 (t60) REVERT: B 453 CYS cc_start: 0.7980 (m) cc_final: 0.7681 (m) REVERT: B 489 MET cc_start: 0.8010 (tpt) cc_final: 0.7591 (tpt) REVERT: B 508 MET cc_start: 0.6270 (tpp) cc_final: 0.5642 (tpt) REVERT: B 516 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8473 (p) REVERT: B 525 THR cc_start: 0.7451 (p) cc_final: 0.7128 (p) REVERT: B 528 TRP cc_start: 0.7867 (t-100) cc_final: 0.7545 (t60) REVERT: B 530 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9019 (mp) REVERT: B 618 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7642 (p0) outliers start: 40 outliers final: 19 residues processed: 183 average time/residue: 0.0635 time to fit residues: 16.6743 Evaluate side-chains 168 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 573 TRP Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 618 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 79 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS A 452 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS B 452 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.178414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.137775 restraints weight = 8781.805| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.39 r_work: 0.3546 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7514 Z= 0.164 Angle : 0.629 8.885 10170 Z= 0.312 Chirality : 0.044 0.348 1094 Planarity : 0.004 0.055 1172 Dihedral : 12.801 96.742 1757 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 6.20 % Allowed : 24.65 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.30), residues: 798 helix: 1.88 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -1.22 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 263 TYR 0.022 0.001 TYR A 518 PHE 0.027 0.001 PHE A 487 TRP 0.024 0.002 TRP B 514 HIS 0.004 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 7512) covalent geometry : angle 0.62895 (10166) SS BOND : bond 0.00356 ( 2) SS BOND : angle 0.66973 ( 4) hydrogen bonds : bond 0.04759 ( 461) hydrogen bonds : angle 4.18648 ( 1377) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.221 Fit side-chains REVERT: A 282 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8098 (mt) REVERT: A 298 ASN cc_start: 0.8344 (t0) cc_final: 0.8096 (t0) REVERT: A 516 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8417 (p) REVERT: A 528 TRP cc_start: 0.8157 (t-100) cc_final: 0.7901 (t60) REVERT: B 236 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.7142 (mtm180) REVERT: B 282 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8089 (mt) REVERT: B 284 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8540 (mt) REVERT: B 345 TYR cc_start: 0.8283 (p90) cc_final: 0.7676 (p90) REVERT: B 373 TRP cc_start: 0.8339 (t60) cc_final: 0.8122 (t60) REVERT: B 453 CYS cc_start: 0.7974 (m) cc_final: 0.7649 (m) REVERT: B 489 MET cc_start: 0.8086 (tpt) cc_final: 0.7812 (tpt) REVERT: B 516 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8442 (p) REVERT: B 525 THR cc_start: 0.7425 (p) cc_final: 0.7123 (p) REVERT: B 528 TRP cc_start: 0.7934 (t-100) cc_final: 0.7678 (t60) REVERT: B 530 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9020 (mp) outliers start: 44 outliers final: 25 residues processed: 185 average time/residue: 0.0664 time to fit residues: 17.3402 Evaluate side-chains 177 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 573 TRP Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 605 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 9 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.178099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.137637 restraints weight = 8762.738| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.39 r_work: 0.3543 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7514 Z= 0.167 Angle : 0.633 8.391 10170 Z= 0.316 Chirality : 0.044 0.341 1094 Planarity : 0.004 0.054 1172 Dihedral : 12.869 95.824 1757 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 6.90 % Allowed : 24.65 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.30), residues: 798 helix: 1.92 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -1.20 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 263 TYR 0.021 0.002 TYR A 518 PHE 0.029 0.001 PHE A 487 TRP 0.024 0.002 TRP A 373 HIS 0.003 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 7512) covalent geometry : angle 0.63316 (10166) SS BOND : bond 0.00388 ( 2) SS BOND : angle 0.70045 ( 4) hydrogen bonds : bond 0.04793 ( 461) hydrogen bonds : angle 4.20125 ( 1377) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 151 time to evaluate : 0.204 Fit side-chains REVERT: A 282 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8099 (mt) REVERT: A 298 ASN cc_start: 0.8357 (t0) cc_final: 0.8086 (t0) REVERT: A 369 LYS cc_start: 0.8498 (mmtp) cc_final: 0.8279 (mmtt) REVERT: A 489 MET cc_start: 0.7843 (tpt) cc_final: 0.7460 (tpt) REVERT: A 516 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8409 (p) REVERT: B 236 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7150 (mtm180) REVERT: B 282 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8101 (mt) REVERT: B 284 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8530 (mt) REVERT: B 345 TYR cc_start: 0.8292 (p90) cc_final: 0.7607 (p90) REVERT: B 373 TRP cc_start: 0.8328 (t60) cc_final: 0.8081 (t60) REVERT: B 423 TRP cc_start: 0.6897 (m100) cc_final: 0.6191 (m100) REVERT: B 453 CYS cc_start: 0.7975 (m) cc_final: 0.7599 (m) REVERT: B 489 MET cc_start: 0.8076 (tpt) cc_final: 0.7862 (tpt) REVERT: B 516 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8386 (p) REVERT: B 525 THR cc_start: 0.7409 (p) cc_final: 0.7102 (p) REVERT: B 528 TRP cc_start: 0.8025 (t-100) cc_final: 0.7657 (t60) REVERT: B 530 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8994 (mp) REVERT: B 618 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7694 (p0) outliers start: 49 outliers final: 28 residues processed: 182 average time/residue: 0.0750 time to fit residues: 18.9569 Evaluate side-chains 180 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 573 TRP Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 618 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.8427 > 50: distance: 68 - 98: 26.903 distance: 73 - 107: 16.031 distance: 85 - 90: 30.964 distance: 86 - 115: 32.271 distance: 90 - 91: 24.172 distance: 91 - 92: 34.553 distance: 91 - 94: 24.043 distance: 92 - 93: 30.905 distance: 92 - 98: 20.287 distance: 93 - 121: 21.488 distance: 94 - 95: 27.868 distance: 94 - 96: 35.417 distance: 95 - 97: 16.424 distance: 98 - 99: 26.090 distance: 99 - 100: 16.907 distance: 99 - 102: 24.016 distance: 100 - 101: 11.351 distance: 100 - 107: 3.839 distance: 102 - 103: 33.357 distance: 103 - 104: 13.819 distance: 104 - 105: 16.156 distance: 104 - 106: 10.712 distance: 107 - 108: 13.753 distance: 108 - 109: 5.716 distance: 108 - 111: 22.153 distance: 109 - 110: 25.494 distance: 109 - 115: 33.548 distance: 111 - 112: 22.121 distance: 111 - 113: 15.911 distance: 112 - 114: 34.875 distance: 115 - 116: 20.171 distance: 116 - 117: 30.450 distance: 116 - 119: 28.484 distance: 117 - 118: 5.114 distance: 117 - 121: 16.241 distance: 119 - 120: 23.504 distance: 121 - 122: 15.796 distance: 122 - 123: 27.193 distance: 122 - 125: 25.637 distance: 123 - 124: 27.736 distance: 123 - 129: 25.015 distance: 125 - 126: 27.286 distance: 125 - 127: 25.803 distance: 126 - 128: 12.514 distance: 129 - 130: 22.680 distance: 130 - 131: 14.351 distance: 131 - 132: 9.168 distance: 131 - 136: 14.092 distance: 133 - 135: 18.123 distance: 136 - 137: 15.827 distance: 137 - 138: 17.032 distance: 137 - 140: 15.372 distance: 138 - 139: 22.610 distance: 138 - 142: 19.339 distance: 140 - 141: 38.501 distance: 142 - 143: 24.886 distance: 143 - 144: 21.971 distance: 143 - 146: 22.188 distance: 144 - 145: 32.123 distance: 144 - 149: 14.823 distance: 146 - 147: 40.111 distance: 146 - 148: 51.259 distance: 149 - 150: 8.633 distance: 150 - 151: 19.576 distance: 150 - 153: 10.484 distance: 151 - 152: 32.809 distance: 151 - 156: 22.834 distance: 153 - 154: 14.977 distance: 153 - 155: 20.145 distance: 156 - 157: 27.895 distance: 157 - 158: 28.556 distance: 157 - 160: 21.847 distance: 158 - 159: 26.755 distance: 158 - 164: 18.848 distance: 160 - 161: 18.422 distance: 161 - 162: 17.355 distance: 161 - 163: 14.833