Starting phenix.real_space_refine on Wed Jul 1 22:14:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k9i_22749/07_2026/7k9i_22749.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k9i_22749/07_2026/7k9i_22749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k9i_22749/07_2026/7k9i_22749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k9i_22749/07_2026/7k9i_22749.map" model { file = "/net/cci-nas-00/data/ceres_data/7k9i_22749/07_2026/7k9i_22749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k9i_22749/07_2026/7k9i_22749.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7k9i_22749/07_2026/7k9i_22749.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k9i_22749/07_2026/7k9i_22749.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.053 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 14 5.16 5 C 2095 2.51 5 N 554 2.21 5 O 632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3295 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 812 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} 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 chiralities: 1 Time building chain proxies: 0.93, per 1000 atoms: 0.28 Number of scatterers: 3295 At special positions: 0 Unit cell: (64.9, 85.8, 86.9, 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 14 16.00 O 632 8.00 N 554 7.00 C 2095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 0.18 Conformation dependent library (CDL) restraints added in 123.7 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 9.9% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.605A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.200A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.896A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.277A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.569A pdb=" N THR H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.703A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.834A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.306A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.769A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR H 109 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.769A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.846A pdb=" N VAL L 18 " --> pdb=" O ILE L 77 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE L 77 " --> pdb=" O VAL L 18 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER L 67 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER L 65 " --> pdb=" O THR L 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 55 through 56 removed outlier: 3.754A pdb=" N LEU L 45 " --> pdb=" O LYS L 41 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY L 51 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA L 35 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 55 through 56 removed outlier: 3.754A pdb=" N LEU L 45 " --> pdb=" O LYS L 41 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY L 51 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA L 35 " --> pdb=" O GLY L 51 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 291 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: 0.38 Time building geometry restraints manager: 0.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1051 1.34 - 1.47: 910 1.47 - 1.59: 1402 1.59 - 1.71: 0 1.71 - 1.83: 16 Bond restraints: 3379 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C TYR A 505 " pdb=" N GLN A 506 " ideal model delta sigma weight residual 1.340 1.269 0.071 5.87e-02 2.90e+02 1.47e+00 bond pdb=" CB ASN L 36 " pdb=" CG ASN L 36 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.36e+00 bond pdb=" CB ILE A 434 " pdb=" CG2 ILE A 434 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.69e-01 ... (remaining 3374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 4390 1.51 - 3.01: 171 3.01 - 4.52: 31 4.52 - 6.03: 6 6.03 - 7.54: 3 Bond angle restraints: 4601 Sorted by residual: angle pdb=" CA CYS H 95 " pdb=" CB CYS H 95 " pdb=" SG CYS H 95 " ideal model delta sigma weight residual 114.40 120.30 -5.90 2.30e+00 1.89e-01 6.58e+00 angle pdb=" N CYS H 95 " pdb=" CA CYS H 95 " pdb=" C CYS H 95 " ideal model delta sigma weight residual 110.32 106.37 3.95 1.59e+00 3.96e-01 6.17e+00 angle pdb=" CA GLU A 516 " pdb=" CB GLU A 516 " pdb=" CG GLU A 516 " ideal model delta sigma weight residual 114.10 118.67 -4.57 2.00e+00 2.50e-01 5.23e+00 angle pdb=" C GLY L 52 " pdb=" N THR L 53 " pdb=" CA THR L 53 " ideal model delta sigma weight residual 121.54 125.86 -4.32 1.91e+00 2.74e-01 5.12e+00 angle pdb=" N GLY L 70 " pdb=" CA GLY L 70 " pdb=" C GLY L 70 " ideal model delta sigma weight residual 112.10 108.16 3.94 1.82e+00 3.02e-01 4.68e+00 ... (remaining 4596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 1804 17.83 - 35.66: 138 35.66 - 53.48: 15 53.48 - 71.31: 3 71.31 - 89.14: 2 Dihedral angle restraints: 1962 sinusoidal: 749 harmonic: 1213 Sorted by residual: dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 90 " pdb=" CB CYS L 90 " ideal model delta sinusoidal sigma weight residual 93.00 51.32 41.68 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CA TRP L 93 " pdb=" C TRP L 93 " pdb=" N TYR L 94 " pdb=" CA TYR L 94 " ideal model delta harmonic sigma weight residual 180.00 157.34 22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 129.94 -36.94 1 1.00e+01 1.00e-02 1.93e+01 ... (remaining 1959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 317 0.039 - 0.078: 118 0.078 - 0.116: 59 0.116 - 0.155: 8 0.155 - 0.193: 1 Chirality restraints: 503 Sorted by residual: chirality pdb=" CB THR A 430 " pdb=" CA THR A 430 " pdb=" OG1 THR A 430 " pdb=" CG2 THR A 430 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.35e-01 chirality pdb=" CB THR H 90 " pdb=" CA THR H 90 " pdb=" OG1 THR H 90 " pdb=" CG2 THR H 90 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA ILE L 87 " pdb=" N ILE L 87 " pdb=" C ILE L 87 " pdb=" CB ILE L 87 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 500 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 355 " -0.073 9.50e-02 1.11e+02 4.13e-02 8.64e+00 pdb=" NE ARG A 355 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 355 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG A 355 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG A 355 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS L 41 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO L 42 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO L 42 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 42 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO A 463 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " -0.019 5.00e-02 4.00e+02 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 72 2.67 - 3.23: 3219 3.23 - 3.79: 4886 3.79 - 4.34: 6660 4.34 - 4.90: 11314 Nonbonded interactions: 26151 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.118 3.040 nonbonded pdb=" O ILE H 30 " pdb=" OG1 THR H 53 " model vdw 2.140 3.040 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.173 3.120 nonbonded pdb=" OG1 THR L 12 " pdb=" O GLU L 16 " model vdw 2.189 3.040 nonbonded pdb=" OG SER H 17 " pdb=" O MET H 82 " model vdw 2.239 3.040 ... (remaining 26146 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.810 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.630 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 0.005 0.071 3386 Z= 0.237 Angle : 0.723 7.536 4616 Z= 0.386 Chirality : 0.049 0.193 503 Planarity : 0.005 0.043 591 Dihedral : 12.700 89.140 1178 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.40), residues: 417 helix: -1.66 (0.85), residues: 32 sheet: 0.51 (0.45), residues: 133 loop : -1.05 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.003 ARG A 355 TYR 0.015 0.001 TYR A 380 PHE 0.012 0.002 PHE A 490 TRP 0.020 0.002 TRP H 47 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.24 ( 3379) covalent geometry : angle 0.71925 / 0.39 ( 4601) SS BOND : bond 0.00560 / 0.40 ( 6) SS BOND : angle 1.22432 / 0.71 ( 12) hydrogen bonds : bond 0.24723 / 16.83 ( 94) hydrogen bonds : angle 9.73332 / 6.62 ( 291) link_NAG-ASN : bond 0.00159 / 0.08 ( 1) link_NAG-ASN : angle 2.19598 / 1.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 16 GLN cc_start: 0.7615 (pt0) cc_final: 0.7371 (pt0) REVERT: H 108 ASP cc_start: 0.7834 (t0) cc_final: 0.7624 (t0) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0853 time to fit residues: 6.4024 Evaluate side-chains 54 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.0060 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 1 GLN H 3 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 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 = 0.3565 r_free = 0.3565 target = 0.090444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.074904 restraints weight = 8103.409| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.36 r_work: 0.3152 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3386 Z= 0.183 Angle : 0.699 6.956 4616 Z= 0.364 Chirality : 0.047 0.132 503 Planarity : 0.005 0.043 591 Dihedral : 5.694 19.601 464 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.13 % Allowed : 14.08 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.40), residues: 417 helix: -1.40 (0.95), residues: 33 sheet: 0.04 (0.43), residues: 142 loop : -0.80 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 466 TYR 0.011 0.001 TYR A 380 PHE 0.010 0.001 PHE A 490 TRP 0.016 0.002 TRP H 47 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 3379) covalent geometry : angle 0.69752 / 0.36 ( 4601) SS BOND : bond 0.00623 / 0.46 ( 6) SS BOND : angle 0.85134 / 0.51 ( 12) hydrogen bonds : bond 0.04282 / 2.86 ( 94) hydrogen bonds : angle 6.80073 / 4.73 ( 291) link_NAG-ASN : bond 0.00010 / 0.01 ( 1) link_NAG-ASN : angle 1.60303 / 0.85 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8554 (tppt) REVERT: A 420 ASP cc_start: 0.8761 (m-30) cc_final: 0.8212 (m-30) outliers start: 4 outliers final: 3 residues processed: 70 average time/residue: 0.0813 time to fit residues: 6.8090 Evaluate side-chains 64 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 0.0980 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 16 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.093007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.077263 restraints weight = 8028.347| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.47 r_work: 0.3200 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3386 Z= 0.115 Angle : 0.636 6.966 4616 Z= 0.324 Chirality : 0.045 0.161 503 Planarity : 0.004 0.038 591 Dihedral : 5.166 18.079 464 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.38 % Allowed : 17.46 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.40), residues: 417 helix: -1.11 (1.13), residues: 27 sheet: 0.24 (0.43), residues: 142 loop : -0.79 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 466 TYR 0.007 0.001 TYR A 451 PHE 0.006 0.001 PHE A 400 TRP 0.012 0.002 TRP H 47 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 3379) covalent geometry : angle 0.63555 / 0.32 ( 4601) SS BOND : bond 0.00451 / 0.34 ( 6) SS BOND : angle 0.58383 / 0.32 ( 12) hydrogen bonds : bond 0.03527 / 2.40 ( 94) hydrogen bonds : angle 6.19071 / 4.31 ( 291) link_NAG-ASN : bond 0.00277 / 0.15 ( 1) link_NAG-ASN : angle 1.12361 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.128 Fit side-chains REVERT: A 414 GLN cc_start: 0.7989 (mp10) cc_final: 0.7722 (mp10) REVERT: A 417 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8476 (tppt) REVERT: A 420 ASP cc_start: 0.8742 (m-30) cc_final: 0.8220 (m-30) REVERT: H 16 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7304 (pm20) REVERT: L 7 GLU cc_start: 0.7296 (pm20) cc_final: 0.7071 (pm20) REVERT: L 39 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7656 (tm-30) outliers start: 12 outliers final: 4 residues processed: 80 average time/residue: 0.0823 time to fit residues: 7.8215 Evaluate side-chains 70 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 39 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.090396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.074817 restraints weight = 7973.091| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.35 r_work: 0.3155 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3386 Z= 0.186 Angle : 0.628 6.170 4616 Z= 0.324 Chirality : 0.045 0.132 503 Planarity : 0.004 0.039 591 Dihedral : 5.320 17.680 464 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.66 % Allowed : 17.46 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.40), residues: 417 helix: -1.29 (1.09), residues: 27 sheet: 0.30 (0.43), residues: 142 loop : -0.85 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 346 TYR 0.014 0.001 TYR A 451 PHE 0.010 0.001 PHE A 490 TRP 0.011 0.002 TRP H 110 HIS 0.001 0.001 HIS L 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 ( 3379) covalent geometry : angle 0.62683 / 0.32 ( 4601) SS BOND : bond 0.00477 / 0.34 ( 6) SS BOND : angle 0.67714 / 0.39 ( 12) hydrogen bonds : bond 0.03453 / 2.32 ( 94) hydrogen bonds : angle 6.10071 / 4.22 ( 291) link_NAG-ASN : bond 0.00062 / 0.03 ( 1) link_NAG-ASN : angle 1.38759 / 0.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.146 Fit side-chains REVERT: A 417 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8554 (tppt) REVERT: A 420 ASP cc_start: 0.8770 (m-30) cc_final: 0.8262 (m-30) REVERT: H 16 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7413 (pm20) REVERT: H 108 ASP cc_start: 0.8241 (t0) cc_final: 0.7967 (t0) REVERT: L 39 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7794 (tm-30) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.0800 time to fit residues: 6.9664 Evaluate side-chains 78 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 60 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 28 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.090473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.074666 restraints weight = 8063.656| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.46 r_work: 0.3145 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3386 Z= 0.176 Angle : 0.631 5.960 4616 Z= 0.326 Chirality : 0.046 0.126 503 Planarity : 0.004 0.042 591 Dihedral : 5.325 17.250 464 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.23 % Allowed : 18.59 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.40), residues: 417 helix: -1.55 (1.01), residues: 27 sheet: 0.31 (0.44), residues: 142 loop : -0.86 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 346 TYR 0.015 0.001 TYR A 451 PHE 0.010 0.001 PHE A 490 TRP 0.011 0.002 TRP H 47 HIS 0.002 0.001 HIS L 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 ( 3379) covalent geometry : angle 0.63031 / 0.33 ( 4601) SS BOND : bond 0.00440 / 0.31 ( 6) SS BOND : angle 0.62712 / 0.36 ( 12) hydrogen bonds : bond 0.03356 / 2.28 ( 94) hydrogen bonds : angle 6.06203 / 4.19 ( 291) link_NAG-ASN : bond 0.00045 / 0.02 ( 1) link_NAG-ASN : angle 1.42052 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.127 Fit side-chains REVERT: A 417 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8548 (tppt) REVERT: A 420 ASP cc_start: 0.8789 (m-30) cc_final: 0.8312 (m-30) REVERT: H 4 LEU cc_start: 0.8764 (mm) cc_final: 0.8558 (mm) REVERT: H 16 GLN cc_start: 0.7949 (pt0) cc_final: 0.7537 (pm20) REVERT: H 18 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7133 (mm) REVERT: H 108 ASP cc_start: 0.8359 (t0) cc_final: 0.8036 (t0) outliers start: 15 outliers final: 11 residues processed: 77 average time/residue: 0.0674 time to fit residues: 6.2778 Evaluate side-chains 78 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.092200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.076612 restraints weight = 7993.184| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.38 r_work: 0.3192 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3386 Z= 0.116 Angle : 0.599 5.755 4616 Z= 0.307 Chirality : 0.045 0.128 503 Planarity : 0.004 0.039 591 Dihedral : 5.046 16.060 464 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.07 % Allowed : 19.15 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.41), residues: 417 helix: -1.64 (0.98), residues: 27 sheet: 0.21 (0.46), residues: 135 loop : -0.69 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 66 TYR 0.012 0.001 TYR A 451 PHE 0.007 0.001 PHE A 490 TRP 0.011 0.002 TRP H 47 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 3379) covalent geometry : angle 0.59859 / 0.31 ( 4601) SS BOND : bond 0.00371 / 0.27 ( 6) SS BOND : angle 0.52061 / 0.30 ( 12) hydrogen bonds : bond 0.03015 / 2.04 ( 94) hydrogen bonds : angle 5.89009 / 4.07 ( 291) link_NAG-ASN : bond 0.00209 / 0.11 ( 1) link_NAG-ASN : angle 1.26074 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8757 (mmtt) cc_final: 0.8499 (tppt) REVERT: A 420 ASP cc_start: 0.8782 (m-30) cc_final: 0.8259 (m-30) REVERT: A 517 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8335 (tt) REVERT: H 3 GLN cc_start: 0.8571 (tt0) cc_final: 0.8333 (tm-30) REVERT: H 4 LEU cc_start: 0.8728 (mm) cc_final: 0.8486 (mm) REVERT: H 16 GLN cc_start: 0.7922 (pt0) cc_final: 0.7473 (pm20) outliers start: 18 outliers final: 13 residues processed: 79 average time/residue: 0.0630 time to fit residues: 5.9766 Evaluate side-chains 78 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 20 optimal weight: 0.0670 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.092854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.077197 restraints weight = 8124.540| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.42 r_work: 0.3205 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3386 Z= 0.110 Angle : 0.598 5.757 4616 Z= 0.305 Chirality : 0.045 0.133 503 Planarity : 0.004 0.039 591 Dihedral : 4.877 15.536 464 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.66 % Allowed : 20.56 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.41), residues: 417 helix: -1.57 (0.99), residues: 27 sheet: 0.25 (0.46), residues: 135 loop : -0.65 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 66 TYR 0.007 0.001 TYR H 109 PHE 0.006 0.001 PHE A 490 TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 3379) covalent geometry : angle 0.59798 / 0.30 ( 4601) SS BOND : bond 0.00355 / 0.26 ( 6) SS BOND : angle 0.48307 / 0.27 ( 12) hydrogen bonds : bond 0.02870 / 1.96 ( 94) hydrogen bonds : angle 5.78324 / 3.98 ( 291) link_NAG-ASN : bond 0.00206 / 0.11 ( 1) link_NAG-ASN : angle 1.28689 / 0.69 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 417 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8482 (tppt) REVERT: A 420 ASP cc_start: 0.8687 (m-30) cc_final: 0.8196 (m-30) REVERT: A 517 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8327 (tt) REVERT: H 16 GLN cc_start: 0.7964 (pt0) cc_final: 0.7495 (pm20) outliers start: 13 outliers final: 11 residues processed: 79 average time/residue: 0.0691 time to fit residues: 6.6949 Evaluate side-chains 74 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.2036 > 50: distance: 31 - 35: 23.017 distance: 35 - 36: 20.292 distance: 36 - 37: 25.274 distance: 36 - 39: 23.707 distance: 37 - 38: 22.653 distance: 37 - 43: 26.965 distance: 39 - 40: 29.777 distance: 40 - 41: 33.137 distance: 40 - 42: 18.055 distance: 43 - 44: 13.165 distance: 44 - 45: 40.065 distance: 44 - 47: 39.658 distance: 45 - 46: 7.572 distance: 45 - 49: 40.100 distance: 47 - 48: 56.731 distance: 49 - 50: 4.934 distance: 50 - 51: 25.353 distance: 50 - 53: 27.911 distance: 51 - 52: 16.788 distance: 51 - 58: 4.133 distance: 53 - 54: 8.795 distance: 54 - 55: 26.378 distance: 55 - 56: 9.123 distance: 56 - 57: 40.120 distance: 58 - 59: 28.741 distance: 59 - 60: 7.998 distance: 59 - 62: 31.106 distance: 60 - 61: 16.901 distance: 60 - 65: 7.172 distance: 62 - 63: 33.350 distance: 62 - 64: 30.574 distance: 65 - 66: 8.203 distance: 66 - 67: 33.590 distance: 67 - 68: 47.423 distance: 67 - 69: 23.430 distance: 70 - 71: 15.038 distance: 71 - 72: 25.416 distance: 71 - 73: 42.309 distance: 73 - 74: 5.726 distance: 74 - 75: 7.520 distance: 74 - 77: 48.796 distance: 75 - 76: 33.067 distance: 75 - 81: 12.838 distance: 77 - 78: 47.784 distance: 78 - 79: 41.135 distance: 78 - 80: 12.957 distance: 81 - 82: 34.940 distance: 82 - 83: 37.376 distance: 82 - 85: 13.319 distance: 83 - 84: 10.804 distance: 83 - 93: 28.501 distance: 85 - 86: 20.982 distance: 86 - 87: 15.749 distance: 86 - 88: 16.293 distance: 87 - 89: 12.499 distance: 88 - 90: 39.629 distance: 89 - 91: 24.415 distance: 91 - 92: 26.572 distance: 94 - 95: 13.048 distance: 94 - 97: 40.493 distance: 95 - 96: 27.527 distance: 95 - 101: 12.782 distance: 97 - 98: 43.659 distance: 98 - 99: 20.413 distance: 98 - 100: 39.012 distance: 101 - 102: 18.468 distance: 102 - 103: 17.344 distance: 102 - 105: 12.899 distance: 103 - 104: 18.071 distance: 103 - 113: 28.830 distance: 105 - 106: 29.543 distance: 106 - 107: 7.870 distance: 106 - 108: 9.446 distance: 107 - 109: 22.758 distance: 108 - 110: 19.476 distance: 109 - 111: 17.031 distance: 110 - 111: 29.806 distance: 111 - 112: 16.885