Starting phenix.real_space_refine on Sun Apr 5 00:58:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ib1_52789/04_2026/9ib1_52789_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ib1_52789/04_2026/9ib1_52789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ib1_52789/04_2026/9ib1_52789_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ib1_52789/04_2026/9ib1_52789_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ib1_52789/04_2026/9ib1_52789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ib1_52789/04_2026/9ib1_52789.map" } resolution = 3.2 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= 1.000 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 S 15 5.16 5 C 2092 2.51 5 N 550 2.21 5 O 640 1.98 5 H 3120 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6417 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3049 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 11, 'TRANS': 186} Chain: "L" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1600 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1740 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.35, per 1000 atoms: 0.21 Number of scatterers: 6417 At special positions: 0 Unit cell: (77.104, 62.464, 108.336, 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 15 16.00 O 640 8.00 N 550 7.00 C 2092 6.00 H 3120 1.00 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=2.01 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.04 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 A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 255.0 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 8 sheets defined 14.5% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.201A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.433A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.628A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'L' and resid 95 through 99 removed outlier: 3.855A pdb=" N PHE L 99 " --> pdb=" O PRO L 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 Processing helix chain 'H' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.794A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 5 removed outlier: 5.719A pdb=" N THR L 85 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N GLN L 27 " --> pdb=" O SER L 83 " (cutoff:3.500A) removed outlier: 9.891A pdb=" N SER L 83 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 12.041A pdb=" N ILE L 29 " --> pdb=" O SER L 79 " (cutoff:3.500A) removed outlier: 12.048A pdb=" N SER L 79 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.582A pdb=" N ASN L 40 " --> pdb=" O GLN L 105 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLN L 43 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LEU L 52 " --> pdb=" O GLN L 43 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER L 66 " --> pdb=" O TYR L 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.674A pdb=" N SER H 79 " --> pdb=" O TYR H 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.174A pdb=" N LEU H 50 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA H 45 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR H 38 " --> pdb=" O GLY H 107 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR H 117 " --> pdb=" O ARG H 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.174A pdb=" N LEU H 50 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA H 45 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR H 38 " --> pdb=" O GLY H 107 " (cutoff:3.500A) 109 hydrogen bonds defined for protein. 264 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: 1.30 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 3120 1.03 - 1.23: 148 1.23 - 1.43: 1388 1.43 - 1.63: 1827 1.63 - 1.83: 18 Bond restraints: 6501 Sorted by residual: bond pdb=" N GLN H 3 " pdb=" CA GLN H 3 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.67e+00 bond pdb=" N GLN L 3 " pdb=" CA GLN L 3 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.32e+00 bond pdb=" N GLN H 3 " pdb=" H GLN H 3 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" N GLN L 3 " pdb=" H GLN L 3 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" N ARG L 18 " pdb=" CA ARG L 18 " ideal model delta sigma weight residual 1.462 1.479 -0.017 1.46e-02 4.69e+03 1.34e+00 ... (remaining 6496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 10673 1.33 - 2.67: 819 2.67 - 4.00: 99 4.00 - 5.34: 22 5.34 - 6.67: 7 Bond angle restraints: 11620 Sorted by residual: angle pdb=" N ASP L 17 " pdb=" CA ASP L 17 " pdb=" C ASP L 17 " ideal model delta sigma weight residual 113.19 119.86 -6.67 1.19e+00 7.06e-01 3.15e+01 angle pdb=" N ALA L 56 " pdb=" CA ALA L 56 " pdb=" C ALA L 56 " ideal model delta sigma weight residual 108.00 102.58 5.42 1.48e+00 4.57e-01 1.34e+01 angle pdb=" CA LYS A 417 " pdb=" CB LYS A 417 " pdb=" CG LYS A 417 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" C GLY A 416 " pdb=" N LYS A 417 " pdb=" CA LYS A 417 " ideal model delta sigma weight residual 121.18 115.25 5.93 1.98e+00 2.55e-01 8.97e+00 angle pdb=" CA TYR L 55 " pdb=" CB TYR L 55 " pdb=" CG TYR L 55 " ideal model delta sigma weight residual 113.90 119.14 -5.24 1.80e+00 3.09e-01 8.46e+00 ... (remaining 11615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.03: 2834 15.03 - 30.05: 190 30.05 - 45.08: 84 45.08 - 60.11: 51 60.11 - 75.13: 20 Dihedral angle restraints: 3179 sinusoidal: 1692 harmonic: 1487 Sorted by residual: dihedral pdb=" CD ARG A 457 " pdb=" NE ARG A 457 " pdb=" CZ ARG A 457 " pdb=" NH1 ARG A 457 " ideal model delta sinusoidal sigma weight residual 0.00 -39.69 39.69 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" CA ALA L 56 " pdb=" C ALA L 56 " pdb=" N ALA L 57 " pdb=" CA ALA L 57 " ideal model delta harmonic sigma weight residual 180.00 160.73 19.27 0 5.00e+00 4.00e-02 1.49e+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 63.39 29.61 1 1.00e+01 1.00e-02 1.25e+01 ... (remaining 3176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 353 0.047 - 0.095: 105 0.095 - 0.142: 24 0.142 - 0.190: 9 0.190 - 0.237: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA LYS A 417 " pdb=" N LYS A 417 " pdb=" C LYS A 417 " pdb=" CB LYS A 417 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ASP L 17 " pdb=" N ASP L 17 " pdb=" C ASP L 17 " pdb=" CB ASP L 17 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA THR A 415 " pdb=" N THR A 415 " pdb=" C THR A 415 " pdb=" CB THR A 415 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 489 not shown) Planarity restraints: 992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 457 " -0.608 9.50e-02 1.11e+02 2.04e-01 4.98e+01 pdb=" NE ARG A 457 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 457 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG A 457 " 0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG A 457 " 0.014 2.00e-02 2.50e+03 pdb="HH11 ARG A 457 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 457 " -0.014 2.00e-02 2.50e+03 pdb="HH21 ARG A 457 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 457 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 495 " -0.009 2.00e-02 2.50e+03 2.83e-02 2.40e+01 pdb=" CG TYR A 495 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR A 495 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 495 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 495 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR A 495 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR A 495 " 0.048 2.00e-02 2.50e+03 pdb=" OH TYR A 495 " -0.051 2.00e-02 2.50e+03 pdb=" HD1 TYR A 495 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 TYR A 495 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR A 495 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR A 495 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 403 " -0.168 9.50e-02 1.11e+02 5.99e-02 1.29e+01 pdb=" NE ARG A 403 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 403 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A 403 " 0.039 2.00e-02 2.50e+03 pdb=" NH2 ARG A 403 " 0.020 2.00e-02 2.50e+03 pdb="HH11 ARG A 403 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 403 " -0.033 2.00e-02 2.50e+03 pdb="HH21 ARG A 403 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 403 " -0.019 2.00e-02 2.50e+03 ... (remaining 989 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 365 2.20 - 2.80: 12791 2.80 - 3.40: 16934 3.40 - 4.00: 22913 4.00 - 4.60: 34739 Nonbonded interactions: 87742 Sorted by model distance: nonbonded pdb="HH12 ARG H 75 " pdb=" OD2 ASP H 98 " model vdw 1.601 2.450 nonbonded pdb=" HG SER L 26 " pdb=" OE1 GLN L 27 " model vdw 1.623 2.450 nonbonded pdb=" OH TYR A 489 " pdb=" HG1 THR H 66 " model vdw 1.638 2.450 nonbonded pdb=" OD1 ASP H 69 " pdb=" HZ1 LYS H 72 " model vdw 1.641 2.450 nonbonded pdb="HH12 ARG L 75 " pdb=" OD2 ASP L 98 " model vdw 1.647 2.450 ... (remaining 87737 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: 10.040 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: 0.030 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.130 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 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 0.036 3389 Z= 0.186 Angle : 0.956 8.511 4608 Z= 0.544 Chirality : 0.051 0.237 492 Planarity : 0.013 0.260 591 Dihedral : 11.464 75.135 1231 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.61 (0.37), residues: 415 helix: -4.32 (0.47), residues: 32 sheet: -0.04 (0.47), residues: 120 loop : -1.15 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.004 ARG A 457 TYR 0.058 0.006 TYR A 495 PHE 0.015 0.003 PHE A 486 TRP 0.019 0.005 TRP H 118 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3381) covalent geometry : angle 0.93616 ( 4590) SS BOND : bond 0.00868 ( 6) SS BOND : angle 1.66251 ( 12) hydrogen bonds : bond 0.20078 ( 96) hydrogen bonds : angle 10.05497 ( 264) link_NAG-ASN : bond 0.00637 ( 2) link_NAG-ASN : angle 5.11943 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.8691 (t0) cc_final: 0.8433 (p0) REVERT: A 356 LYS cc_start: 0.8767 (tttt) cc_final: 0.8557 (tttp) REVERT: A 369 TYR cc_start: 0.8510 (t80) cc_final: 0.8301 (t80) REVERT: A 377 PHE cc_start: 0.8140 (t80) cc_final: 0.7827 (t80) REVERT: A 384 PRO cc_start: 0.8415 (Cg_exo) cc_final: 0.8178 (Cg_endo) REVERT: A 385 THR cc_start: 0.9025 (p) cc_final: 0.8753 (p) REVERT: L 17 ASP cc_start: 0.7800 (t0) cc_final: 0.7394 (t70) REVERT: L 97 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8593 (pt0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2141 time to fit residues: 31.3941 Evaluate side-chains 77 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.105536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.090993 restraints weight = 19240.316| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.78 r_work: 0.3179 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3389 Z= 0.172 Angle : 0.645 5.675 4608 Z= 0.346 Chirality : 0.045 0.154 492 Planarity : 0.004 0.039 591 Dihedral : 5.893 50.739 512 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.54 % Allowed : 9.04 % Favored : 88.42 % 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: -0.88 (0.39), residues: 415 helix: -4.01 (0.63), residues: 26 sheet: -0.11 (0.47), residues: 124 loop : -0.40 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 111 TYR 0.016 0.001 TYR H 55 PHE 0.012 0.002 PHE H 30 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 3381) covalent geometry : angle 0.63751 ( 4590) SS BOND : bond 0.00553 ( 6) SS BOND : angle 1.76667 ( 12) hydrogen bonds : bond 0.04929 ( 96) hydrogen bonds : angle 7.42527 ( 264) link_NAG-ASN : bond 0.00173 ( 2) link_NAG-ASN : angle 1.58700 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.8596 (m-80) cc_final: 0.8163 (m-80) REVERT: L 17 ASP cc_start: 0.8062 (t0) cc_final: 0.7349 (t70) REVERT: H 76 PHE cc_start: 0.8578 (m-10) cc_final: 0.8180 (m-10) outliers start: 9 outliers final: 8 residues processed: 84 average time/residue: 0.1913 time to fit residues: 18.5974 Evaluate side-chains 73 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 127 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.104084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.089891 restraints weight = 19427.820| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.78 r_work: 0.3154 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3389 Z= 0.138 Angle : 0.565 4.610 4608 Z= 0.299 Chirality : 0.043 0.151 492 Planarity : 0.004 0.026 591 Dihedral : 5.381 46.010 512 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.39 % Allowed : 9.89 % Favored : 86.72 % 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 (0.40), residues: 415 helix: -3.48 (0.77), residues: 26 sheet: -0.09 (0.47), residues: 124 loop : -0.26 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 111 TYR 0.016 0.001 TYR H 55 PHE 0.014 0.001 PHE A 377 TRP 0.009 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 3381) covalent geometry : angle 0.56022 ( 4590) SS BOND : bond 0.00469 ( 6) SS BOND : angle 1.28039 ( 12) hydrogen bonds : bond 0.04315 ( 96) hydrogen bonds : angle 6.66067 ( 264) link_NAG-ASN : bond 0.00028 ( 2) link_NAG-ASN : angle 1.43180 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7587 (tm-30) REVERT: A 396 TYR cc_start: 0.8577 (m-80) cc_final: 0.8214 (m-80) REVERT: L 17 ASP cc_start: 0.8235 (t0) cc_final: 0.7539 (t70) outliers start: 12 outliers final: 11 residues processed: 77 average time/residue: 0.2062 time to fit residues: 18.2647 Evaluate side-chains 75 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 125 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.104105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.089959 restraints weight = 19697.081| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.81 r_work: 0.3159 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3389 Z= 0.121 Angle : 0.527 4.214 4608 Z= 0.276 Chirality : 0.042 0.157 492 Planarity : 0.003 0.025 591 Dihedral : 4.981 42.174 512 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.67 % Allowed : 9.89 % Favored : 86.44 % 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: -0.56 (0.40), residues: 415 helix: -3.19 (0.83), residues: 26 sheet: -0.16 (0.45), residues: 124 loop : -0.08 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.015 0.001 TYR H 55 PHE 0.014 0.001 PHE A 377 TRP 0.008 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3381) covalent geometry : angle 0.52354 ( 4590) SS BOND : bond 0.00386 ( 6) SS BOND : angle 1.09014 ( 12) hydrogen bonds : bond 0.03651 ( 96) hydrogen bonds : angle 6.18096 ( 264) link_NAG-ASN : bond 0.00055 ( 2) link_NAG-ASN : angle 1.23787 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.8615 (m-80) cc_final: 0.8277 (m-80) REVERT: L 17 ASP cc_start: 0.8270 (t0) cc_final: 0.7575 (t70) outliers start: 13 outliers final: 11 residues processed: 79 average time/residue: 0.1932 time to fit residues: 17.6342 Evaluate side-chains 77 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 127 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.0030 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.103209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.089240 restraints weight = 19871.963| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.79 r_work: 0.3151 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3389 Z= 0.119 Angle : 0.517 4.165 4608 Z= 0.269 Chirality : 0.042 0.151 492 Planarity : 0.003 0.025 591 Dihedral : 4.829 40.641 512 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.67 % Allowed : 11.86 % Favored : 84.46 % 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: -0.48 (0.40), residues: 415 helix: -3.04 (0.85), residues: 26 sheet: -0.14 (0.44), residues: 124 loop : -0.02 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.014 0.001 TYR H 55 PHE 0.008 0.001 PHE A 377 TRP 0.007 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3381) covalent geometry : angle 0.51285 ( 4590) SS BOND : bond 0.00368 ( 6) SS BOND : angle 1.06041 ( 12) hydrogen bonds : bond 0.03541 ( 96) hydrogen bonds : angle 6.00458 ( 264) link_NAG-ASN : bond 0.00043 ( 2) link_NAG-ASN : angle 1.30400 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.8641 (m-80) cc_final: 0.8340 (m-80) REVERT: L 17 ASP cc_start: 0.8281 (t0) cc_final: 0.7568 (t70) REVERT: L 67 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8686 (mm) outliers start: 13 outliers final: 10 residues processed: 75 average time/residue: 0.1954 time to fit residues: 16.8859 Evaluate side-chains 78 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 127 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.101677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.087448 restraints weight = 19830.519| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.82 r_work: 0.3109 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3389 Z= 0.163 Angle : 0.538 4.233 4608 Z= 0.280 Chirality : 0.043 0.149 492 Planarity : 0.004 0.025 591 Dihedral : 4.819 35.403 512 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.24 % Allowed : 12.15 % Favored : 83.62 % 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: -0.41 (0.41), residues: 415 helix: -2.96 (0.84), residues: 26 sheet: -0.22 (0.44), residues: 130 loop : 0.11 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 106 TYR 0.013 0.001 TYR H 55 PHE 0.009 0.001 PHE A 342 TRP 0.005 0.001 TRP H 118 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 3381) covalent geometry : angle 0.53367 ( 4590) SS BOND : bond 0.00418 ( 6) SS BOND : angle 1.06405 ( 12) hydrogen bonds : bond 0.03610 ( 96) hydrogen bonds : angle 5.91666 ( 264) link_NAG-ASN : bond 0.00024 ( 2) link_NAG-ASN : angle 1.50324 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.8672 (m-80) cc_final: 0.8398 (m-80) REVERT: L 17 ASP cc_start: 0.8346 (t0) cc_final: 0.7696 (t70) REVERT: L 65 SER cc_start: 0.9007 (m) cc_final: 0.8741 (p) REVERT: L 67 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8718 (mm) outliers start: 15 outliers final: 12 residues processed: 78 average time/residue: 0.1981 time to fit residues: 17.9209 Evaluate side-chains 82 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 127 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 0.0570 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.087125 restraints weight = 19609.013| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.80 r_work: 0.3098 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3389 Z= 0.154 Angle : 0.539 4.237 4608 Z= 0.281 Chirality : 0.043 0.149 492 Planarity : 0.003 0.025 591 Dihedral : 4.814 32.782 512 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.80 % Allowed : 12.43 % Favored : 82.77 % 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: -0.38 (0.41), residues: 415 helix: -2.93 (0.83), residues: 26 sheet: -0.14 (0.44), residues: 130 loop : 0.10 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.014 0.001 TYR H 55 PHE 0.013 0.001 PHE A 377 TRP 0.005 0.001 TRP H 118 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3381) covalent geometry : angle 0.53458 ( 4590) SS BOND : bond 0.00421 ( 6) SS BOND : angle 1.07605 ( 12) hydrogen bonds : bond 0.03591 ( 96) hydrogen bonds : angle 5.88464 ( 264) link_NAG-ASN : bond 0.00055 ( 2) link_NAG-ASN : angle 1.41955 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.8668 (m-80) cc_final: 0.8389 (m-80) REVERT: L 17 ASP cc_start: 0.8337 (t0) cc_final: 0.7682 (t70) REVERT: L 67 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8714 (mm) REVERT: H 76 PHE cc_start: 0.8515 (m-10) cc_final: 0.8287 (m-10) outliers start: 17 outliers final: 12 residues processed: 78 average time/residue: 0.1854 time to fit residues: 16.8308 Evaluate side-chains 79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 127 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.101960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.087678 restraints weight = 19840.919| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.79 r_work: 0.3111 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3389 Z= 0.134 Angle : 0.532 4.347 4608 Z= 0.276 Chirality : 0.043 0.150 492 Planarity : 0.003 0.026 591 Dihedral : 4.540 29.205 512 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.95 % Allowed : 12.43 % Favored : 83.62 % 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: -0.36 (0.42), residues: 415 helix: -2.71 (0.87), residues: 26 sheet: -0.17 (0.44), residues: 133 loop : 0.12 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.014 0.001 TYR H 55 PHE 0.012 0.001 PHE A 377 TRP 0.006 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3381) covalent geometry : angle 0.52874 ( 4590) SS BOND : bond 0.00373 ( 6) SS BOND : angle 1.05246 ( 12) hydrogen bonds : bond 0.03464 ( 96) hydrogen bonds : angle 5.75749 ( 264) link_NAG-ASN : bond 0.00076 ( 2) link_NAG-ASN : angle 1.29294 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.8630 (m-80) cc_final: 0.8349 (m-80) REVERT: L 17 ASP cc_start: 0.8299 (t0) cc_final: 0.7638 (t70) REVERT: L 67 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8702 (mm) outliers start: 14 outliers final: 12 residues processed: 74 average time/residue: 0.1901 time to fit residues: 16.3353 Evaluate side-chains 77 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 127 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.102144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.087820 restraints weight = 20079.320| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.82 r_work: 0.3112 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3389 Z= 0.117 Angle : 0.527 4.455 4608 Z= 0.273 Chirality : 0.042 0.149 492 Planarity : 0.003 0.027 591 Dihedral : 4.544 28.168 512 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.82 % Allowed : 13.28 % Favored : 83.90 % 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: -0.21 (0.42), residues: 415 helix: -2.43 (0.91), residues: 26 sheet: 0.02 (0.45), residues: 127 loop : 0.14 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.014 0.001 TYR H 55 PHE 0.010 0.001 PHE A 377 TRP 0.006 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 3381) covalent geometry : angle 0.52327 ( 4590) SS BOND : bond 0.00349 ( 6) SS BOND : angle 1.04840 ( 12) hydrogen bonds : bond 0.03391 ( 96) hydrogen bonds : angle 5.70049 ( 264) link_NAG-ASN : bond 0.00103 ( 2) link_NAG-ASN : angle 1.20443 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.8623 (m-80) cc_final: 0.8339 (m-80) REVERT: L 17 ASP cc_start: 0.8285 (t0) cc_final: 0.7635 (t70) REVERT: L 67 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8730 (mm) outliers start: 10 outliers final: 9 residues processed: 72 average time/residue: 0.1979 time to fit residues: 16.5510 Evaluate side-chains 74 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.103040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.088965 restraints weight = 19610.154| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.76 r_work: 0.3127 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3389 Z= 0.107 Angle : 0.539 6.079 4608 Z= 0.276 Chirality : 0.042 0.148 492 Planarity : 0.004 0.033 591 Dihedral : 4.280 26.381 512 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.54 % Allowed : 13.84 % Favored : 83.62 % 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: -0.25 (0.42), residues: 415 helix: -2.24 (0.93), residues: 26 sheet: -0.04 (0.44), residues: 133 loop : 0.11 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.014 0.001 TYR H 55 PHE 0.013 0.001 PHE H 76 TRP 0.007 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3381) covalent geometry : angle 0.53590 ( 4590) SS BOND : bond 0.00337 ( 6) SS BOND : angle 0.98294 ( 12) hydrogen bonds : bond 0.03262 ( 96) hydrogen bonds : angle 5.60640 ( 264) link_NAG-ASN : bond 0.00109 ( 2) link_NAG-ASN : angle 1.06460 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.8565 (m-80) cc_final: 0.8223 (m-80) REVERT: L 17 ASP cc_start: 0.8255 (t0) cc_final: 0.7618 (t70) REVERT: L 67 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8744 (mm) REVERT: H 76 PHE cc_start: 0.8228 (m-10) cc_final: 0.8017 (m-10) outliers start: 9 outliers final: 8 residues processed: 71 average time/residue: 0.1878 time to fit residues: 15.5605 Evaluate side-chains 72 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.102240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.088029 restraints weight = 19717.510| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.79 r_work: 0.3112 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3389 Z= 0.128 Angle : 0.543 7.313 4608 Z= 0.281 Chirality : 0.042 0.146 492 Planarity : 0.003 0.032 591 Dihedral : 4.215 23.177 512 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.82 % Allowed : 14.41 % Favored : 82.77 % 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: -0.25 (0.42), residues: 415 helix: -2.11 (0.95), residues: 26 sheet: 0.05 (0.46), residues: 128 loop : 0.03 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.014 0.001 TYR L 116 PHE 0.010 0.001 PHE H 76 TRP 0.005 0.001 TRP H 118 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 3381) covalent geometry : angle 0.54011 ( 4590) SS BOND : bond 0.00386 ( 6) SS BOND : angle 1.03019 ( 12) hydrogen bonds : bond 0.03387 ( 96) hydrogen bonds : angle 5.63599 ( 264) link_NAG-ASN : bond 0.00068 ( 2) link_NAG-ASN : angle 1.19067 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2578.70 seconds wall clock time: 44 minutes 19.58 seconds (2659.58 seconds total)