Starting phenix.real_space_refine on Sun Apr 5 00:58:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ib3_52791/04_2026/9ib3_52791_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ib3_52791/04_2026/9ib3_52791.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/9ib3_52791/04_2026/9ib3_52791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ib3_52791/04_2026/9ib3_52791.map" model { file = "/net/cci-nas-00/data/ceres_data/9ib3_52791/04_2026/9ib3_52791_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ib3_52791/04_2026/9ib3_52791_trim.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= 0.000 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: 1.25, per 1000 atoms: 0.19 Number of scatterers: 6417 At special positions: 0 Unit cell: (77.104, 62.464, 106.384, 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=2.03 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=2.03 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 A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 280.1 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 7 sheets defined 14.5% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 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: 4.076A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.642A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.687A 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: 3.567A 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: 3.661A 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: 3.663A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 5 removed outlier: 5.888A 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: 9.935A pdb=" N SER L 83 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 12.122A pdb=" N ILE L 29 " --> pdb=" O SER L 79 " (cutoff:3.500A) removed outlier: 12.413A pdb=" N SER L 79 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.052A pdb=" N GLN L 43 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU L 52 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.845A pdb=" N SER H 79 " --> pdb=" O TYR H 88 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.345A pdb=" N LEU H 50 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA H 45 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR H 38 " --> pdb=" O GLY H 107 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR H 117 " --> pdb=" O ARG H 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.345A pdb=" N LEU H 50 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA H 45 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 3.753A 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: 1.37 Time building geometry restraints manager: 0.63 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: 78 1.23 - 1.43: 1444 1.43 - 1.63: 1841 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 3.57e+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 3.37e+00 bond pdb=" N GLN L 3 " pdb=" H GLN L 3 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.47e+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 2.27e+00 bond pdb=" N ARG L 18 " pdb=" CA ARG L 18 " ideal model delta sigma weight residual 1.462 1.475 -0.013 1.50e-02 4.44e+03 7.72e-01 ... (remaining 6496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 10676 1.31 - 2.63: 828 2.63 - 3.94: 94 3.94 - 5.25: 16 5.25 - 6.57: 6 Bond angle restraints: 11620 Sorted by residual: angle pdb=" C GLY A 416 " pdb=" N LYS A 417 " pdb=" CA LYS A 417 " ideal model delta sigma weight residual 121.18 114.61 6.57 1.98e+00 2.55e-01 1.10e+01 angle pdb=" CA LYS A 417 " pdb=" CB LYS A 417 " pdb=" CG LYS A 417 " ideal model delta sigma weight residual 114.10 120.60 -6.50 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CA TYR A 473 " pdb=" CB TYR A 473 " pdb=" CG TYR A 473 " ideal model delta sigma weight residual 113.90 119.38 -5.48 1.80e+00 3.09e-01 9.27e+00 angle pdb=" CA TYR L 55 " pdb=" CB TYR L 55 " pdb=" CG TYR L 55 " ideal model delta sigma weight residual 113.90 119.36 -5.46 1.80e+00 3.09e-01 9.22e+00 angle pdb=" N LYS H 72 " pdb=" CA LYS H 72 " pdb=" C LYS H 72 " ideal model delta sigma weight residual 111.37 116.09 -4.72 1.65e+00 3.67e-01 8.19e+00 ... (remaining 11615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.82: 2814 14.82 - 29.64: 207 29.64 - 44.45: 76 44.45 - 59.27: 61 59.27 - 74.09: 21 Dihedral angle restraints: 3179 sinusoidal: 1692 harmonic: 1487 Sorted by residual: 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 62.77 30.23 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" CA LYS A 417 " pdb=" C LYS A 417 " pdb=" N ILE A 418 " pdb=" CA ILE A 418 " ideal model delta harmonic sigma weight residual 180.00 164.57 15.43 0 5.00e+00 4.00e-02 9.52e+00 dihedral pdb=" CA GLN A 493 " pdb=" CB GLN A 493 " pdb=" CG GLN A 493 " pdb=" CD GLN A 493 " ideal model delta sinusoidal sigma weight residual -60.00 -105.98 45.98 3 1.50e+01 4.44e-03 8.26e+00 ... (remaining 3176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 357 0.049 - 0.098: 108 0.098 - 0.147: 21 0.147 - 0.196: 4 0.196 - 0.245: 2 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 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.14e+00 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 6.49e-01 ... (remaining 489 not shown) Planarity restraints: 992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 408 " 0.235 9.50e-02 1.11e+02 8.26e-02 2.20e+01 pdb=" NE ARG A 408 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG A 408 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 408 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 408 " -0.055 2.00e-02 2.50e+03 pdb="HH11 ARG A 408 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 408 " -0.016 2.00e-02 2.50e+03 pdb="HH21 ARG A 408 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 408 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 457 " -0.345 9.50e-02 1.11e+02 1.16e-01 1.81e+01 pdb=" NE ARG A 457 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 457 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A 457 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG A 457 " -0.000 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 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 106 " -0.340 9.50e-02 1.11e+02 1.14e-01 1.61e+01 pdb=" NE ARG H 106 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG H 106 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG H 106 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG H 106 " 0.013 2.00e-02 2.50e+03 pdb="HH11 ARG H 106 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG H 106 " -0.006 2.00e-02 2.50e+03 pdb="HH21 ARG H 106 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 106 " -0.013 2.00e-02 2.50e+03 ... (remaining 989 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 542 2.23 - 2.82: 13695 2.82 - 3.41: 16460 3.41 - 4.01: 22988 4.01 - 4.60: 34391 Nonbonded interactions: 88076 Sorted by model distance: nonbonded pdb=" OD1 ASN A 422 " pdb=" H ARG A 454 " model vdw 1.636 2.450 nonbonded pdb=" O GLN A 414 " pdb=" HG1 THR A 415 " model vdw 1.647 2.450 nonbonded pdb=" OD1 ASP H 69 " pdb=" HZ1 LYS H 72 " model vdw 1.659 2.450 nonbonded pdb=" OH TYR A 489 " pdb=" HG1 THR H 66 " model vdw 1.669 2.450 nonbonded pdb=" O ARG H 111 " pdb=" HG SER H 113 " model vdw 1.675 2.450 ... (remaining 88071 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: 4.520 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: 0.040 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.690 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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= 0.179 Angle : 0.897 6.566 4608 Z= 0.514 Chirality : 0.052 0.245 492 Planarity : 0.013 0.152 591 Dihedral : 11.882 73.657 1231 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.28 % Allowed : 0.56 % 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: -1.75 (0.37), residues: 415 helix: -4.55 (0.37), residues: 33 sheet: -0.08 (0.50), residues: 111 loop : -1.22 (0.32), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.005 ARG A 457 TYR 0.032 0.006 TYR A 489 PHE 0.019 0.003 PHE L 87 TRP 0.019 0.006 TRP H 118 HIS 0.006 0.004 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3381) covalent geometry : angle 0.89275 ( 4590) SS BOND : bond 0.00391 ( 6) SS BOND : angle 1.54058 ( 12) hydrogen bonds : bond 0.21371 ( 96) hydrogen bonds : angle 10.28438 ( 264) link_NAG-ASN : bond 0.00631 ( 2) link_NAG-ASN : angle 1.70874 ( 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 102 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8901 (mp0) REVERT: A 406 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8398 (mp0) REVERT: L 27 GLN cc_start: 0.8327 (mp10) cc_final: 0.8109 (mp10) outliers start: 1 outliers final: 1 residues processed: 101 average time/residue: 0.2065 time to fit residues: 23.7705 Evaluate side-chains 80 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 TYR 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: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.082895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.071152 restraints weight = 31842.820| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 4.29 r_work: 0.3211 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3389 Z= 0.151 Angle : 0.643 6.375 4608 Z= 0.346 Chirality : 0.044 0.183 492 Planarity : 0.004 0.026 591 Dihedral : 6.337 51.032 514 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.13 % Allowed : 9.32 % Favored : 89.55 % 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: -1.36 (0.38), residues: 415 helix: -4.21 (0.46), residues: 33 sheet: -0.29 (0.46), residues: 129 loop : -0.72 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.011 0.001 TYR L 55 PHE 0.021 0.002 PHE A 374 TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 3381) covalent geometry : angle 0.63948 ( 4590) SS BOND : bond 0.00424 ( 6) SS BOND : angle 1.44251 ( 12) hydrogen bonds : bond 0.04931 ( 96) hydrogen bonds : angle 7.49191 ( 264) link_NAG-ASN : bond 0.00109 ( 2) link_NAG-ASN : angle 0.82370 ( 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 81 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9227 (mm-30) cc_final: 0.9010 (mp0) REVERT: L 27 GLN cc_start: 0.8415 (mp10) cc_final: 0.8059 (mp10) REVERT: L 44 GLN cc_start: 0.8884 (tt0) cc_final: 0.8578 (tt0) REVERT: L 48 LYS cc_start: 0.9177 (mmmm) cc_final: 0.8923 (mmmm) REVERT: H 91 MET cc_start: 0.8475 (mtm) cc_final: 0.8218 (mtp) REVERT: H 99 THR cc_start: 0.9346 (m) cc_final: 0.9103 (p) REVERT: H 108 ASP cc_start: 0.8795 (t0) cc_final: 0.8372 (t0) outliers start: 4 outliers final: 4 residues processed: 80 average time/residue: 0.2048 time to fit residues: 18.7763 Evaluate side-chains 73 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain H residue 72 LYS 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: 2.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.083115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.071705 restraints weight = 32441.022| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 4.11 r_work: 0.3239 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3389 Z= 0.130 Angle : 0.572 5.129 4608 Z= 0.302 Chirality : 0.042 0.171 492 Planarity : 0.004 0.038 591 Dihedral : 5.978 49.032 514 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.13 % Allowed : 12.99 % Favored : 85.88 % 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: -1.12 (0.40), residues: 415 helix: -3.63 (0.65), residues: 33 sheet: -0.29 (0.47), residues: 124 loop : -0.50 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 95 TYR 0.013 0.001 TYR L 108 PHE 0.012 0.001 PHE H 30 TRP 0.008 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 3381) covalent geometry : angle 0.56850 ( 4590) SS BOND : bond 0.00403 ( 6) SS BOND : angle 1.27523 ( 12) hydrogen bonds : bond 0.04211 ( 96) hydrogen bonds : angle 6.89564 ( 264) link_NAG-ASN : bond 0.00129 ( 2) link_NAG-ASN : angle 0.66914 ( 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 78 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8413 (mp10) cc_final: 0.8076 (mp10) REVERT: L 44 GLN cc_start: 0.8935 (tt0) cc_final: 0.8562 (tt0) REVERT: L 48 LYS cc_start: 0.9193 (mmmm) cc_final: 0.8960 (mmmm) REVERT: H 85 ASN cc_start: 0.8773 (m-40) cc_final: 0.8556 (t0) REVERT: H 108 ASP cc_start: 0.8800 (t0) cc_final: 0.8577 (t0) outliers start: 4 outliers final: 3 residues processed: 78 average time/residue: 0.2050 time to fit residues: 18.4626 Evaluate side-chains 72 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain H residue 72 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 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 = 0.3591 r_free = 0.3591 target = 0.082361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.070731 restraints weight = 32419.142| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 4.12 r_work: 0.3225 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3389 Z= 0.141 Angle : 0.551 4.576 4608 Z= 0.289 Chirality : 0.042 0.169 492 Planarity : 0.003 0.022 591 Dihedral : 5.448 43.835 512 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.98 % Allowed : 12.15 % Favored : 85.88 % 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: -1.14 (0.39), residues: 415 helix: -3.26 (0.81), residues: 33 sheet: -0.32 (0.46), residues: 119 loop : -0.58 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.015 0.001 TYR L 108 PHE 0.011 0.001 PHE H 30 TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3381) covalent geometry : angle 0.54844 ( 4590) SS BOND : bond 0.00349 ( 6) SS BOND : angle 1.13158 ( 12) hydrogen bonds : bond 0.03685 ( 96) hydrogen bonds : angle 6.52235 ( 264) link_NAG-ASN : bond 0.00053 ( 2) link_NAG-ASN : angle 0.65541 ( 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 81 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8373 (mp10) cc_final: 0.7972 (mp10) REVERT: L 44 GLN cc_start: 0.8899 (tt0) cc_final: 0.8479 (tt0) REVERT: L 48 LYS cc_start: 0.9192 (mmmm) cc_final: 0.8955 (mmmm) REVERT: H 108 ASP cc_start: 0.8778 (t0) cc_final: 0.8531 (t0) outliers start: 7 outliers final: 5 residues processed: 77 average time/residue: 0.2055 time to fit residues: 18.2146 Evaluate side-chains 73 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain L residue 67 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.081410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.069598 restraints weight = 32637.357| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 4.16 r_work: 0.3201 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3389 Z= 0.160 Angle : 0.541 4.425 4608 Z= 0.284 Chirality : 0.042 0.161 492 Planarity : 0.003 0.023 591 Dihedral : 5.258 39.059 512 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.98 % Allowed : 12.43 % Favored : 85.59 % 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: -1.26 (0.40), residues: 415 helix: -3.41 (0.73), residues: 33 sheet: -0.44 (0.47), residues: 115 loop : -0.63 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 403 TYR 0.015 0.001 TYR L 108 PHE 0.011 0.001 PHE H 30 TRP 0.006 0.001 TRP A 353 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 3381) covalent geometry : angle 0.53841 ( 4590) SS BOND : bond 0.00318 ( 6) SS BOND : angle 1.06971 ( 12) hydrogen bonds : bond 0.03511 ( 96) hydrogen bonds : angle 6.41051 ( 264) link_NAG-ASN : bond 0.00062 ( 2) link_NAG-ASN : angle 0.57467 ( 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 78 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.188 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: L 27 GLN cc_start: 0.8405 (mp10) cc_final: 0.7970 (mp10) REVERT: H 108 ASP cc_start: 0.8787 (t0) cc_final: 0.8507 (t0) outliers start: 7 outliers final: 6 residues processed: 74 average time/residue: 0.1851 time to fit residues: 15.9324 Evaluate side-chains 75 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 67 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.081144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.069147 restraints weight = 32934.844| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 4.33 r_work: 0.3181 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3389 Z= 0.118 Angle : 0.534 4.885 4608 Z= 0.276 Chirality : 0.042 0.156 492 Planarity : 0.003 0.022 591 Dihedral : 5.078 37.863 512 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.69 % Allowed : 13.56 % Favored : 84.75 % 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: -1.03 (0.41), residues: 415 helix: -3.25 (0.88), residues: 25 sheet: -0.89 (0.44), residues: 126 loop : -0.21 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.016 0.001 TYR L 108 PHE 0.008 0.001 PHE H 30 TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3381) covalent geometry : angle 0.53063 ( 4590) SS BOND : bond 0.00336 ( 6) SS BOND : angle 1.32423 ( 12) hydrogen bonds : bond 0.03263 ( 96) hydrogen bonds : angle 6.16089 ( 264) link_NAG-ASN : bond 0.00080 ( 2) link_NAG-ASN : angle 0.53970 ( 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 76 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8394 (mp10) cc_final: 0.7961 (mp10) REVERT: L 44 GLN cc_start: 0.8971 (tt0) cc_final: 0.8465 (tt0) REVERT: L 48 LYS cc_start: 0.9121 (mmmm) cc_final: 0.8813 (mmmm) REVERT: H 97 GLU cc_start: 0.8731 (mp0) cc_final: 0.8410 (pm20) REVERT: H 108 ASP cc_start: 0.8719 (t0) cc_final: 0.8437 (t0) outliers start: 6 outliers final: 5 residues processed: 73 average time/residue: 0.1971 time to fit residues: 16.7077 Evaluate side-chains 75 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain L residue 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.079420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.067256 restraints weight = 32671.676| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 4.27 r_work: 0.3131 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3389 Z= 0.217 Angle : 0.570 4.423 4608 Z= 0.299 Chirality : 0.042 0.157 492 Planarity : 0.003 0.022 591 Dihedral : 5.169 29.093 512 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % 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: -1.42 (0.40), residues: 415 helix: -3.20 (0.87), residues: 27 sheet: -0.80 (0.44), residues: 117 loop : -0.73 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 18 TYR 0.015 0.002 TYR L 108 PHE 0.012 0.001 PHE H 30 TRP 0.007 0.001 TRP A 353 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 3381) covalent geometry : angle 0.56730 ( 4590) SS BOND : bond 0.00315 ( 6) SS BOND : angle 1.15468 ( 12) hydrogen bonds : bond 0.03643 ( 96) hydrogen bonds : angle 6.39001 ( 264) link_NAG-ASN : bond 0.00151 ( 2) link_NAG-ASN : angle 0.61148 ( 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 81 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8399 (mp10) cc_final: 0.7845 (mp10) REVERT: H 97 GLU cc_start: 0.8747 (mp0) cc_final: 0.8418 (pm20) REVERT: H 108 ASP cc_start: 0.8657 (t0) cc_final: 0.8365 (t0) outliers start: 10 outliers final: 8 residues processed: 76 average time/residue: 0.1859 time to fit residues: 16.3282 Evaluate side-chains 75 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain H residue 104 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.080522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.068647 restraints weight = 32701.272| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 4.27 r_work: 0.3168 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3389 Z= 0.120 Angle : 0.536 4.560 4608 Z= 0.277 Chirality : 0.042 0.146 492 Planarity : 0.003 0.023 591 Dihedral : 4.780 27.777 512 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.26 % Allowed : 14.12 % 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: -1.31 (0.40), residues: 415 helix: -3.12 (0.89), residues: 27 sheet: -0.69 (0.45), residues: 117 loop : -0.68 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 75 TYR 0.015 0.001 TYR L 108 PHE 0.008 0.001 PHE H 30 TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3381) covalent geometry : angle 0.53362 ( 4590) SS BOND : bond 0.00254 ( 6) SS BOND : angle 1.21194 ( 12) hydrogen bonds : bond 0.03253 ( 96) hydrogen bonds : angle 6.13424 ( 264) link_NAG-ASN : bond 0.00080 ( 2) link_NAG-ASN : angle 0.49087 ( 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 83 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8771 (pt0) cc_final: 0.8539 (pt0) REVERT: L 27 GLN cc_start: 0.8436 (mp10) cc_final: 0.7920 (mp-120) REVERT: L 44 GLN cc_start: 0.8966 (tt0) cc_final: 0.8456 (tt0) REVERT: L 48 LYS cc_start: 0.9147 (mmmm) cc_final: 0.8817 (mmmm) REVERT: L 103 TYR cc_start: 0.8446 (m-80) cc_final: 0.8234 (m-80) REVERT: H 97 GLU cc_start: 0.8770 (mp0) cc_final: 0.8451 (pm20) REVERT: H 108 ASP cc_start: 0.8617 (t0) cc_final: 0.8309 (t0) outliers start: 8 outliers final: 8 residues processed: 80 average time/residue: 0.1883 time to fit residues: 17.3867 Evaluate side-chains 80 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain H residue 104 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.081370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.069654 restraints weight = 32570.009| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 4.28 r_work: 0.3174 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3389 Z= 0.102 Angle : 0.526 4.424 4608 Z= 0.270 Chirality : 0.041 0.146 492 Planarity : 0.003 0.020 591 Dihedral : 4.556 27.430 512 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.26 % Allowed : 14.41 % Favored : 83.33 % 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: -1.21 (0.40), residues: 415 helix: -3.04 (0.88), residues: 27 sheet: -0.69 (0.44), residues: 122 loop : -0.55 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 20 TYR 0.013 0.001 TYR L 108 PHE 0.007 0.001 PHE H 30 TRP 0.006 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 3381) covalent geometry : angle 0.52332 ( 4590) SS BOND : bond 0.00170 ( 6) SS BOND : angle 1.10212 ( 12) hydrogen bonds : bond 0.03016 ( 96) hydrogen bonds : angle 5.92098 ( 264) link_NAG-ASN : bond 0.00105 ( 2) link_NAG-ASN : angle 0.53502 ( 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 79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8786 (pt0) cc_final: 0.8535 (pt0) REVERT: L 27 GLN cc_start: 0.8428 (mp10) cc_final: 0.7901 (mp-120) REVERT: L 44 GLN cc_start: 0.8942 (tt0) cc_final: 0.8368 (tt0) REVERT: L 48 LYS cc_start: 0.9141 (mmmm) cc_final: 0.8817 (mmmm) REVERT: H 97 GLU cc_start: 0.8791 (mp0) cc_final: 0.8483 (pm20) REVERT: H 108 ASP cc_start: 0.8561 (t0) cc_final: 0.8213 (t0) outliers start: 8 outliers final: 8 residues processed: 76 average time/residue: 0.1767 time to fit residues: 15.6374 Evaluate side-chains 76 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain H residue 104 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.081064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.069491 restraints weight = 31822.044| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 4.16 r_work: 0.3171 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3389 Z= 0.126 Angle : 0.529 4.784 4608 Z= 0.274 Chirality : 0.041 0.147 492 Planarity : 0.003 0.019 591 Dihedral : 4.546 25.014 512 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.26 % Allowed : 14.41 % Favored : 83.33 % 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: -1.17 (0.40), residues: 415 helix: -3.01 (0.89), residues: 27 sheet: -0.45 (0.45), residues: 117 loop : -0.65 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 20 TYR 0.007 0.001 TYR H 55 PHE 0.008 0.001 PHE H 30 TRP 0.004 0.001 TRP A 353 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3381) covalent geometry : angle 0.52634 ( 4590) SS BOND : bond 0.00226 ( 6) SS BOND : angle 1.14224 ( 12) hydrogen bonds : bond 0.03106 ( 96) hydrogen bonds : angle 5.87871 ( 264) link_NAG-ASN : bond 0.00069 ( 2) link_NAG-ASN : angle 0.54575 ( 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 79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 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 406 GLU cc_start: 0.8791 (pt0) cc_final: 0.8542 (pt0) REVERT: L 27 GLN cc_start: 0.8430 (mp10) cc_final: 0.7880 (mp10) REVERT: L 44 GLN cc_start: 0.8943 (tt0) cc_final: 0.8358 (tt0) REVERT: L 48 LYS cc_start: 0.9138 (mmmm) cc_final: 0.8817 (mmmm) REVERT: H 97 GLU cc_start: 0.8785 (mp0) cc_final: 0.8482 (pm20) REVERT: H 108 ASP cc_start: 0.8584 (t0) cc_final: 0.8243 (t0) outliers start: 8 outliers final: 8 residues processed: 76 average time/residue: 0.1563 time to fit residues: 14.0624 Evaluate side-chains 77 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain H residue 104 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.0170 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.081317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.069548 restraints weight = 32081.463| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 4.22 r_work: 0.3173 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3389 Z= 0.115 Angle : 0.521 4.556 4608 Z= 0.268 Chirality : 0.041 0.145 492 Planarity : 0.003 0.020 591 Dihedral : 4.411 22.892 512 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.26 % Allowed : 14.41 % Favored : 83.33 % 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: -1.08 (0.40), residues: 415 helix: -2.96 (0.89), residues: 27 sheet: -0.31 (0.45), residues: 116 loop : -0.63 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.007 0.001 TYR H 88 PHE 0.008 0.001 PHE H 30 TRP 0.006 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3381) covalent geometry : angle 0.51875 ( 4590) SS BOND : bond 0.00198 ( 6) SS BOND : angle 1.07434 ( 12) hydrogen bonds : bond 0.03025 ( 96) hydrogen bonds : angle 5.80394 ( 264) link_NAG-ASN : bond 0.00094 ( 2) link_NAG-ASN : angle 0.53583 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2267.84 seconds wall clock time: 39 minutes 2.84 seconds (2342.84 seconds total)