Starting phenix.real_space_refine on Fri Aug 22 15:43:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zhg_60102/08_2025/8zhg_60102.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zhg_60102/08_2025/8zhg_60102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zhg_60102/08_2025/8zhg_60102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zhg_60102/08_2025/8zhg_60102.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zhg_60102/08_2025/8zhg_60102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zhg_60102/08_2025/8zhg_60102.map" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2345 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2100 2.51 5 N 556 2.21 5 O 655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3326 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1552 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 926 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 820 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} 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: 0.83, per 1000 atoms: 0.25 Number of scatterers: 3326 At special positions: 0 Unit cell: (71.1776, 88.972, 79.3904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 655 8.00 N 556 7.00 C 2100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " 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 BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN C 343 " Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 133.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 8.7% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.895A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.611A pdb=" N LYS C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.567A pdb=" N ILE C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 411' Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.926A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.625A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.509A pdb=" N ASP L 85 " --> pdb=" O LYS L 82 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU L 86 " --> pdb=" O THR L 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 82 through 86' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.817A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL C 433 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE C 377 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 435 " --> pdb=" O SER C 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 59 removed outlier: 4.874A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN H 39 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N CYS H 96 " --> pdb=" O TRP H 110 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N TRP H 110 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG H 98 " --> pdb=" O ASP H 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 58 through 59 removed outlier: 4.874A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN H 39 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR H 114 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'L' and resid 46 through 49 removed outlier: 3.965A pdb=" N VAL L 48 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR L 90 " --> pdb=" O TYR L 37 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN L 39 " --> pdb=" O ASP L 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 46 through 49 removed outlier: 3.965A pdb=" N VAL L 48 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR L 90 " --> pdb=" O TYR L 37 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN L 39 " --> pdb=" O ASP L 88 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR L 89 " --> pdb=" O THR L 105 " (cutoff:3.500A) 88 hydrogen bonds defined for protein. 216 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.37 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1070 1.35 - 1.47: 932 1.47 - 1.59: 1391 1.59 - 1.71: 0 1.71 - 1.84: 18 Bond restraints: 3411 Sorted by residual: bond pdb=" N TYR C 473 " pdb=" CA TYR C 473 " ideal model delta sigma weight residual 1.455 1.484 -0.030 1.27e-02 6.20e+03 5.42e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" CB GLU L 86 " pdb=" CG GLU L 86 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.11e+00 bond pdb=" C TYR C 473 " pdb=" O TYR C 473 " ideal model delta sigma weight residual 1.234 1.251 -0.017 1.27e-02 6.20e+03 1.88e+00 ... (remaining 3406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 4447 1.40 - 2.80: 153 2.80 - 4.20: 26 4.20 - 5.61: 8 5.61 - 7.01: 5 Bond angle restraints: 4639 Sorted by residual: angle pdb=" CB GLU L 86 " pdb=" CG GLU L 86 " pdb=" CD GLU L 86 " ideal model delta sigma weight residual 112.60 118.01 -5.41 1.70e+00 3.46e-01 1.01e+01 angle pdb=" CA LYS H 43 " pdb=" CB LYS H 43 " pdb=" CG LYS H 43 " ideal model delta sigma weight residual 114.10 120.30 -6.20 2.00e+00 2.50e-01 9.62e+00 angle pdb=" C CYS C 480 " pdb=" N ASN C 481 " pdb=" CA ASN C 481 " ideal model delta sigma weight residual 121.54 127.17 -5.63 1.91e+00 2.74e-01 8.68e+00 angle pdb=" CA GLU L 86 " pdb=" CB GLU L 86 " pdb=" CG GLU L 86 " ideal model delta sigma weight residual 114.10 119.36 -5.26 2.00e+00 2.50e-01 6.92e+00 angle pdb=" CA LYS L 16 " pdb=" CB LYS L 16 " pdb=" CG LYS L 16 " ideal model delta sigma weight residual 114.10 119.22 -5.12 2.00e+00 2.50e-01 6.55e+00 ... (remaining 4634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 1709 17.23 - 34.45: 227 34.45 - 51.68: 67 51.68 - 68.91: 13 68.91 - 86.14: 7 Dihedral angle restraints: 2023 sinusoidal: 803 harmonic: 1220 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 60.96 32.04 1 1.00e+01 1.00e-02 1.46e+01 dihedral pdb=" CA ASP L 68 " pdb=" CB ASP L 68 " pdb=" CG ASP L 68 " pdb=" OD1 ASP L 68 " ideal model delta sinusoidal sigma weight residual -30.00 -89.46 59.46 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 66.49 26.51 1 1.00e+01 1.00e-02 1.01e+01 ... (remaining 2020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 303 0.033 - 0.067: 136 0.067 - 0.100: 36 0.100 - 0.133: 20 0.133 - 0.166: 2 Chirality restraints: 497 Sorted by residual: chirality pdb=" CG LEU H 86 " pdb=" CB LEU H 86 " pdb=" CD1 LEU H 86 " pdb=" CD2 LEU H 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CG LEU C 452 " pdb=" CB LEU C 452 " pdb=" CD1 LEU C 452 " pdb=" CD2 LEU C 452 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CB ILE L 49 " pdb=" CA ILE L 49 " pdb=" CG1 ILE L 49 " pdb=" CG2 ILE L 49 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 494 not shown) Planarity restraints: 603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 13 " -0.059 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO L 14 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO L 14 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO L 14 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO C 463 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO C 521 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.019 5.00e-02 4.00e+02 ... (remaining 600 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 888 2.80 - 3.32: 2682 3.32 - 3.85: 5331 3.85 - 4.37: 5856 4.37 - 4.90: 10330 Nonbonded interactions: 25087 Sorted by model distance: nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR C 415 " pdb=" OD1 ASP C 420 " model vdw 2.323 3.040 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.339 3.040 nonbonded pdb=" OG1 THR C 430 " pdb=" O PHE C 515 " model vdw 2.347 3.040 nonbonded pdb=" OE1 GLU H 57 " pdb=" OH TYR H 59 " model vdw 2.353 3.040 ... (remaining 25082 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 group one per residue 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.490 Find NCS groups from input model: 0.010 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 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 0.051 3419 Z= 0.152 Angle : 0.662 7.007 4657 Z= 0.337 Chirality : 0.044 0.166 497 Planarity : 0.007 0.090 602 Dihedral : 17.545 86.137 1235 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.11 % Allowed : 32.69 % Favored : 66.20 % 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 aren not related in a simple way. whole: -1.47 (0.40), residues: 419 helix: -4.79 (0.32), residues: 19 sheet: 1.06 (0.51), residues: 119 loop : -1.75 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 40 TYR 0.019 0.001 TYR C 453 PHE 0.009 0.001 PHE C 456 TRP 0.017 0.001 TRP H 110 HIS 0.002 0.001 HIS L 8 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 3411) covalent geometry : angle 0.65737 ( 4639) SS BOND : bond 0.00150 ( 6) SS BOND : angle 1.57542 ( 12) hydrogen bonds : bond 0.32078 ( 71) hydrogen bonds : angle 10.83789 ( 216) link_BETA1-4 : bond 0.00445 ( 1) link_BETA1-4 : angle 0.89168 ( 3) link_NAG-ASN : bond 0.00118 ( 1) link_NAG-ASN : angle 1.54311 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.073 Fit side-chains REVERT: C 465 GLU cc_start: 0.6576 (mt-10) cc_final: 0.6116 (mt-10) REVERT: H 115 LEU cc_start: 0.8755 (tp) cc_final: 0.8505 (tt) outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 0.0826 time to fit residues: 4.8711 Evaluate side-chains 46 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain H residue 77 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.0050 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.0570 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.5114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 437 ASN C 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.169845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.137567 restraints weight = 4088.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.139606 restraints weight = 3932.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.140680 restraints weight = 2718.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141289 restraints weight = 2399.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.141702 restraints weight = 2095.684| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3419 Z= 0.157 Angle : 0.562 5.122 4657 Z= 0.297 Chirality : 0.043 0.151 497 Planarity : 0.006 0.072 602 Dihedral : 4.537 41.224 514 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.26 % Allowed : 26.59 % Favored : 68.14 % 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 aren not related in a simple way. whole: -1.45 (0.39), residues: 419 helix: -4.59 (0.47), residues: 18 sheet: 0.60 (0.47), residues: 131 loop : -1.61 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 454 TYR 0.019 0.001 TYR C 495 PHE 0.013 0.001 PHE C 429 TRP 0.013 0.001 TRP C 436 HIS 0.001 0.000 HIS L 8 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 3411) covalent geometry : angle 0.55752 ( 4639) SS BOND : bond 0.00411 ( 6) SS BOND : angle 1.20277 ( 12) hydrogen bonds : bond 0.04487 ( 71) hydrogen bonds : angle 6.51690 ( 216) link_BETA1-4 : bond 0.00376 ( 1) link_BETA1-4 : angle 1.11617 ( 3) link_NAG-ASN : bond 0.00091 ( 1) link_NAG-ASN : angle 1.76849 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.116 Fit side-chains REVERT: C 346 ARG cc_start: 0.7357 (mtp85) cc_final: 0.6959 (mtp85) REVERT: C 457 ARG cc_start: 0.7469 (ttt90) cc_final: 0.7086 (ttt90) REVERT: C 508 TYR cc_start: 0.8297 (m-80) cc_final: 0.8068 (m-80) REVERT: L 10 VAL cc_start: 0.4541 (OUTLIER) cc_final: 0.4341 (p) outliers start: 19 outliers final: 12 residues processed: 59 average time/residue: 0.0681 time to fit residues: 4.8953 Evaluate side-chains 53 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.162020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.130509 restraints weight = 4040.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.131604 restraints weight = 3411.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.132656 restraints weight = 2734.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.132988 restraints weight = 2259.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.133215 restraints weight = 2061.619| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3419 Z= 0.169 Angle : 0.588 5.509 4657 Z= 0.307 Chirality : 0.044 0.132 497 Planarity : 0.005 0.069 602 Dihedral : 4.050 14.102 510 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 6.37 % Allowed : 28.81 % Favored : 64.82 % 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 aren not related in a simple way. whole: -1.53 (0.39), residues: 419 helix: -4.63 (0.47), residues: 18 sheet: 0.43 (0.48), residues: 136 loop : -1.62 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 40 TYR 0.025 0.002 TYR C 495 PHE 0.020 0.002 PHE C 429 TRP 0.011 0.001 TRP C 436 HIS 0.002 0.001 HIS L 8 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 3411) covalent geometry : angle 0.58147 ( 4639) SS BOND : bond 0.00481 ( 6) SS BOND : angle 1.47526 ( 12) hydrogen bonds : bond 0.04372 ( 71) hydrogen bonds : angle 5.76940 ( 216) link_BETA1-4 : bond 0.00284 ( 1) link_BETA1-4 : angle 1.12840 ( 3) link_NAG-ASN : bond 0.00178 ( 1) link_NAG-ASN : angle 2.12586 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 0.083 Fit side-chains REVERT: C 334 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7444 (p0) REVERT: C 346 ARG cc_start: 0.7476 (mtp85) cc_final: 0.7054 (mtp85) REVERT: C 495 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.5860 (t80) REVERT: C 508 TYR cc_start: 0.8447 (m-80) cc_final: 0.8136 (m-10) REVERT: C 516 GLU cc_start: 0.7778 (pm20) cc_final: 0.7086 (pt0) REVERT: L 97 SER cc_start: 0.7619 (m) cc_final: 0.7228 (p) outliers start: 23 outliers final: 18 residues processed: 63 average time/residue: 0.0749 time to fit residues: 5.6747 Evaluate side-chains 63 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 26 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.160885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.128176 restraints weight = 4033.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.129648 restraints weight = 3967.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.130856 restraints weight = 2781.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131248 restraints weight = 2444.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.131822 restraints weight = 2163.635| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3419 Z= 0.142 Angle : 0.556 5.086 4657 Z= 0.289 Chirality : 0.043 0.137 497 Planarity : 0.005 0.063 602 Dihedral : 3.952 13.829 510 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.26 % Allowed : 29.36 % Favored : 65.37 % 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 aren not related in a simple way. whole: -1.38 (0.39), residues: 419 helix: -4.47 (0.57), residues: 18 sheet: 0.65 (0.48), residues: 130 loop : -1.56 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 72 TYR 0.022 0.001 TYR C 495 PHE 0.014 0.001 PHE C 429 TRP 0.010 0.001 TRP C 436 HIS 0.001 0.000 HIS L 8 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3411) covalent geometry : angle 0.54975 ( 4639) SS BOND : bond 0.00505 ( 6) SS BOND : angle 1.25088 ( 12) hydrogen bonds : bond 0.03576 ( 71) hydrogen bonds : angle 5.49577 ( 216) link_BETA1-4 : bond 0.00356 ( 1) link_BETA1-4 : angle 1.17880 ( 3) link_NAG-ASN : bond 0.00188 ( 1) link_NAG-ASN : angle 2.12014 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.073 Fit side-chains REVERT: C 334 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.7083 (p0) REVERT: C 346 ARG cc_start: 0.7480 (mtp85) cc_final: 0.7066 (mtp85) REVERT: C 430 THR cc_start: 0.8599 (p) cc_final: 0.8361 (p) REVERT: C 495 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.6166 (t80) REVERT: C 508 TYR cc_start: 0.8441 (m-80) cc_final: 0.8170 (m-10) REVERT: C 516 GLU cc_start: 0.7657 (pm20) cc_final: 0.7134 (pt0) REVERT: L 97 SER cc_start: 0.7683 (m) cc_final: 0.7311 (p) outliers start: 19 outliers final: 16 residues processed: 59 average time/residue: 0.0645 time to fit residues: 4.5581 Evaluate side-chains 59 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN C 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.157783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.123979 restraints weight = 4080.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.125440 restraints weight = 3394.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126562 restraints weight = 2462.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.127407 restraints weight = 2136.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.127639 restraints weight = 1964.521| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3419 Z= 0.189 Angle : 0.615 6.387 4657 Z= 0.324 Chirality : 0.045 0.140 497 Planarity : 0.005 0.065 602 Dihedral : 4.383 19.033 510 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 6.93 % Allowed : 27.98 % Favored : 65.10 % 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 aren not related in a simple way. whole: -1.54 (0.39), residues: 419 helix: -4.55 (0.53), residues: 18 sheet: 0.42 (0.47), residues: 132 loop : -1.61 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 72 TYR 0.032 0.002 TYR C 495 PHE 0.020 0.002 PHE C 429 TRP 0.012 0.002 TRP H 47 HIS 0.001 0.000 HIS L 8 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 3411) covalent geometry : angle 0.60669 ( 4639) SS BOND : bond 0.00575 ( 6) SS BOND : angle 1.44695 ( 12) hydrogen bonds : bond 0.03856 ( 71) hydrogen bonds : angle 5.38162 ( 216) link_BETA1-4 : bond 0.00289 ( 1) link_BETA1-4 : angle 1.31864 ( 3) link_NAG-ASN : bond 0.00304 ( 1) link_NAG-ASN : angle 2.67823 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 44 time to evaluate : 0.139 Fit side-chains REVERT: C 346 ARG cc_start: 0.7450 (mtp85) cc_final: 0.7115 (mtp85) REVERT: C 390 LEU cc_start: 0.7906 (mp) cc_final: 0.7667 (mt) REVERT: C 442 ASP cc_start: 0.8147 (m-30) cc_final: 0.7615 (m-30) REVERT: C 495 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.6002 (t80) REVERT: C 516 GLU cc_start: 0.7972 (pm20) cc_final: 0.7536 (pt0) REVERT: H 11 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5741 (tt) outliers start: 25 outliers final: 18 residues processed: 65 average time/residue: 0.0907 time to fit residues: 6.9420 Evaluate side-chains 61 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 14 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.158599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.123905 restraints weight = 4072.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126559 restraints weight = 2835.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.128257 restraints weight = 2277.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.129575 restraints weight = 1994.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.130032 restraints weight = 1825.227| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3419 Z= 0.125 Angle : 0.546 5.549 4657 Z= 0.288 Chirality : 0.042 0.138 497 Planarity : 0.005 0.061 602 Dihedral : 4.092 19.221 510 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 6.09 % Allowed : 27.98 % Favored : 65.93 % 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 aren not related in a simple way. whole: -1.30 (0.39), residues: 419 helix: -4.35 (0.58), residues: 18 sheet: 0.67 (0.47), residues: 131 loop : -1.49 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 454 TYR 0.019 0.001 TYR C 495 PHE 0.013 0.001 PHE C 429 TRP 0.010 0.001 TRP C 436 HIS 0.001 0.000 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3411) covalent geometry : angle 0.54012 ( 4639) SS BOND : bond 0.00513 ( 6) SS BOND : angle 1.21287 ( 12) hydrogen bonds : bond 0.03315 ( 71) hydrogen bonds : angle 5.16094 ( 216) link_BETA1-4 : bond 0.00352 ( 1) link_BETA1-4 : angle 1.18555 ( 3) link_NAG-ASN : bond 0.00022 ( 1) link_NAG-ASN : angle 2.02363 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 38 time to evaluate : 0.124 Fit side-chains REVERT: C 346 ARG cc_start: 0.7427 (mtp85) cc_final: 0.7089 (mtp85) REVERT: C 430 THR cc_start: 0.8485 (p) cc_final: 0.8268 (t) REVERT: C 454 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8071 (ttm-80) REVERT: C 495 TYR cc_start: 0.7594 (OUTLIER) cc_final: 0.6229 (t80) REVERT: C 516 GLU cc_start: 0.7896 (pm20) cc_final: 0.7596 (pt0) outliers start: 22 outliers final: 17 residues processed: 56 average time/residue: 0.0959 time to fit residues: 6.3442 Evaluate side-chains 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 83 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.0870 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.0020 chunk 15 optimal weight: 4.9990 overall best weight: 0.5770 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.157286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.122668 restraints weight = 4169.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.125452 restraints weight = 2882.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.127317 restraints weight = 2302.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.128259 restraints weight = 2000.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.129009 restraints weight = 1845.306| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3419 Z= 0.157 Angle : 0.583 7.217 4657 Z= 0.304 Chirality : 0.044 0.142 497 Planarity : 0.005 0.060 602 Dihedral : 4.211 19.038 510 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 5.54 % Allowed : 28.81 % Favored : 65.65 % 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 aren not related in a simple way. whole: -1.38 (0.39), residues: 419 helix: -4.24 (0.55), residues: 19 sheet: 0.36 (0.45), residues: 137 loop : -1.43 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 454 TYR 0.026 0.002 TYR C 495 PHE 0.013 0.001 PHE C 429 TRP 0.010 0.001 TRP C 436 HIS 0.001 0.000 HIS L 8 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 3411) covalent geometry : angle 0.57646 ( 4639) SS BOND : bond 0.00527 ( 6) SS BOND : angle 1.26950 ( 12) hydrogen bonds : bond 0.03580 ( 71) hydrogen bonds : angle 5.11903 ( 216) link_BETA1-4 : bond 0.00347 ( 1) link_BETA1-4 : angle 1.33138 ( 3) link_NAG-ASN : bond 0.00218 ( 1) link_NAG-ASN : angle 2.41191 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.127 Fit side-chains REVERT: C 346 ARG cc_start: 0.7438 (mtp85) cc_final: 0.7112 (mtp85) REVERT: C 390 LEU cc_start: 0.7714 (mt) cc_final: 0.7506 (mt) REVERT: C 430 THR cc_start: 0.8570 (p) cc_final: 0.8241 (t) REVERT: C 442 ASP cc_start: 0.8105 (m-30) cc_final: 0.7685 (m-30) REVERT: C 454 ARG cc_start: 0.8597 (ttm-80) cc_final: 0.7973 (ttm-80) REVERT: C 495 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.5944 (t80) REVERT: C 516 GLU cc_start: 0.8018 (pm20) cc_final: 0.7735 (pt0) outliers start: 20 outliers final: 17 residues processed: 56 average time/residue: 0.0923 time to fit residues: 6.1405 Evaluate side-chains 55 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 83 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.156819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.121395 restraints weight = 4165.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.124433 restraints weight = 2743.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126468 restraints weight = 2138.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.127480 restraints weight = 1841.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.128174 restraints weight = 1694.056| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3419 Z= 0.166 Angle : 0.596 6.430 4657 Z= 0.312 Chirality : 0.044 0.143 497 Planarity : 0.005 0.061 602 Dihedral : 4.357 18.564 510 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.82 % Allowed : 27.15 % Favored : 67.04 % 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 aren not related in a simple way. whole: -1.60 (0.39), residues: 419 helix: -4.42 (0.41), residues: 27 sheet: 0.29 (0.45), residues: 137 loop : -1.51 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 457 TYR 0.027 0.002 TYR C 495 PHE 0.014 0.002 PHE C 429 TRP 0.011 0.002 TRP C 436 HIS 0.001 0.000 HIS L 8 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 3411) covalent geometry : angle 0.58956 ( 4639) SS BOND : bond 0.00577 ( 6) SS BOND : angle 1.33760 ( 12) hydrogen bonds : bond 0.03615 ( 71) hydrogen bonds : angle 5.14292 ( 216) link_BETA1-4 : bond 0.00251 ( 1) link_BETA1-4 : angle 1.26373 ( 3) link_NAG-ASN : bond 0.00156 ( 1) link_NAG-ASN : angle 2.31309 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 37 time to evaluate : 0.126 Fit side-chains REVERT: C 346 ARG cc_start: 0.7445 (mtp85) cc_final: 0.7119 (mtp85) REVERT: C 430 THR cc_start: 0.8565 (p) cc_final: 0.8244 (t) REVERT: C 442 ASP cc_start: 0.8087 (m-30) cc_final: 0.7661 (m-30) REVERT: C 454 ARG cc_start: 0.8584 (ttm-80) cc_final: 0.7999 (ttm-80) REVERT: C 495 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.5923 (t80) outliers start: 21 outliers final: 15 residues processed: 55 average time/residue: 0.0855 time to fit residues: 5.6004 Evaluate side-chains 53 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 0.0870 chunk 5 optimal weight: 0.0070 chunk 20 optimal weight: 0.0970 chunk 3 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 32 optimal weight: 0.3980 overall best weight: 0.0774 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.164409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.130797 restraints weight = 4059.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.133318 restraints weight = 3358.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.133818 restraints weight = 2448.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.134377 restraints weight = 2203.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.134556 restraints weight = 1984.778| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3419 Z= 0.093 Angle : 0.515 5.845 4657 Z= 0.270 Chirality : 0.042 0.145 497 Planarity : 0.005 0.054 602 Dihedral : 3.835 17.973 510 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.05 % Allowed : 30.47 % Favored : 66.48 % 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 aren not related in a simple way. whole: -0.95 (0.41), residues: 419 helix: -3.78 (0.83), residues: 13 sheet: 0.50 (0.47), residues: 135 loop : -1.11 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 457 TYR 0.011 0.001 TYR H 60 PHE 0.009 0.001 PHE C 429 TRP 0.011 0.001 TRP C 436 HIS 0.001 0.000 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 3411) covalent geometry : angle 0.51021 ( 4639) SS BOND : bond 0.00458 ( 6) SS BOND : angle 1.08896 ( 12) hydrogen bonds : bond 0.02769 ( 71) hydrogen bonds : angle 4.78729 ( 216) link_BETA1-4 : bond 0.00459 ( 1) link_BETA1-4 : angle 0.98427 ( 3) link_NAG-ASN : bond 0.00152 ( 1) link_NAG-ASN : angle 1.64233 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: C 346 ARG cc_start: 0.7453 (mtp85) cc_final: 0.7036 (mtp85) REVERT: C 454 ARG cc_start: 0.8512 (ttm-80) cc_final: 0.7964 (ttm-80) REVERT: C 495 TYR cc_start: 0.7746 (OUTLIER) cc_final: 0.6721 (t80) outliers start: 11 outliers final: 9 residues processed: 48 average time/residue: 0.0978 time to fit residues: 5.4832 Evaluate side-chains 46 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.156876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.122466 restraints weight = 4113.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.125030 restraints weight = 2907.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.126805 restraints weight = 2359.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.127893 restraints weight = 2081.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.128395 restraints weight = 1920.827| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3419 Z= 0.158 Angle : 0.587 5.865 4657 Z= 0.307 Chirality : 0.045 0.164 497 Planarity : 0.005 0.056 602 Dihedral : 4.135 17.634 510 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.22 % Allowed : 31.02 % Favored : 66.76 % 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 aren not related in a simple way. whole: -1.19 (0.40), residues: 419 helix: -4.26 (0.56), residues: 19 sheet: 0.27 (0.45), residues: 142 loop : -1.16 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 457 TYR 0.026 0.002 TYR C 495 PHE 0.011 0.001 PHE C 429 TRP 0.010 0.002 TRP C 436 HIS 0.001 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 3411) covalent geometry : angle 0.58050 ( 4639) SS BOND : bond 0.00511 ( 6) SS BOND : angle 1.33125 ( 12) hydrogen bonds : bond 0.03588 ( 71) hydrogen bonds : angle 4.88732 ( 216) link_BETA1-4 : bond 0.00271 ( 1) link_BETA1-4 : angle 1.23276 ( 3) link_NAG-ASN : bond 0.00235 ( 1) link_NAG-ASN : angle 2.40782 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.125 Fit side-chains REVERT: C 346 ARG cc_start: 0.7436 (mtp85) cc_final: 0.7114 (mtp85) REVERT: C 430 THR cc_start: 0.8545 (p) cc_final: 0.8198 (t) REVERT: C 442 ASP cc_start: 0.8043 (m-30) cc_final: 0.7710 (m-30) REVERT: C 454 ARG cc_start: 0.8589 (ttm-80) cc_final: 0.8039 (ttm-80) REVERT: C 495 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.6230 (t80) REVERT: H 98 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7681 (ptt180) outliers start: 8 outliers final: 6 residues processed: 42 average time/residue: 0.1066 time to fit residues: 5.2620 Evaluate side-chains 42 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 16 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.156448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.124825 restraints weight = 4212.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.126592 restraints weight = 3418.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.127691 restraints weight = 2767.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.128079 restraints weight = 2311.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.128260 restraints weight = 2151.770| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3419 Z= 0.170 Angle : 0.604 6.538 4657 Z= 0.316 Chirality : 0.045 0.168 497 Planarity : 0.005 0.059 602 Dihedral : 4.372 17.065 510 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.05 % Allowed : 30.47 % Favored : 66.48 % 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 aren not related in a simple way. whole: -1.48 (0.39), residues: 419 helix: -4.35 (0.42), residues: 27 sheet: 0.13 (0.44), residues: 143 loop : -1.29 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 457 TYR 0.027 0.002 TYR C 495 PHE 0.013 0.002 PHE C 429 TRP 0.011 0.002 TRP C 436 HIS 0.001 0.000 HIS L 8 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 3411) covalent geometry : angle 0.59718 ( 4639) SS BOND : bond 0.00575 ( 6) SS BOND : angle 1.37265 ( 12) hydrogen bonds : bond 0.03582 ( 71) hydrogen bonds : angle 5.00229 ( 216) link_BETA1-4 : bond 0.00237 ( 1) link_BETA1-4 : angle 1.25642 ( 3) link_NAG-ASN : bond 0.00185 ( 1) link_NAG-ASN : angle 2.37596 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 843.55 seconds wall clock time: 15 minutes 4.98 seconds (904.98 seconds total)