Starting phenix.real_space_refine on Tue Mar 3 14:07:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i4f_35171/03_2026/8i4f_35171.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i4f_35171/03_2026/8i4f_35171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i4f_35171/03_2026/8i4f_35171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i4f_35171/03_2026/8i4f_35171.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i4f_35171/03_2026/8i4f_35171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i4f_35171/03_2026/8i4f_35171.map" } resolution = 3.44 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= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 3733 2.51 5 N 964 2.21 5 O 1102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5824 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4902 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 34, 'TRANS': 584} Chain breaks: 5 Chain: "C" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 922 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Time building chain proxies: 1.34, per 1000 atoms: 0.23 Number of scatterers: 5824 At special positions: 0 Unit cell: (71.764, 86.676, 128.616, 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 25 16.00 O 1102 8.00 N 964 7.00 C 3733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 532 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 545 " - pdb=" SG CYS A 597 " distance=2.03 Simple disulfide: pdb=" SG CYS A 624 " - pdb=" SG CYS A 656 " distance=2.03 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 678 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 249.2 milliseconds 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1374 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 13 sheets defined 2.7% alpha, 26.8% 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 301 through 308 removed outlier: 3.751A pdb=" N GLU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.921A pdb=" N TYR A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 377' Processing helix chain 'A' and resid 626 through 631 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38 removed outlier: 7.811A pdb=" N ASN A 69 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TYR A 276 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 200 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 236 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE A 210 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N VAL A 234 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER A 212 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 63 Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.623A pdb=" N GLY A 115 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 125 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 128 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 135 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.623A pdb=" N GLY A 115 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 125 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS A 139 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 321 removed outlier: 3.543A pdb=" N THR A 606 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A 619 " --> pdb=" O CYS A 656 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 331 through 333 removed outlier: 6.804A pdb=" N GLU A 331 " --> pdb=" O ASN A 547 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASN A 549 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ILE A 333 " --> pdb=" O ASN A 549 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 363 through 365 removed outlier: 3.605A pdb=" N LYS A 385 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA A 442 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA A 383 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 460 through 461 Processing sheet with id=AB1, first strand: chain 'A' and resid 661 through 662 removed outlier: 6.155A pdb=" N GLU A 661 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 682 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 671 through 674 removed outlier: 6.734A pdb=" N ILE A 677 " --> pdb=" O ILE A 673 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 6 through 7 removed outlier: 3.554A pdb=" N SER C 7 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU C 18 " --> pdb=" O MET C 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET C 83 " --> pdb=" O LEU C 18 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.830A pdb=" N MET C 34 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) 133 hydrogen bonds defined for protein. 333 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: 0.65 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1856 1.34 - 1.46: 1532 1.46 - 1.58: 2557 1.58 - 1.70: 0 1.70 - 1.82: 29 Bond restraints: 5974 Sorted by residual: bond pdb=" CB PRO A 147 " pdb=" CG PRO A 147 " ideal model delta sigma weight residual 1.492 1.534 -0.042 5.00e-02 4.00e+02 7.08e-01 bond pdb=" C ALA A 379 " pdb=" N PRO A 380 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 6.19e-01 bond pdb=" C VAL A 627 " pdb=" N PRO A 628 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.28e-02 6.10e+03 4.27e-01 bond pdb=" C ASP A 301 " pdb=" N PRO A 302 " ideal model delta sigma weight residual 1.334 1.349 -0.015 2.34e-02 1.83e+03 4.05e-01 bond pdb=" C PHE A 336 " pdb=" N PRO A 337 " ideal model delta sigma weight residual 1.334 1.349 -0.015 2.34e-02 1.83e+03 4.02e-01 ... (remaining 5969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 7889 1.13 - 2.26: 187 2.26 - 3.38: 47 3.38 - 4.51: 3 4.51 - 5.64: 3 Bond angle restraints: 8129 Sorted by residual: angle pdb=" CA TYR A 502 " pdb=" CB TYR A 502 " pdb=" CG TYR A 502 " ideal model delta sigma weight residual 113.90 117.01 -3.11 1.80e+00 3.09e-01 2.99e+00 angle pdb=" C GLY A 573 " pdb=" N ARG A 574 " pdb=" CA ARG A 574 " ideal model delta sigma weight residual 121.54 124.84 -3.30 1.91e+00 2.74e-01 2.98e+00 angle pdb=" C ALA A 379 " pdb=" N PRO A 380 " pdb=" CA PRO A 380 " ideal model delta sigma weight residual 119.84 121.96 -2.12 1.25e+00 6.40e-01 2.88e+00 angle pdb=" N PRO A 380 " pdb=" CA PRO A 380 " pdb=" C PRO A 380 " ideal model delta sigma weight residual 112.47 115.73 -3.26 2.06e+00 2.36e-01 2.50e+00 angle pdb=" C SER A 647 " pdb=" N ASN A 648 " pdb=" CA ASN A 648 " ideal model delta sigma weight residual 122.82 125.03 -2.21 1.42e+00 4.96e-01 2.43e+00 ... (remaining 8124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 3330 17.65 - 35.30: 160 35.30 - 52.95: 19 52.95 - 70.61: 5 70.61 - 88.26: 2 Dihedral angle restraints: 3516 sinusoidal: 1367 harmonic: 2149 Sorted by residual: dihedral pdb=" CB GLU A 668 " pdb=" CG GLU A 668 " pdb=" CD GLU A 668 " pdb=" OE1 GLU A 668 " ideal model delta sinusoidal sigma weight residual 0.00 -88.26 88.26 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" SG CYS A 139 " pdb=" CB CYS A 173 " pdb=" SG CYS A 173 " pdb=" CA CYS A 173 " ideal model delta sinusoidal sigma weight residual 79.00 26.43 52.57 1 2.00e+01 2.50e-03 9.41e+00 dihedral pdb=" N PHE A 282 " pdb=" CA PHE A 282 " pdb=" CB PHE A 282 " pdb=" CG PHE A 282 " ideal model delta sinusoidal sigma weight residual -60.00 -115.68 55.68 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 3513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 498 0.026 - 0.052: 238 0.052 - 0.078: 81 0.078 - 0.104: 54 0.104 - 0.130: 23 Chirality restraints: 894 Sorted by residual: chirality pdb=" CB ILE A 417 " pdb=" CA ILE A 417 " pdb=" CG1 ILE A 417 " pdb=" CG2 ILE A 417 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE A 127 " pdb=" N ILE A 127 " pdb=" C ILE A 127 " pdb=" CB ILE A 127 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE A 210 " pdb=" N ILE A 210 " pdb=" C ILE A 210 " pdb=" CB ILE A 210 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 891 not shown) Planarity restraints: 1051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 451 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A 452 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 452 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 452 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 343 " 0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 344 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 92 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO A 93 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.015 5.00e-02 4.00e+02 ... (remaining 1048 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 869 2.77 - 3.30: 5359 3.30 - 3.83: 9549 3.83 - 4.37: 10883 4.37 - 4.90: 18833 Nonbonded interactions: 45493 Sorted by model distance: nonbonded pdb=" OH TYR A 45 " pdb=" O LEU A 62 " model vdw 2.232 3.040 nonbonded pdb=" O GLU A 668 " pdb=" OH TYR A 702 " model vdw 2.284 3.040 nonbonded pdb=" O VAL A 138 " pdb=" OG1 THR A 174 " model vdw 2.314 3.040 nonbonded pdb=" OG1 THR A 116 " pdb=" O ASN A 241 " model vdw 2.315 3.040 nonbonded pdb=" OG1 THR A 400 " pdb=" O GLU A 523 " model vdw 2.323 3.040 ... (remaining 45488 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.070 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 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 : 0.002 0.042 5984 Z= 0.086 Angle : 0.451 5.640 8149 Z= 0.250 Chirality : 0.041 0.130 894 Planarity : 0.004 0.049 1051 Dihedral : 9.629 88.256 2112 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.44 % Allowed : 7.62 % Favored : 86.94 % 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: -4.30 (0.25), residues: 724 helix: -4.59 (0.40), residues: 33 sheet: -1.27 (0.38), residues: 171 loop : -3.60 (0.21), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 86 TYR 0.005 0.001 TYR A 376 PHE 0.010 0.001 PHE A 407 TRP 0.005 0.001 TRP A 640 HIS 0.001 0.000 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00178 ( 5974) covalent geometry : angle 0.45040 ( 8129) SS BOND : bond 0.00152 ( 10) SS BOND : angle 0.65693 ( 20) hydrogen bonds : bond 0.18493 ( 125) hydrogen bonds : angle 6.95181 ( 333) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7567 (p) REVERT: A 74 HIS cc_start: 0.5942 (m-70) cc_final: 0.5624 (m-70) REVERT: A 118 LEU cc_start: 0.7341 (mp) cc_final: 0.6988 (mp) REVERT: A 136 ILE cc_start: 0.8337 (mm) cc_final: 0.8079 (mt) REVERT: A 196 LEU cc_start: 0.8265 (tp) cc_final: 0.7882 (tp) REVERT: A 212 SER cc_start: 0.7213 (t) cc_final: 0.6868 (m) REVERT: A 251 LEU cc_start: 0.7681 (tp) cc_final: 0.7426 (tp) REVERT: A 349 PHE cc_start: 0.7400 (m-80) cc_final: 0.6648 (m-80) REVERT: A 399 PHE cc_start: 0.7868 (m-80) cc_final: 0.7545 (m-10) REVERT: A 432 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7923 (mp) REVERT: A 443 TRP cc_start: 0.8199 (p90) cc_final: 0.7131 (p90) REVERT: A 477 THR cc_start: 0.8672 (p) cc_final: 0.8460 (t) REVERT: A 544 LYS cc_start: 0.8212 (ttmt) cc_final: 0.7849 (ttmm) REVERT: A 585 ASP cc_start: 0.7531 (t70) cc_final: 0.6839 (t70) REVERT: A 651 GLN cc_start: 0.7513 (tp40) cc_final: 0.7164 (tp-100) REVERT: A 673 ILE cc_start: 0.7721 (mt) cc_final: 0.7520 (mt) outliers start: 35 outliers final: 11 residues processed: 207 average time/residue: 0.0778 time to fit residues: 20.5928 Evaluate side-chains 165 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0020 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 overall best weight: 0.3366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 218 ASN A 416 GLN A 421 GLN A 429 ASN A 481 GLN A 551 ASN A 570 GLN A 614 GLN A 664 ASN A 682 GLN C 112 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.163511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.145916 restraints weight = 9623.596| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.63 r_work: 0.3803 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5984 Z= 0.116 Angle : 0.559 7.167 8149 Z= 0.292 Chirality : 0.044 0.169 894 Planarity : 0.005 0.048 1051 Dihedral : 6.953 92.499 835 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.44 % Allowed : 13.53 % Favored : 81.03 % 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: -3.76 (0.26), residues: 724 helix: -4.18 (0.56), residues: 34 sheet: -1.07 (0.37), residues: 176 loop : -3.16 (0.22), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 335 TYR 0.030 0.001 TYR A 502 PHE 0.032 0.002 PHE A 378 TRP 0.032 0.002 TRP C 36 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 5974) covalent geometry : angle 0.55772 ( 8129) SS BOND : bond 0.00307 ( 10) SS BOND : angle 1.00711 ( 20) hydrogen bonds : bond 0.03102 ( 125) hydrogen bonds : angle 5.20982 ( 333) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7079 (p) REVERT: A 60 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7494 (tm-30) REVERT: A 136 ILE cc_start: 0.8568 (mm) cc_final: 0.8315 (mt) REVERT: A 212 SER cc_start: 0.7409 (t) cc_final: 0.6964 (m) REVERT: A 251 LEU cc_start: 0.7715 (tp) cc_final: 0.7512 (tp) REVERT: A 381 PHE cc_start: 0.5194 (m-10) cc_final: 0.4937 (m-80) REVERT: A 429 ASN cc_start: 0.7434 (m-40) cc_final: 0.7000 (m-40) REVERT: A 443 TRP cc_start: 0.8288 (p90) cc_final: 0.7687 (p90) REVERT: A 477 THR cc_start: 0.8721 (p) cc_final: 0.8459 (t) REVERT: A 544 LYS cc_start: 0.8420 (ttmt) cc_final: 0.8142 (ttmm) REVERT: A 585 ASP cc_start: 0.7810 (t70) cc_final: 0.7420 (t70) REVERT: A 665 ASN cc_start: 0.7892 (t0) cc_final: 0.7443 (t0) REVERT: C 69 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7393 (p) outliers start: 35 outliers final: 19 residues processed: 194 average time/residue: 0.0824 time to fit residues: 20.4429 Evaluate side-chains 171 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 42 optimal weight: 0.0060 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 70 optimal weight: 0.8980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 ASN A 682 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.161004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.143248 restraints weight = 9529.299| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 3.63 r_work: 0.3763 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5984 Z= 0.130 Angle : 0.594 11.442 8149 Z= 0.303 Chirality : 0.045 0.206 894 Planarity : 0.005 0.050 1051 Dihedral : 6.943 90.977 833 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 5.75 % Allowed : 17.26 % Favored : 76.98 % 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: -3.51 (0.27), residues: 724 helix: -3.86 (0.67), residues: 34 sheet: -0.81 (0.40), residues: 156 loop : -2.95 (0.22), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 335 TYR 0.028 0.002 TYR A 502 PHE 0.034 0.002 PHE A 569 TRP 0.018 0.002 TRP C 36 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 5974) covalent geometry : angle 0.58513 ( 8129) SS BOND : bond 0.00682 ( 10) SS BOND : angle 2.14587 ( 20) hydrogen bonds : bond 0.03002 ( 125) hydrogen bonds : angle 5.03962 ( 333) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7147 (p) REVERT: A 60 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7626 (tm-30) REVERT: A 72 TRP cc_start: 0.8522 (t60) cc_final: 0.8233 (t60) REVERT: A 136 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8297 (mt) REVERT: A 212 SER cc_start: 0.7470 (t) cc_final: 0.6969 (m) REVERT: A 251 LEU cc_start: 0.7765 (tp) cc_final: 0.7516 (tp) REVERT: A 399 PHE cc_start: 0.8183 (m-80) cc_final: 0.7955 (m-10) REVERT: A 429 ASN cc_start: 0.7334 (m-40) cc_final: 0.6992 (m-40) REVERT: A 477 THR cc_start: 0.8751 (p) cc_final: 0.8545 (t) REVERT: A 544 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8228 (ttmm) REVERT: A 651 GLN cc_start: 0.7676 (tp-100) cc_final: 0.7059 (tp-100) REVERT: A 665 ASN cc_start: 0.7848 (t0) cc_final: 0.7340 (t0) REVERT: A 673 ILE cc_start: 0.7903 (mt) cc_final: 0.7665 (mt) REVERT: C 69 THR cc_start: 0.7727 (OUTLIER) cc_final: 0.7471 (p) outliers start: 37 outliers final: 26 residues processed: 190 average time/residue: 0.0733 time to fit residues: 18.0903 Evaluate side-chains 188 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 ASN ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN A 664 ASN ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.157984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.140329 restraints weight = 9476.253| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 3.60 r_work: 0.3719 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5984 Z= 0.154 Angle : 0.629 10.440 8149 Z= 0.321 Chirality : 0.046 0.275 894 Planarity : 0.005 0.045 1051 Dihedral : 7.230 90.761 833 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 5.44 % Allowed : 20.06 % Favored : 74.49 % 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: -3.25 (0.28), residues: 724 helix: -3.24 (0.91), residues: 28 sheet: -0.77 (0.40), residues: 170 loop : -2.81 (0.23), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 473 TYR 0.029 0.002 TYR A 502 PHE 0.021 0.002 PHE A 569 TRP 0.016 0.002 TRP A 360 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 5974) covalent geometry : angle 0.62243 ( 8129) SS BOND : bond 0.00517 ( 10) SS BOND : angle 1.97505 ( 20) hydrogen bonds : bond 0.03223 ( 125) hydrogen bonds : angle 5.02637 ( 333) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7207 (p) REVERT: A 60 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7642 (tm-30) REVERT: A 136 ILE cc_start: 0.8538 (mm) cc_final: 0.8291 (mt) REVERT: A 176 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7418 (tm-30) REVERT: A 212 SER cc_start: 0.7515 (t) cc_final: 0.6989 (m) REVERT: A 251 LEU cc_start: 0.7772 (tp) cc_final: 0.7549 (tp) REVERT: A 368 CYS cc_start: 0.6205 (OUTLIER) cc_final: 0.5872 (t) REVERT: A 378 PHE cc_start: 0.6146 (t80) cc_final: 0.5479 (t80) REVERT: A 429 ASN cc_start: 0.7255 (m-40) cc_final: 0.6938 (m110) REVERT: A 477 THR cc_start: 0.8824 (p) cc_final: 0.8583 (t) REVERT: A 523 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6485 (mt-10) REVERT: A 544 LYS cc_start: 0.8470 (ttmt) cc_final: 0.8231 (ttmm) REVERT: A 651 GLN cc_start: 0.7786 (tp-100) cc_final: 0.7134 (tp-100) REVERT: A 665 ASN cc_start: 0.7904 (t0) cc_final: 0.7364 (t0) REVERT: A 673 ILE cc_start: 0.7869 (mt) cc_final: 0.7653 (mt) REVERT: C 69 THR cc_start: 0.7755 (OUTLIER) cc_final: 0.7454 (p) REVERT: C 71 SER cc_start: 0.8245 (m) cc_final: 0.7827 (p) outliers start: 35 outliers final: 26 residues processed: 184 average time/residue: 0.0688 time to fit residues: 16.4353 Evaluate side-chains 191 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 599 PHE Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 30 optimal weight: 0.0470 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 0.0570 chunk 63 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.158812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.141268 restraints weight = 9662.452| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 3.61 r_work: 0.3723 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5984 Z= 0.130 Angle : 0.622 10.574 8149 Z= 0.317 Chirality : 0.045 0.230 894 Planarity : 0.004 0.047 1051 Dihedral : 7.380 92.136 833 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 5.75 % Allowed : 21.31 % Favored : 72.94 % 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: -3.07 (0.28), residues: 724 helix: -3.12 (0.95), residues: 28 sheet: -0.62 (0.41), residues: 157 loop : -2.65 (0.23), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 473 TYR 0.029 0.002 TYR A 502 PHE 0.020 0.002 PHE A 504 TRP 0.014 0.001 TRP C 36 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5974) covalent geometry : angle 0.61793 ( 8129) SS BOND : bond 0.00571 ( 10) SS BOND : angle 1.58041 ( 20) hydrogen bonds : bond 0.03109 ( 125) hydrogen bonds : angle 5.07588 ( 333) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.7141 (p) REVERT: A 60 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7559 (tm-30) REVERT: A 134 VAL cc_start: 0.5946 (OUTLIER) cc_final: 0.5622 (p) REVERT: A 136 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8232 (mt) REVERT: A 212 SER cc_start: 0.7424 (t) cc_final: 0.6953 (m) REVERT: A 251 LEU cc_start: 0.7717 (tp) cc_final: 0.7510 (tp) REVERT: A 335 ARG cc_start: 0.7547 (mtp85) cc_final: 0.7271 (mtp85) REVERT: A 378 PHE cc_start: 0.5991 (t80) cc_final: 0.5295 (t80) REVERT: A 429 ASN cc_start: 0.7173 (m-40) cc_final: 0.6842 (m110) REVERT: A 523 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6541 (mt-10) REVERT: A 538 THR cc_start: 0.7525 (p) cc_final: 0.6206 (m) REVERT: A 544 LYS cc_start: 0.8467 (ttmt) cc_final: 0.8227 (ttmm) REVERT: A 651 GLN cc_start: 0.7825 (tp-100) cc_final: 0.7088 (tp-100) REVERT: A 665 ASN cc_start: 0.7853 (t0) cc_final: 0.7369 (t0) REVERT: A 670 ASP cc_start: 0.7604 (t70) cc_final: 0.7341 (t0) REVERT: C 69 THR cc_start: 0.7716 (OUTLIER) cc_final: 0.7410 (p) REVERT: C 71 SER cc_start: 0.8227 (m) cc_final: 0.7823 (p) REVERT: C 72 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8228 (tpp80) outliers start: 37 outliers final: 23 residues processed: 181 average time/residue: 0.0768 time to fit residues: 17.6316 Evaluate side-chains 184 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 76 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 0.3980 chunk 65 optimal weight: 0.0170 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.157833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.140495 restraints weight = 9463.617| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.55 r_work: 0.3726 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5984 Z= 0.131 Angle : 0.622 12.132 8149 Z= 0.316 Chirality : 0.045 0.174 894 Planarity : 0.005 0.042 1051 Dihedral : 7.326 92.085 832 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 4.98 % Allowed : 22.71 % Favored : 72.32 % 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: -2.88 (0.29), residues: 724 helix: -3.01 (0.99), residues: 28 sheet: -0.45 (0.39), residues: 179 loop : -2.60 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 653 TYR 0.034 0.002 TYR A 502 PHE 0.024 0.001 PHE A 63 TRP 0.016 0.001 TRP C 36 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 5974) covalent geometry : angle 0.61673 ( 8129) SS BOND : bond 0.00465 ( 10) SS BOND : angle 1.76619 ( 20) hydrogen bonds : bond 0.03053 ( 125) hydrogen bonds : angle 5.12849 ( 333) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.7861 (OUTLIER) cc_final: 0.7079 (p) REVERT: A 60 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7328 (tm-30) REVERT: A 72 TRP cc_start: 0.8531 (t60) cc_final: 0.8066 (t60) REVERT: A 136 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8274 (mt) REVERT: A 212 SER cc_start: 0.7509 (t) cc_final: 0.7028 (m) REVERT: A 251 LEU cc_start: 0.7762 (tp) cc_final: 0.7540 (tp) REVERT: A 363 LYS cc_start: 0.8523 (tttm) cc_final: 0.8302 (ttpp) REVERT: A 378 PHE cc_start: 0.5984 (t80) cc_final: 0.5253 (t80) REVERT: A 417 ILE cc_start: 0.6737 (pt) cc_final: 0.6353 (pt) REVERT: A 429 ASN cc_start: 0.7223 (m-40) cc_final: 0.6953 (m-40) REVERT: A 523 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6622 (mt-10) REVERT: A 538 THR cc_start: 0.7525 (p) cc_final: 0.6213 (m) REVERT: A 544 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8259 (ttmm) REVERT: A 651 GLN cc_start: 0.7860 (tp-100) cc_final: 0.7256 (tp-100) REVERT: A 665 ASN cc_start: 0.7870 (t0) cc_final: 0.7382 (t0) REVERT: A 670 ASP cc_start: 0.7490 (t70) cc_final: 0.6916 (t70) REVERT: C 36 TRP cc_start: 0.7851 (m100) cc_final: 0.7280 (m100) REVERT: C 69 THR cc_start: 0.7747 (OUTLIER) cc_final: 0.7440 (p) REVERT: C 71 SER cc_start: 0.8257 (m) cc_final: 0.7858 (p) REVERT: C 72 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.8217 (tpp80) outliers start: 32 outliers final: 26 residues processed: 174 average time/residue: 0.0720 time to fit residues: 16.2261 Evaluate side-chains 182 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 76 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 0.0370 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.157752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.140902 restraints weight = 9480.581| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.42 r_work: 0.3727 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5984 Z= 0.136 Angle : 0.620 11.983 8149 Z= 0.317 Chirality : 0.045 0.160 894 Planarity : 0.005 0.041 1051 Dihedral : 7.280 90.362 832 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 5.60 % Allowed : 23.02 % Favored : 71.38 % 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: -2.72 (0.29), residues: 724 helix: -3.00 (1.00), residues: 28 sheet: -0.35 (0.40), residues: 179 loop : -2.48 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 326 TYR 0.026 0.002 TYR A 502 PHE 0.027 0.001 PHE A 63 TRP 0.014 0.001 TRP A 360 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5974) covalent geometry : angle 0.61583 ( 8129) SS BOND : bond 0.00416 ( 10) SS BOND : angle 1.61424 ( 20) hydrogen bonds : bond 0.02968 ( 125) hydrogen bonds : angle 5.16728 ( 333) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.7925 (OUTLIER) cc_final: 0.7077 (p) REVERT: A 60 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7317 (tm-30) REVERT: A 72 TRP cc_start: 0.8530 (t60) cc_final: 0.8039 (t60) REVERT: A 136 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8269 (mt) REVERT: A 212 SER cc_start: 0.7630 (t) cc_final: 0.7159 (m) REVERT: A 251 LEU cc_start: 0.7806 (tp) cc_final: 0.7588 (tp) REVERT: A 335 ARG cc_start: 0.7536 (mtp85) cc_final: 0.7270 (mtp85) REVERT: A 363 LYS cc_start: 0.8535 (tttm) cc_final: 0.8312 (ttpp) REVERT: A 378 PHE cc_start: 0.5933 (t80) cc_final: 0.5204 (t80) REVERT: A 425 ILE cc_start: 0.8708 (pp) cc_final: 0.8418 (pt) REVERT: A 429 ASN cc_start: 0.7251 (m-40) cc_final: 0.6985 (m-40) REVERT: A 523 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6666 (mt-10) REVERT: A 538 THR cc_start: 0.7515 (p) cc_final: 0.6345 (m) REVERT: A 544 LYS cc_start: 0.8529 (ttmt) cc_final: 0.8279 (ttmm) REVERT: A 651 GLN cc_start: 0.7930 (tp-100) cc_final: 0.7277 (tp-100) REVERT: A 665 ASN cc_start: 0.7914 (t0) cc_final: 0.7438 (t0) REVERT: A 670 ASP cc_start: 0.7491 (t70) cc_final: 0.6897 (t70) REVERT: C 36 TRP cc_start: 0.7814 (m100) cc_final: 0.7303 (m100) REVERT: C 69 THR cc_start: 0.7780 (OUTLIER) cc_final: 0.7488 (p) REVERT: C 71 SER cc_start: 0.8275 (m) cc_final: 0.7911 (p) REVERT: C 72 ARG cc_start: 0.8379 (ttm-80) cc_final: 0.8169 (tpp80) outliers start: 36 outliers final: 29 residues processed: 182 average time/residue: 0.0892 time to fit residues: 20.6389 Evaluate side-chains 192 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 41 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.154091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.137960 restraints weight = 9408.840| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 3.24 r_work: 0.3708 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5984 Z= 0.185 Angle : 0.704 18.908 8149 Z= 0.355 Chirality : 0.047 0.204 894 Planarity : 0.005 0.041 1051 Dihedral : 7.555 90.474 832 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 6.69 % Allowed : 22.71 % Favored : 70.61 % 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: -2.73 (0.30), residues: 724 helix: -3.07 (0.98), residues: 28 sheet: -0.46 (0.38), residues: 191 loop : -2.47 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 326 TYR 0.026 0.002 TYR A 502 PHE 0.033 0.002 PHE A 63 TRP 0.022 0.002 TRP A 360 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 5974) covalent geometry : angle 0.68705 ( 8129) SS BOND : bond 0.00384 ( 10) SS BOND : angle 3.14600 ( 20) hydrogen bonds : bond 0.03475 ( 125) hydrogen bonds : angle 5.51091 ( 333) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7496 (tm-30) REVERT: A 72 TRP cc_start: 0.8556 (t60) cc_final: 0.8032 (t60) REVERT: A 134 VAL cc_start: 0.5966 (OUTLIER) cc_final: 0.5688 (p) REVERT: A 136 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8235 (mt) REVERT: A 241 ASN cc_start: 0.5685 (OUTLIER) cc_final: 0.5238 (p0) REVERT: A 345 PHE cc_start: 0.7996 (m-80) cc_final: 0.7658 (m-80) REVERT: A 363 LYS cc_start: 0.8512 (tttm) cc_final: 0.8294 (ttpp) REVERT: A 378 PHE cc_start: 0.5890 (t80) cc_final: 0.5670 (t80) REVERT: A 425 ILE cc_start: 0.8762 (pp) cc_final: 0.8483 (pt) REVERT: A 429 ASN cc_start: 0.7459 (m-40) cc_final: 0.7229 (m-40) REVERT: A 443 TRP cc_start: 0.8396 (p90) cc_final: 0.7834 (p90) REVERT: A 523 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6725 (mt-10) REVERT: A 531 VAL cc_start: 0.8219 (m) cc_final: 0.7982 (p) REVERT: A 538 THR cc_start: 0.7637 (p) cc_final: 0.6574 (m) REVERT: A 544 LYS cc_start: 0.8522 (ttmt) cc_final: 0.8246 (ttmm) REVERT: A 588 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.8155 (p) REVERT: A 651 GLN cc_start: 0.7906 (tp-100) cc_final: 0.7292 (tp-100) REVERT: A 665 ASN cc_start: 0.7938 (t0) cc_final: 0.7440 (t0) REVERT: A 670 ASP cc_start: 0.7620 (t70) cc_final: 0.7041 (t70) REVERT: C 36 TRP cc_start: 0.7846 (m100) cc_final: 0.7345 (m100) REVERT: C 69 THR cc_start: 0.7851 (OUTLIER) cc_final: 0.7602 (p) REVERT: C 71 SER cc_start: 0.8287 (m) cc_final: 0.7947 (p) REVERT: C 81 LEU cc_start: 0.7853 (tp) cc_final: 0.7572 (tp) outliers start: 43 outliers final: 35 residues processed: 180 average time/residue: 0.0856 time to fit residues: 19.8100 Evaluate side-chains 194 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 48 optimal weight: 0.0970 chunk 36 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 41 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 0.0170 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 ASN A 682 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.156562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.140560 restraints weight = 9445.582| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 3.25 r_work: 0.3726 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5984 Z= 0.130 Angle : 0.683 20.192 8149 Z= 0.341 Chirality : 0.045 0.151 894 Planarity : 0.005 0.050 1051 Dihedral : 7.273 89.588 831 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 6.22 % Allowed : 24.88 % Favored : 68.90 % 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: -2.66 (0.30), residues: 724 helix: -3.02 (1.00), residues: 28 sheet: -0.43 (0.39), residues: 189 loop : -2.41 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 641 TYR 0.024 0.001 TYR A 502 PHE 0.037 0.002 PHE A 63 TRP 0.013 0.001 TRP A 360 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5974) covalent geometry : angle 0.67315 ( 8129) SS BOND : bond 0.00589 ( 10) SS BOND : angle 2.44772 ( 20) hydrogen bonds : bond 0.02996 ( 125) hydrogen bonds : angle 5.38318 ( 333) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7763 (tm-30) cc_final: 0.7216 (tm-30) REVERT: A 74 HIS cc_start: 0.6609 (m90) cc_final: 0.6210 (m90) REVERT: A 134 VAL cc_start: 0.5943 (OUTLIER) cc_final: 0.5660 (p) REVERT: A 136 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8231 (mt) REVERT: A 241 ASN cc_start: 0.5680 (OUTLIER) cc_final: 0.5240 (p0) REVERT: A 345 PHE cc_start: 0.7843 (m-80) cc_final: 0.7522 (m-80) REVERT: A 378 PHE cc_start: 0.5784 (t80) cc_final: 0.5068 (t80) REVERT: A 429 ASN cc_start: 0.7437 (m-40) cc_final: 0.7183 (m-40) REVERT: A 443 TRP cc_start: 0.8434 (p90) cc_final: 0.7778 (p90) REVERT: A 523 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6666 (mt-10) REVERT: A 538 THR cc_start: 0.7501 (p) cc_final: 0.6305 (m) REVERT: A 544 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8257 (ttmm) REVERT: A 651 GLN cc_start: 0.7924 (tp-100) cc_final: 0.7274 (tp-100) REVERT: A 665 ASN cc_start: 0.7980 (t0) cc_final: 0.7497 (t0) REVERT: C 36 TRP cc_start: 0.7793 (m100) cc_final: 0.7274 (m100) REVERT: C 69 THR cc_start: 0.7781 (OUTLIER) cc_final: 0.7507 (p) REVERT: C 71 SER cc_start: 0.8286 (m) cc_final: 0.7906 (p) REVERT: C 81 LEU cc_start: 0.7756 (tp) cc_final: 0.7533 (tp) outliers start: 40 outliers final: 29 residues processed: 180 average time/residue: 0.0864 time to fit residues: 19.9656 Evaluate side-chains 190 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 43 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 429 ASN A 682 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.155961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.139669 restraints weight = 9458.707| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 3.33 r_work: 0.3714 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5984 Z= 0.145 Angle : 0.698 20.456 8149 Z= 0.350 Chirality : 0.046 0.174 894 Planarity : 0.005 0.049 1051 Dihedral : 7.230 88.662 831 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 5.75 % Allowed : 25.51 % Favored : 68.74 % 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: -2.59 (0.30), residues: 724 helix: -3.01 (1.01), residues: 28 sheet: -0.42 (0.39), residues: 195 loop : -2.36 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 641 TYR 0.030 0.002 TYR A 502 PHE 0.039 0.002 PHE A 63 TRP 0.013 0.001 TRP A 360 HIS 0.004 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 5974) covalent geometry : angle 0.68993 ( 8129) SS BOND : bond 0.00548 ( 10) SS BOND : angle 2.24089 ( 20) hydrogen bonds : bond 0.03165 ( 125) hydrogen bonds : angle 5.39782 ( 333) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7206 (tm-30) REVERT: A 134 VAL cc_start: 0.5977 (OUTLIER) cc_final: 0.5702 (p) REVERT: A 136 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8238 (mt) REVERT: A 241 ASN cc_start: 0.5675 (OUTLIER) cc_final: 0.5235 (p0) REVERT: A 345 PHE cc_start: 0.7826 (m-80) cc_final: 0.7521 (m-80) REVERT: A 363 LYS cc_start: 0.8514 (tttm) cc_final: 0.8312 (ttpp) REVERT: A 429 ASN cc_start: 0.7458 (m110) cc_final: 0.7209 (m-40) REVERT: A 443 TRP cc_start: 0.8449 (p90) cc_final: 0.7826 (p90) REVERT: A 467 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8104 (mtpp) REVERT: A 523 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6722 (mt-10) REVERT: A 538 THR cc_start: 0.7579 (p) cc_final: 0.6532 (m) REVERT: A 544 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8245 (ttmm) REVERT: A 588 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8164 (p) REVERT: A 651 GLN cc_start: 0.7938 (tp-100) cc_final: 0.7273 (tp-100) REVERT: A 665 ASN cc_start: 0.7998 (t0) cc_final: 0.7485 (t0) REVERT: A 670 ASP cc_start: 0.7499 (t70) cc_final: 0.7025 (t70) REVERT: C 36 TRP cc_start: 0.7818 (m100) cc_final: 0.7349 (m100) REVERT: C 69 THR cc_start: 0.7820 (OUTLIER) cc_final: 0.7548 (p) REVERT: C 71 SER cc_start: 0.8289 (m) cc_final: 0.7920 (p) REVERT: C 81 LEU cc_start: 0.7809 (tp) cc_final: 0.7579 (tp) outliers start: 37 outliers final: 28 residues processed: 176 average time/residue: 0.0871 time to fit residues: 19.7699 Evaluate side-chains 186 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.155214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.138834 restraints weight = 9484.629| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 3.33 r_work: 0.3706 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5984 Z= 0.156 Angle : 0.704 20.509 8149 Z= 0.353 Chirality : 0.046 0.183 894 Planarity : 0.005 0.049 1051 Dihedral : 7.097 88.678 827 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 5.44 % Allowed : 26.13 % Favored : 68.43 % 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: -2.57 (0.30), residues: 724 helix: -3.00 (1.01), residues: 28 sheet: -0.40 (0.39), residues: 195 loop : -2.34 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 641 TYR 0.028 0.002 TYR A 502 PHE 0.041 0.002 PHE A 63 TRP 0.015 0.002 TRP A 360 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 5974) covalent geometry : angle 0.69711 ( 8129) SS BOND : bond 0.00535 ( 10) SS BOND : angle 2.14967 ( 20) hydrogen bonds : bond 0.03186 ( 125) hydrogen bonds : angle 5.42013 ( 333) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1329.53 seconds wall clock time: 23 minutes 28.63 seconds (1408.63 seconds total)