Starting phenix.real_space_refine on Wed Feb 4 00:48:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nda_49269/02_2026/9nda_49269_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nda_49269/02_2026/9nda_49269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nda_49269/02_2026/9nda_49269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nda_49269/02_2026/9nda_49269.map" model { file = "/net/cci-nas-00/data/ceres_data/9nda_49269/02_2026/9nda_49269_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nda_49269/02_2026/9nda_49269_neut.cif" } resolution = 2.9 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= 0.020 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 30 5.16 5 C 5126 2.51 5 N 1430 2.21 5 O 1374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7960 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2746 Classifications: {'peptide': 357} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 327} Chain breaks: 7 Chain: "C" Number of atoms: 5214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5214 Classifications: {'peptide': 687} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 632} Chain breaks: 13 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 1.89, per 1000 atoms: 0.24 Number of scatterers: 7960 At special positions: 0 Unit cell: (94.041, 104.247, 131.949, 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 30 16.00 O 1374 8.00 N 1430 7.00 C 5126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 754 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 469 " 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: 0.78 Conformation dependent library (CDL) restraints added in 297.1 milliseconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 11 sheets defined 42.9% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 427 through 438 Processing helix chain 'A' and resid 457 through 469 Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 565 through 571 Processing helix chain 'A' and resid 578 through 590 removed outlier: 3.723A pdb=" N ILE A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 Processing helix chain 'A' and resid 638 through 661 removed outlier: 4.131A pdb=" N ARG A 651 " --> pdb=" O GLY A 647 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 652 " --> pdb=" O HIS A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 792 Processing helix chain 'A' and resid 796 through 801 removed outlier: 4.332A pdb=" N ALA A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 858 Processing helix chain 'A' and resid 862 through 866 Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.515A pdb=" N TRP C 98 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 172 Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 189 through 194 removed outlier: 3.978A pdb=" N SER C 193 " --> pdb=" O PRO C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 228 Processing helix chain 'C' and resid 267 through 283 Processing helix chain 'C' and resid 297 through 301 removed outlier: 3.704A pdb=" N GLU C 301 " --> pdb=" O PRO C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 344 Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.924A pdb=" N VAL C 355 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 361 through 372 Processing helix chain 'C' and resid 374 through 383 Processing helix chain 'C' and resid 412 through 426 Processing helix chain 'C' and resid 427 through 429 No H-bonds generated for 'chain 'C' and resid 427 through 429' Processing helix chain 'C' and resid 435 through 448 Processing helix chain 'C' and resid 451 through 466 Proline residue: C 463 - end of helix removed outlier: 4.349A pdb=" N CYS C 466 " --> pdb=" O VAL C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 492 Processing helix chain 'C' and resid 520 through 542 Processing helix chain 'C' and resid 588 through 607 Processing helix chain 'C' and resid 619 through 639 Processing helix chain 'C' and resid 660 through 666 Processing helix chain 'C' and resid 668 through 673 removed outlier: 3.568A pdb=" N ASP C 671 " --> pdb=" O ALA C 668 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 673 " --> pdb=" O LEU C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 697 No H-bonds generated for 'chain 'C' and resid 695 through 697' Processing helix chain 'C' and resid 707 through 731 Processing helix chain 'C' and resid 746 through 750 Processing sheet with id=AA1, first strand: chain 'A' and resid 421 through 425 removed outlier: 6.639A pdb=" N ARG A 421 " --> pdb=" O HIS A 885 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 773 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N SER A 886 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 456 removed outlier: 5.444A pdb=" N VAL A 535 " --> pdb=" O ILE A 615 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 624 through 627 removed outlier: 3.564A pdb=" N VAL A 764 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE A 675 " --> pdb=" O VAL A 843 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 841 " --> pdb=" O LYS A 677 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 56 removed outlier: 6.889A pdb=" N HIS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL C 21 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU C 34 " --> pdb=" O TYR C 19 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA C 15 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG C 40 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL C 13 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 150 through 151 removed outlier: 6.300A pdb=" N ALA C 150 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE C 259 " --> pdb=" O PHE C 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 153 through 158 removed outlier: 3.893A pdb=" N SER C 196 " --> pdb=" O ASN C 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 230 through 237 Processing sheet with id=AA8, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AA9, first strand: chain 'C' and resid 398 through 400 Processing sheet with id=AB1, first strand: chain 'C' and resid 496 through 501 removed outlier: 6.243A pdb=" N TRP C 507 " --> pdb=" O CYS C 499 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY C 501 " --> pdb=" O ALA C 505 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA C 505 " --> pdb=" O GLY C 501 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 508 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR C 405 " --> pdb=" O VAL C 557 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL C 557 " --> pdb=" O THR C 405 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ARG C 407 " --> pdb=" O GLU C 555 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 648 through 650 365 hydrogen bonds defined for protein. 996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 1.01 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: 2632 1.35 - 1.47: 2000 1.47 - 1.59: 3490 1.59 - 1.72: 0 1.72 - 1.84: 39 Bond restraints: 8161 Sorted by residual: bond pdb=" CA ALA C 284 " pdb=" C ALA C 284 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.80e-02 3.09e+03 2.61e+00 bond pdb=" C VAL A 472 " pdb=" N PRO A 473 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.52e+00 bond pdb=" CB TRP C 98 " pdb=" CG TRP C 98 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.04e+00 bond pdb=" C SER C 87 " pdb=" N PRO C 88 " ideal model delta sigma weight residual 1.332 1.321 0.011 8.20e-03 1.49e+04 1.86e+00 bond pdb=" CE2 TRP C 98 " pdb=" CZ2 TRP C 98 " ideal model delta sigma weight residual 1.394 1.367 0.027 2.10e-02 2.27e+03 1.69e+00 ... (remaining 8156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 10981 2.86 - 5.72: 148 5.72 - 8.58: 9 8.58 - 11.44: 1 11.44 - 14.30: 2 Bond angle restraints: 11141 Sorted by residual: angle pdb=" N ALA C 80 " pdb=" CA ALA C 80 " pdb=" C ALA C 80 " ideal model delta sigma weight residual 112.72 106.36 6.36 1.36e+00 5.41e-01 2.19e+01 angle pdb=" C ALA A 670 " pdb=" N TYR A 671 " pdb=" CA TYR A 671 " ideal model delta sigma weight residual 121.27 106.97 14.30 3.40e+00 8.65e-02 1.77e+01 angle pdb=" N VAL C 75 " pdb=" CA VAL C 75 " pdb=" C VAL C 75 " ideal model delta sigma weight residual 113.00 108.40 4.60 1.30e+00 5.92e-01 1.25e+01 angle pdb=" C PRO A 636 " pdb=" N VAL A 637 " pdb=" CA VAL A 637 " ideal model delta sigma weight residual 123.33 120.61 2.72 8.70e-01 1.32e+00 9.79e+00 angle pdb=" N CYS A 754 " pdb=" CA CYS A 754 " pdb=" C CYS A 754 " ideal model delta sigma weight residual 113.21 109.72 3.49 1.15e+00 7.56e-01 9.19e+00 ... (remaining 11136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 4350 15.04 - 30.08: 364 30.08 - 45.11: 89 45.11 - 60.15: 20 60.15 - 75.19: 8 Dihedral angle restraints: 4831 sinusoidal: 1845 harmonic: 2986 Sorted by residual: dihedral pdb=" CB CYS C 466 " pdb=" SG CYS C 466 " pdb=" SG CYS C 469 " pdb=" CB CYS C 469 " ideal model delta sinusoidal sigma weight residual 93.00 33.48 59.52 1 1.00e+01 1.00e-02 4.73e+01 dihedral pdb=" CB CYS A 754 " pdb=" SG CYS A 754 " pdb=" SG CYS A 756 " pdb=" CB CYS A 756 " ideal model delta sinusoidal sigma weight residual 93.00 141.67 -48.67 1 1.00e+01 1.00e-02 3.26e+01 dihedral pdb=" CA SER C 87 " pdb=" C SER C 87 " pdb=" N PRO C 88 " pdb=" CA PRO C 88 " ideal model delta harmonic sigma weight residual -180.00 -155.04 -24.96 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 4828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 841 0.047 - 0.094: 328 0.094 - 0.141: 89 0.141 - 0.187: 10 0.187 - 0.234: 1 Chirality restraints: 1269 Sorted by residual: chirality pdb=" CG LEU A 810 " pdb=" CB LEU A 810 " pdb=" CD1 LEU A 810 " pdb=" CD2 LEU A 810 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CG LEU C 289 " pdb=" CB LEU C 289 " pdb=" CD1 LEU C 289 " pdb=" CD2 LEU C 289 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CG LEU C 89 " pdb=" CB LEU C 89 " pdb=" CD1 LEU C 89 " pdb=" CD2 LEU C 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.62e-01 ... (remaining 1266 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 83 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO C 84 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 84 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 84 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 697 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO C 698 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 698 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 698 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 24 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO C 25 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 25 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 25 " 0.032 5.00e-02 4.00e+02 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 3243 2.93 - 3.42: 7881 3.42 - 3.91: 13161 3.91 - 4.41: 15360 4.41 - 4.90: 25167 Nonbonded interactions: 64812 Sorted by model distance: nonbonded pdb=" O ALA A 670 " pdb=" CA TYR A 671 " model vdw 2.435 2.776 nonbonded pdb=" O GLU C 714 " pdb=" OE1 GLU C 718 " model vdw 2.471 3.040 nonbonded pdb=" O ALA C 167 " pdb=" OE1 GLU C 171 " model vdw 2.507 3.040 nonbonded pdb=" O LEU A 434 " pdb=" OG1 THR A 438 " model vdw 2.545 3.040 nonbonded pdb=" N ASN C 467 " pdb=" O ASN C 467 " model vdw 2.550 2.496 ... (remaining 64807 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: 5.730 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.280 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 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 : 0.006 0.062 8163 Z= 0.285 Angle : 0.828 14.305 11145 Z= 0.435 Chirality : 0.051 0.234 1269 Planarity : 0.008 0.068 1440 Dihedral : 12.682 75.187 2889 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.26), residues: 1000 helix: -0.14 (0.26), residues: 403 sheet: -1.81 (0.35), residues: 178 loop : -1.86 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 651 TYR 0.035 0.003 TYR C 558 PHE 0.022 0.002 PHE A 649 TRP 0.021 0.003 TRP C 98 HIS 0.005 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00645 ( 8161) covalent geometry : angle 0.82700 (11141) SS BOND : bond 0.00434 ( 2) SS BOND : angle 2.46344 ( 4) hydrogen bonds : bond 0.13426 ( 365) hydrogen bonds : angle 6.28717 ( 996) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 627 ASP cc_start: 0.5906 (t0) cc_final: 0.5650 (t0) REVERT: C 718 GLU cc_start: 0.7035 (mp0) cc_final: 0.6355 (mp0) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.4613 time to fit residues: 88.4543 Evaluate side-chains 171 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.139234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126857 restraints weight = 11661.920| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.96 r_work: 0.3581 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8163 Z= 0.213 Angle : 0.693 9.478 11145 Z= 0.350 Chirality : 0.047 0.162 1269 Planarity : 0.007 0.066 1440 Dihedral : 5.445 22.264 1139 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.13 % Allowed : 9.05 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.26), residues: 1000 helix: 0.19 (0.26), residues: 405 sheet: -1.75 (0.35), residues: 183 loop : -1.71 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 584 TYR 0.026 0.002 TYR C 558 PHE 0.018 0.002 PHE C 37 TRP 0.018 0.002 TRP C 98 HIS 0.005 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 8161) covalent geometry : angle 0.69180 (11141) SS BOND : bond 0.00394 ( 2) SS BOND : angle 1.82316 ( 4) hydrogen bonds : bond 0.04836 ( 365) hydrogen bonds : angle 5.17333 ( 996) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 186 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 VAL cc_start: 0.8583 (m) cc_final: 0.8311 (p) REVERT: C 256 TYR cc_start: 0.7327 (p90) cc_final: 0.6982 (p90) REVERT: C 627 ASP cc_start: 0.6827 (t0) cc_final: 0.6413 (t0) REVERT: C 718 GLU cc_start: 0.7860 (mp0) cc_final: 0.7278 (mp0) outliers start: 9 outliers final: 6 residues processed: 188 average time/residue: 0.4359 time to fit residues: 87.7890 Evaluate side-chains 182 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 176 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 413 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 4 optimal weight: 0.0370 chunk 100 optimal weight: 0.8980 chunk 80 optimal weight: 0.0980 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 overall best weight: 0.2258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.141944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.129640 restraints weight = 11667.386| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.98 r_work: 0.3619 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8163 Z= 0.127 Angle : 0.603 7.370 11145 Z= 0.304 Chirality : 0.043 0.155 1269 Planarity : 0.006 0.062 1440 Dihedral : 4.881 18.259 1139 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.26 % Allowed : 11.43 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.27), residues: 1000 helix: 0.59 (0.27), residues: 407 sheet: -1.52 (0.36), residues: 183 loop : -1.49 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 651 TYR 0.026 0.001 TYR C 558 PHE 0.015 0.001 PHE C 37 TRP 0.014 0.001 TRP C 98 HIS 0.003 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8161) covalent geometry : angle 0.60256 (11141) SS BOND : bond 0.00190 ( 2) SS BOND : angle 1.41260 ( 4) hydrogen bonds : bond 0.03971 ( 365) hydrogen bonds : angle 4.70449 ( 996) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 651 ARG cc_start: 0.7494 (ptt90) cc_final: 0.7279 (ptt90) REVERT: C 10 GLU cc_start: 0.6643 (tt0) cc_final: 0.5434 (tt0) REVERT: C 627 ASP cc_start: 0.6793 (t0) cc_final: 0.6347 (t0) REVERT: C 718 GLU cc_start: 0.7873 (mp0) cc_final: 0.7311 (mp0) outliers start: 18 outliers final: 9 residues processed: 201 average time/residue: 0.4537 time to fit residues: 97.3383 Evaluate side-chains 188 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 179 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 680 CYS Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 569 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 78 optimal weight: 0.5980 chunk 77 optimal weight: 0.0980 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 41 optimal weight: 0.0770 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.138913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.126730 restraints weight = 11897.024| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.95 r_work: 0.3607 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8163 Z= 0.152 Angle : 0.619 10.529 11145 Z= 0.307 Chirality : 0.044 0.144 1269 Planarity : 0.006 0.058 1440 Dihedral : 4.789 19.610 1139 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.51 % Allowed : 13.69 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.27), residues: 1000 helix: 0.56 (0.27), residues: 418 sheet: -1.46 (0.35), residues: 195 loop : -1.54 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 651 TYR 0.023 0.001 TYR C 558 PHE 0.027 0.002 PHE A 649 TRP 0.011 0.001 TRP C 98 HIS 0.003 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8161) covalent geometry : angle 0.61903 (11141) SS BOND : bond 0.00305 ( 2) SS BOND : angle 1.26356 ( 4) hydrogen bonds : bond 0.03981 ( 365) hydrogen bonds : angle 4.54842 ( 996) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 454 VAL cc_start: 0.8566 (m) cc_final: 0.8241 (p) REVERT: A 651 ARG cc_start: 0.7478 (ptt90) cc_final: 0.7152 (ptt90) REVERT: C 79 ARG cc_start: 0.7650 (mpt180) cc_final: 0.7450 (mpt90) REVERT: C 510 PHE cc_start: 0.8171 (m-80) cc_final: 0.7816 (m-80) REVERT: C 627 ASP cc_start: 0.6775 (t0) cc_final: 0.6393 (t0) REVERT: C 714 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7403 (mp0) REVERT: C 718 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7321 (mp0) outliers start: 20 outliers final: 12 residues processed: 184 average time/residue: 0.4230 time to fit residues: 83.4493 Evaluate side-chains 186 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 718 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 10 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 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 = 0.3862 r_free = 0.3862 target = 0.139427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.126842 restraints weight = 11659.665| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.97 r_work: 0.3577 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8163 Z= 0.227 Angle : 0.669 8.878 11145 Z= 0.333 Chirality : 0.047 0.166 1269 Planarity : 0.006 0.058 1440 Dihedral : 5.010 21.314 1139 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.52 % Allowed : 13.82 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.27), residues: 1000 helix: 0.51 (0.27), residues: 412 sheet: -1.44 (0.36), residues: 195 loop : -1.59 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 763 TYR 0.027 0.002 TYR C 558 PHE 0.029 0.002 PHE A 649 TRP 0.038 0.002 TRP C 8 HIS 0.005 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 8161) covalent geometry : angle 0.66836 (11141) SS BOND : bond 0.00458 ( 2) SS BOND : angle 1.32140 ( 4) hydrogen bonds : bond 0.04316 ( 365) hydrogen bonds : angle 4.66416 ( 996) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 651 ARG cc_start: 0.7561 (ptt90) cc_final: 0.7239 (ptt90) REVERT: A 766 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.8016 (mtm) REVERT: C 79 ARG cc_start: 0.7659 (mpt180) cc_final: 0.7444 (mpt90) REVERT: C 417 LEU cc_start: 0.7743 (mt) cc_final: 0.7528 (mp) REVERT: C 627 ASP cc_start: 0.6804 (t0) cc_final: 0.6382 (t0) REVERT: C 718 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7339 (mp0) outliers start: 28 outliers final: 21 residues processed: 194 average time/residue: 0.3883 time to fit residues: 81.0958 Evaluate side-chains 200 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 718 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 15 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 10 optimal weight: 0.0870 chunk 82 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 64 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 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 = 0.3871 r_free = 0.3871 target = 0.139494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.127144 restraints weight = 11588.947| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.94 r_work: 0.3603 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8163 Z= 0.158 Angle : 0.623 8.147 11145 Z= 0.309 Chirality : 0.044 0.142 1269 Planarity : 0.006 0.056 1440 Dihedral : 4.812 19.083 1139 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.64 % Allowed : 14.95 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.27), residues: 1000 helix: 0.62 (0.27), residues: 413 sheet: -1.26 (0.37), residues: 190 loop : -1.53 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 763 TYR 0.024 0.001 TYR C 558 PHE 0.030 0.002 PHE A 649 TRP 0.051 0.002 TRP C 8 HIS 0.004 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8161) covalent geometry : angle 0.62260 (11141) SS BOND : bond 0.00297 ( 2) SS BOND : angle 1.17344 ( 4) hydrogen bonds : bond 0.03935 ( 365) hydrogen bonds : angle 4.53347 ( 996) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 651 ARG cc_start: 0.7522 (ptt90) cc_final: 0.7295 (ptt90) REVERT: C 10 GLU cc_start: 0.6804 (tt0) cc_final: 0.5719 (tt0) REVERT: C 13 VAL cc_start: 0.6862 (OUTLIER) cc_final: 0.6590 (t) REVERT: C 417 LEU cc_start: 0.7730 (mt) cc_final: 0.7502 (mp) REVERT: C 510 PHE cc_start: 0.8161 (m-80) cc_final: 0.7770 (m-80) REVERT: C 627 ASP cc_start: 0.6774 (t0) cc_final: 0.6347 (t0) REVERT: C 718 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7343 (mp0) outliers start: 29 outliers final: 22 residues processed: 189 average time/residue: 0.4127 time to fit residues: 83.8344 Evaluate side-chains 198 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 680 CYS Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 718 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 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 = 0.3853 r_free = 0.3853 target = 0.137898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.125520 restraints weight = 11727.139| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.94 r_work: 0.3581 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8163 Z= 0.222 Angle : 0.670 9.012 11145 Z= 0.333 Chirality : 0.046 0.143 1269 Planarity : 0.006 0.054 1440 Dihedral : 4.985 24.347 1139 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.89 % Allowed : 15.58 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.27), residues: 1000 helix: 0.44 (0.26), residues: 419 sheet: -1.31 (0.36), residues: 195 loop : -1.54 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 584 TYR 0.020 0.002 TYR C 558 PHE 0.031 0.002 PHE A 649 TRP 0.038 0.002 TRP C 8 HIS 0.005 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 8161) covalent geometry : angle 0.66978 (11141) SS BOND : bond 0.00440 ( 2) SS BOND : angle 1.23457 ( 4) hydrogen bonds : bond 0.04233 ( 365) hydrogen bonds : angle 4.60903 ( 996) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: C 13 VAL cc_start: 0.6881 (OUTLIER) cc_final: 0.6617 (t) REVERT: C 256 TYR cc_start: 0.7309 (p90) cc_final: 0.6952 (p90) REVERT: C 417 LEU cc_start: 0.7740 (mt) cc_final: 0.7512 (mp) REVERT: C 627 ASP cc_start: 0.6805 (t0) cc_final: 0.6400 (t0) REVERT: C 718 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7351 (mp0) outliers start: 31 outliers final: 24 residues processed: 198 average time/residue: 0.4075 time to fit residues: 86.9803 Evaluate side-chains 208 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 718 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 98 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 95 optimal weight: 0.0870 chunk 38 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 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 = 0.3865 r_free = 0.3865 target = 0.138952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.126797 restraints weight = 11778.431| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.94 r_work: 0.3591 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8163 Z= 0.161 Angle : 0.646 10.067 11145 Z= 0.318 Chirality : 0.044 0.138 1269 Planarity : 0.006 0.058 1440 Dihedral : 4.847 23.502 1139 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.77 % Allowed : 16.21 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.27), residues: 1000 helix: 0.57 (0.27), residues: 419 sheet: -1.18 (0.37), residues: 190 loop : -1.52 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 763 TYR 0.023 0.002 TYR C 558 PHE 0.032 0.002 PHE A 649 TRP 0.044 0.002 TRP C 8 HIS 0.004 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8161) covalent geometry : angle 0.64596 (11141) SS BOND : bond 0.00309 ( 2) SS BOND : angle 1.15179 ( 4) hydrogen bonds : bond 0.03925 ( 365) hydrogen bonds : angle 4.52045 ( 996) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 651 ARG cc_start: 0.7396 (ptt90) cc_final: 0.7088 (ppt90) REVERT: C 10 GLU cc_start: 0.6789 (tt0) cc_final: 0.5915 (tt0) REVERT: C 13 VAL cc_start: 0.6825 (OUTLIER) cc_final: 0.6557 (t) REVERT: C 256 TYR cc_start: 0.7195 (p90) cc_final: 0.6863 (p90) REVERT: C 417 LEU cc_start: 0.7754 (mt) cc_final: 0.7518 (mp) REVERT: C 627 ASP cc_start: 0.6806 (t0) cc_final: 0.6388 (t0) REVERT: C 718 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7337 (mp0) outliers start: 30 outliers final: 24 residues processed: 190 average time/residue: 0.4181 time to fit residues: 85.0396 Evaluate side-chains 200 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain C residue 721 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 68 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 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 = 0.3857 r_free = 0.3857 target = 0.138249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.126093 restraints weight = 11823.597| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.94 r_work: 0.3583 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8163 Z= 0.197 Angle : 0.680 10.507 11145 Z= 0.334 Chirality : 0.046 0.137 1269 Planarity : 0.006 0.055 1440 Dihedral : 4.932 26.947 1139 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.89 % Allowed : 16.83 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.27), residues: 1000 helix: 0.49 (0.26), residues: 419 sheet: -1.22 (0.36), residues: 195 loop : -1.56 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 245 TYR 0.020 0.002 TYR C 645 PHE 0.020 0.002 PHE C 571 TRP 0.038 0.002 TRP C 8 HIS 0.005 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 8161) covalent geometry : angle 0.67934 (11141) SS BOND : bond 0.00410 ( 2) SS BOND : angle 1.15951 ( 4) hydrogen bonds : bond 0.04100 ( 365) hydrogen bonds : angle 4.56649 ( 996) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 607 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7917 (mm-40) REVERT: A 651 ARG cc_start: 0.7389 (ptt90) cc_final: 0.7146 (ptt90) REVERT: C 13 VAL cc_start: 0.6865 (OUTLIER) cc_final: 0.6596 (t) REVERT: C 256 TYR cc_start: 0.7211 (p90) cc_final: 0.6814 (p90) REVERT: C 313 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8074 (pp) REVERT: C 417 LEU cc_start: 0.7754 (mt) cc_final: 0.7518 (mp) REVERT: C 627 ASP cc_start: 0.6816 (t0) cc_final: 0.6364 (t0) REVERT: C 718 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7355 (mp0) outliers start: 31 outliers final: 23 residues processed: 191 average time/residue: 0.3792 time to fit residues: 78.3120 Evaluate side-chains 199 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain C residue 721 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 31 optimal weight: 0.0570 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.0010 chunk 36 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 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 = 0.3870 r_free = 0.3870 target = 0.139126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.127030 restraints weight = 11658.606| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.92 r_work: 0.3598 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8163 Z= 0.157 Angle : 0.656 9.481 11145 Z= 0.323 Chirality : 0.045 0.140 1269 Planarity : 0.006 0.058 1440 Dihedral : 4.785 25.863 1139 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.39 % Allowed : 17.59 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.27), residues: 1000 helix: 0.62 (0.27), residues: 418 sheet: -1.22 (0.36), residues: 195 loop : -1.55 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 40 TYR 0.017 0.002 TYR C 645 PHE 0.035 0.002 PHE A 649 TRP 0.047 0.002 TRP C 8 HIS 0.004 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8161) covalent geometry : angle 0.65563 (11141) SS BOND : bond 0.00285 ( 2) SS BOND : angle 1.13241 ( 4) hydrogen bonds : bond 0.03871 ( 365) hydrogen bonds : angle 4.48760 ( 996) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 454 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8245 (p) REVERT: A 584 ARG cc_start: 0.7436 (mpp80) cc_final: 0.6565 (mpp80) REVERT: A 651 ARG cc_start: 0.7361 (ptt90) cc_final: 0.7128 (ptt90) REVERT: C 10 GLU cc_start: 0.6751 (tt0) cc_final: 0.5991 (tm-30) REVERT: C 13 VAL cc_start: 0.6803 (OUTLIER) cc_final: 0.6550 (t) REVERT: C 40 ARG cc_start: 0.7802 (mmt90) cc_final: 0.7516 (mtt-85) REVERT: C 256 TYR cc_start: 0.7119 (p90) cc_final: 0.6753 (p90) REVERT: C 313 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8129 (pp) REVERT: C 417 LEU cc_start: 0.7747 (mt) cc_final: 0.7525 (mp) REVERT: C 523 VAL cc_start: 0.7830 (OUTLIER) cc_final: 0.7575 (m) REVERT: C 627 ASP cc_start: 0.6763 (t0) cc_final: 0.6400 (t0) REVERT: C 718 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7335 (mp0) outliers start: 27 outliers final: 22 residues processed: 187 average time/residue: 0.3940 time to fit residues: 79.3334 Evaluate side-chains 199 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 718 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 0.0970 chunk 60 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 99 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 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 = 0.3862 r_free = 0.3862 target = 0.138491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.126260 restraints weight = 11735.248| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.96 r_work: 0.3589 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8163 Z= 0.172 Angle : 0.663 9.734 11145 Z= 0.327 Chirality : 0.045 0.144 1269 Planarity : 0.006 0.053 1440 Dihedral : 4.786 27.283 1139 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.52 % Allowed : 17.59 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.27), residues: 1000 helix: 0.62 (0.26), residues: 418 sheet: -1.13 (0.37), residues: 190 loop : -1.54 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 245 TYR 0.012 0.002 TYR C 558 PHE 0.031 0.002 PHE A 649 TRP 0.032 0.002 TRP C 8 HIS 0.004 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 8161) covalent geometry : angle 0.66319 (11141) SS BOND : bond 0.00334 ( 2) SS BOND : angle 1.11409 ( 4) hydrogen bonds : bond 0.03940 ( 365) hydrogen bonds : angle 4.49160 ( 996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2838.07 seconds wall clock time: 48 minutes 58.16 seconds (2938.16 seconds total)