Starting phenix.real_space_refine on Fri Aug 2 23:14:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q74_18203/08_2024/8q74_18203.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q74_18203/08_2024/8q74_18203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q74_18203/08_2024/8q74_18203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q74_18203/08_2024/8q74_18203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q74_18203/08_2024/8q74_18203.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q74_18203/08_2024/8q74_18203.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Cu 1 5.60 5 S 34 5.16 5 C 3812 2.51 5 N 988 2.21 5 O 1108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 218": "OE1" <-> "OE2" Residue "A ASP 353": "OD1" <-> "OD2" Residue "A TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 573": "OE1" <-> "OE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 782": "OE1" <-> "OE2" Residue "A GLU 831": "OE1" <-> "OE2" Residue "A TYR 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 5943 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 5942 Classifications: {'peptide': 783} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 745} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3243 SG CYS A 597 27.486 24.901 48.334 1.00140.08 S ATOM 3256 SG CYS A 599 28.127 29.237 48.453 1.00142.78 S Time building chain proxies: 4.27, per 1000 atoms: 0.72 Number of scatterers: 5943 At special positions: 0 Unit cell: (80.408, 86.3328, 141.349, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cu 1 28.99 S 34 16.00 O 1108 8.00 N 988 7.00 C 3812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.46 Conformation dependent library (CDL) restraints added in 1.2 seconds 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1448 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 4 sheets defined 53.6% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 197 through 209 removed outlier: 4.285A pdb=" N ARG A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 248 removed outlier: 3.599A pdb=" N ALA A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 296 removed outlier: 3.793A pdb=" N PHE A 286 " --> pdb=" O TRP A 282 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 297 through 300 Processing helix chain 'A' and resid 302 through 308 Processing helix chain 'A' and resid 317 through 332 Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 335 through 348 removed outlier: 6.499A pdb=" N ALA A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 377 removed outlier: 3.696A pdb=" N LEU A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 420 removed outlier: 4.094A pdb=" N ILE A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 531 removed outlier: 3.635A pdb=" N GLN A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 545 Processing helix chain 'A' and resid 546 through 567 removed outlier: 3.520A pdb=" N TRP A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 3.638A pdb=" N LEU A 593 " --> pdb=" O GLY A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 618 removed outlier: 4.010A pdb=" N MET A 610 " --> pdb=" O PRO A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 634 Processing helix chain 'A' and resid 682 through 693 removed outlier: 4.373A pdb=" N THR A 690 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 691 " --> pdb=" O VAL A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 743 through 756 removed outlier: 3.825A pdb=" N GLU A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 768 Processing helix chain 'A' and resid 782 through 794 Processing helix chain 'A' and resid 804 through 816 Processing helix chain 'A' and resid 825 through 839 Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'A' and resid 869 through 876 removed outlier: 3.900A pdb=" N ILE A 873 " --> pdb=" O THR A 869 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 875 " --> pdb=" O VAL A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 922 removed outlier: 4.123A pdb=" N ILE A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 890 " --> pdb=" O GLU A 886 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 892 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 913 " --> pdb=" O ALA A 909 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 915 " --> pdb=" O GLY A 911 " (cutoff:3.500A) Proline residue: A 918 - end of helix Processing helix chain 'A' and resid 924 through 929 Processing helix chain 'A' and resid 933 through 954 removed outlier: 4.146A pdb=" N ALA A 939 " --> pdb=" O TRP A 935 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET A 941 " --> pdb=" O ALA A 937 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 954 " --> pdb=" O CYS A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 958 Processing sheet with id=AA1, first strand: chain 'A' and resid 310 through 312 removed outlier: 3.628A pdb=" N VAL A 311 " --> pdb=" O MET A 315 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N MET A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 424 through 425 Processing sheet with id=AA3, first strand: chain 'A' and resid 454 through 455 removed outlier: 4.082A pdb=" N CYS A 504 " --> pdb=" O GLN A 471 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 820 through 821 removed outlier: 8.929A pdb=" N PHE A 821 " --> pdb=" O SER A 797 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N MET A 799 " --> pdb=" O PHE A 821 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA A 637 " --> pdb=" O ALA A 844 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 831 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: 1.60 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1893 1.34 - 1.46: 801 1.46 - 1.57: 3309 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 6057 Sorted by residual: bond pdb=" CA CYS A 597 " pdb=" C CYS A 597 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.26e-02 6.30e+03 1.59e+01 bond pdb=" CA CYS A 599 " pdb=" C CYS A 599 " ideal model delta sigma weight residual 1.527 1.495 0.032 1.30e-02 5.92e+03 5.93e+00 bond pdb=" CA MET A 352 " pdb=" C MET A 352 " ideal model delta sigma weight residual 1.524 1.497 0.027 1.28e-02 6.10e+03 4.59e+00 bond pdb=" N ALA A 600 " pdb=" CA ALA A 600 " ideal model delta sigma weight residual 1.458 1.433 0.026 1.26e-02 6.30e+03 4.14e+00 bond pdb=" CA ASP A 353 " pdb=" C ASP A 353 " ideal model delta sigma weight residual 1.525 1.499 0.026 1.37e-02 5.33e+03 3.62e+00 ... (remaining 6052 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.57: 184 106.57 - 113.47: 3405 113.47 - 120.36: 2134 120.36 - 127.25: 2444 127.25 - 134.14: 59 Bond angle restraints: 8226 Sorted by residual: angle pdb=" N ALA A 600 " pdb=" CA ALA A 600 " pdb=" C ALA A 600 " ideal model delta sigma weight residual 111.69 103.10 8.59 1.23e+00 6.61e-01 4.88e+01 angle pdb=" C THR A 656 " pdb=" N LYS A 657 " pdb=" CA LYS A 657 " ideal model delta sigma weight residual 122.11 112.10 10.01 1.59e+00 3.96e-01 3.97e+01 angle pdb=" N VAL A 311 " pdb=" CA VAL A 311 " pdb=" C VAL A 311 " ideal model delta sigma weight residual 113.53 108.53 5.00 9.80e-01 1.04e+00 2.60e+01 angle pdb=" C LYS A 657 " pdb=" N VAL A 658 " pdb=" CA VAL A 658 " ideal model delta sigma weight residual 120.13 128.17 -8.04 1.58e+00 4.01e-01 2.59e+01 angle pdb=" N TRP A 335 " pdb=" CA TRP A 335 " pdb=" C TRP A 335 " ideal model delta sigma weight residual 113.43 107.54 5.89 1.26e+00 6.30e-01 2.18e+01 ... (remaining 8221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 3320 17.59 - 35.18: 277 35.18 - 52.77: 34 52.77 - 70.36: 13 70.36 - 87.95: 8 Dihedral angle restraints: 3652 sinusoidal: 1403 harmonic: 2249 Sorted by residual: dihedral pdb=" CA PRO A 250 " pdb=" C PRO A 250 " pdb=" N PRO A 251 " pdb=" CA PRO A 251 " ideal model delta harmonic sigma weight residual 180.00 139.23 40.77 0 5.00e+00 4.00e-02 6.65e+01 dihedral pdb=" CA ASN A 721 " pdb=" C ASN A 721 " pdb=" N VAL A 722 " pdb=" CA VAL A 722 " ideal model delta harmonic sigma weight residual 180.00 -144.73 -35.27 0 5.00e+00 4.00e-02 4.98e+01 dihedral pdb=" CA GLY A 724 " pdb=" C GLY A 724 " pdb=" N LYS A 725 " pdb=" CA LYS A 725 " ideal model delta harmonic sigma weight residual 180.00 -153.04 -26.96 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 3649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 705 0.048 - 0.096: 209 0.096 - 0.144: 50 0.144 - 0.192: 8 0.192 - 0.240: 2 Chirality restraints: 974 Sorted by residual: chirality pdb=" CB ILE A 704 " pdb=" CA ILE A 704 " pdb=" CG1 ILE A 704 " pdb=" CG2 ILE A 704 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA THR A 656 " pdb=" N THR A 656 " pdb=" C THR A 656 " pdb=" CB THR A 656 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.31e-01 chirality pdb=" CB ILE A 662 " pdb=" CA ILE A 662 " pdb=" CG1 ILE A 662 " pdb=" CG2 ILE A 662 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 971 not shown) Planarity restraints: 1041 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 662 " -0.050 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO A 663 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 663 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 663 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 570 " -0.047 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO A 571 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 571 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 571 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 740 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.83e+00 pdb=" N PRO A 741 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 741 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 741 " 0.036 5.00e-02 4.00e+02 ... (remaining 1038 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.29: 12 2.29 - 2.94: 2793 2.94 - 3.59: 9757 3.59 - 4.25: 14043 4.25 - 4.90: 22453 Nonbonded interactions: 49058 Sorted by model distance: nonbonded pdb=" CE MET A 352 " pdb="CU CU A1001 " model vdw 1.633 2.660 nonbonded pdb=" SG CYS A 597 " pdb="CU CU A1001 " model vdw 2.079 2.600 nonbonded pdb=" SD MET A 352 " pdb="CU CU A1001 " model vdw 2.087 2.600 nonbonded pdb=" SD MET A 352 " pdb=" SG CYS A 599 " model vdw 2.135 3.760 nonbonded pdb=" O VAL A 687 " pdb=" OG1 THR A 690 " model vdw 2.178 3.040 ... (remaining 49053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.800 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 26.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.004 0.071 6057 Z= 0.294 Angle : 1.020 12.117 8226 Z= 0.613 Chirality : 0.048 0.240 974 Planarity : 0.008 0.077 1041 Dihedral : 14.005 87.951 2204 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.90 % Allowed : 15.88 % Favored : 83.23 % Rotamer: Outliers : 0.15 % Allowed : 1.23 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 2.78 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.30), residues: 781 helix: 0.65 (0.28), residues: 366 sheet: -3.40 (0.73), residues: 30 loop : -3.90 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 558 HIS 0.009 0.001 HIS A 473 PHE 0.020 0.002 PHE A 582 TYR 0.028 0.002 TYR A 689 ARG 0.008 0.001 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 PHE cc_start: 0.9357 (m-80) cc_final: 0.9065 (m-80) REVERT: A 315 MET cc_start: 0.9055 (ppp) cc_final: 0.8799 (tmm) REVERT: A 319 MET cc_start: 0.8325 (mpp) cc_final: 0.8016 (mtp) REVERT: A 331 PHE cc_start: 0.7861 (m-80) cc_final: 0.7285 (m-80) REVERT: A 686 ILE cc_start: 0.9548 (mt) cc_final: 0.9235 (mt) REVERT: A 790 LEU cc_start: 0.9583 (mt) cc_final: 0.9329 (pp) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.1515 time to fit residues: 16.8727 Evaluate side-chains 46 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 32 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 0.0010 overall best weight: 0.8966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN A 448 GLN A 721 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6057 Z= 0.242 Angle : 0.849 9.258 8226 Z= 0.438 Chirality : 0.047 0.178 974 Planarity : 0.006 0.066 1041 Dihedral : 6.495 38.844 826 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.77 % Allowed : 15.24 % Favored : 83.99 % Rotamer: Outliers : 1.23 % Allowed : 10.48 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 2.78 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.31), residues: 781 helix: 0.92 (0.27), residues: 383 sheet: -3.04 (0.76), residues: 31 loop : -3.68 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 558 HIS 0.012 0.001 HIS A 473 PHE 0.027 0.002 PHE A 293 TYR 0.017 0.002 TYR A 253 ARG 0.006 0.001 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 282 TRP cc_start: 0.8183 (m100) cc_final: 0.7982 (m-10) REVERT: A 315 MET cc_start: 0.9103 (ppp) cc_final: 0.8831 (tmm) REVERT: A 319 MET cc_start: 0.8405 (mpp) cc_final: 0.8127 (mpp) REVERT: A 601 LEU cc_start: 0.9165 (mm) cc_final: 0.8821 (mm) REVERT: A 689 TYR cc_start: 0.8950 (p90) cc_final: 0.8603 (p90) REVERT: A 799 MET cc_start: 0.8990 (ppp) cc_final: 0.8379 (ppp) outliers start: 8 outliers final: 4 residues processed: 62 average time/residue: 0.1306 time to fit residues: 12.0525 Evaluate side-chains 47 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 899 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 53 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6057 Z= 0.206 Angle : 0.782 8.662 8226 Z= 0.403 Chirality : 0.046 0.180 974 Planarity : 0.006 0.062 1041 Dihedral : 6.236 35.898 826 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.77 % Allowed : 13.44 % Favored : 85.79 % Rotamer: Outliers : 2.31 % Allowed : 14.18 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 2.78 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.30), residues: 781 helix: 1.05 (0.27), residues: 389 sheet: -2.16 (0.88), residues: 21 loop : -3.72 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 558 HIS 0.011 0.001 HIS A 473 PHE 0.023 0.002 PHE A 331 TYR 0.012 0.001 TYR A 689 ARG 0.004 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 MET cc_start: 0.8428 (mpp) cc_final: 0.8155 (mpp) REVERT: A 331 PHE cc_start: 0.8726 (m-80) cc_final: 0.8353 (m-80) REVERT: A 689 TYR cc_start: 0.8992 (p90) cc_final: 0.8579 (p90) REVERT: A 799 MET cc_start: 0.8924 (ppp) cc_final: 0.8480 (ppp) outliers start: 15 outliers final: 10 residues processed: 67 average time/residue: 0.1304 time to fit residues: 12.9455 Evaluate side-chains 57 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 946 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6057 Z= 0.196 Angle : 0.760 11.906 8226 Z= 0.387 Chirality : 0.045 0.218 974 Planarity : 0.006 0.061 1041 Dihedral : 6.101 37.192 826 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.77 % Allowed : 13.83 % Favored : 85.40 % Rotamer: Outliers : 2.93 % Allowed : 13.56 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 2.78 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.31), residues: 781 helix: 1.14 (0.27), residues: 402 sheet: -1.89 (0.88), residues: 21 loop : -3.64 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 558 HIS 0.011 0.001 HIS A 473 PHE 0.018 0.002 PHE A 293 TYR 0.020 0.001 TYR A 689 ARG 0.003 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 49 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.9493 (t80) cc_final: 0.9241 (t80) REVERT: A 315 MET cc_start: 0.9241 (tmm) cc_final: 0.8992 (tmm) REVERT: A 319 MET cc_start: 0.8472 (mpp) cc_final: 0.8225 (mpp) REVERT: A 331 PHE cc_start: 0.8760 (m-80) cc_final: 0.8414 (m-80) REVERT: A 689 TYR cc_start: 0.9016 (p90) cc_final: 0.8559 (p90) REVERT: A 705 MET cc_start: 0.8802 (ppp) cc_final: 0.8545 (ppp) REVERT: A 799 MET cc_start: 0.8928 (ppp) cc_final: 0.8652 (tmm) REVERT: A 845 MET cc_start: 0.8466 (ppp) cc_final: 0.7867 (ptm) REVERT: A 881 MET cc_start: 0.9251 (tpp) cc_final: 0.9020 (tmm) outliers start: 19 outliers final: 11 residues processed: 65 average time/residue: 0.1323 time to fit residues: 12.7166 Evaluate side-chains 56 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 946 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 52 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 38 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 30.0000 chunk 14 optimal weight: 1.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 6057 Z= 0.506 Angle : 0.901 10.635 8226 Z= 0.470 Chirality : 0.049 0.165 974 Planarity : 0.006 0.060 1041 Dihedral : 6.302 38.144 826 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.77 % Allowed : 14.60 % Favored : 84.64 % Rotamer: Outliers : 4.31 % Allowed : 16.80 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.30), residues: 781 helix: 0.72 (0.26), residues: 387 sheet: -1.99 (1.12), residues: 23 loop : -3.54 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 558 HIS 0.011 0.002 HIS A 473 PHE 0.032 0.003 PHE A 395 TYR 0.022 0.002 TYR A 253 ARG 0.006 0.001 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 39 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.9407 (t80) cc_final: 0.9091 (t80) REVERT: A 319 MET cc_start: 0.8589 (mpp) cc_final: 0.8292 (mpp) REVERT: A 331 PHE cc_start: 0.8930 (m-80) cc_final: 0.8399 (m-80) REVERT: A 689 TYR cc_start: 0.9277 (p90) cc_final: 0.8841 (p90) REVERT: A 705 MET cc_start: 0.8840 (ppp) cc_final: 0.8529 (ppp) REVERT: A 799 MET cc_start: 0.8977 (ppp) cc_final: 0.8705 (tmm) outliers start: 28 outliers final: 21 residues processed: 64 average time/residue: 0.1399 time to fit residues: 13.0643 Evaluate side-chains 60 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 39 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 949 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 40.0000 chunk 24 optimal weight: 40.0000 chunk 39 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6057 Z= 0.210 Angle : 0.750 10.093 8226 Z= 0.385 Chirality : 0.046 0.148 974 Planarity : 0.006 0.062 1041 Dihedral : 6.129 38.182 826 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.80 % Favored : 86.30 % Rotamer: Outliers : 3.39 % Allowed : 18.64 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.30), residues: 781 helix: 1.04 (0.26), residues: 405 sheet: -2.10 (0.91), residues: 21 loop : -3.69 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 558 HIS 0.011 0.001 HIS A 473 PHE 0.010 0.002 PHE A 710 TYR 0.019 0.001 TYR A 689 ARG 0.002 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 45 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.9430 (t80) cc_final: 0.9135 (t80) REVERT: A 315 MET cc_start: 0.9290 (tmm) cc_final: 0.9000 (tmm) REVERT: A 319 MET cc_start: 0.8459 (mpp) cc_final: 0.8165 (mpp) REVERT: A 331 PHE cc_start: 0.8870 (m-80) cc_final: 0.8387 (m-80) REVERT: A 689 TYR cc_start: 0.9157 (p90) cc_final: 0.8706 (p90) REVERT: A 705 MET cc_start: 0.8841 (ppp) cc_final: 0.8528 (ppp) REVERT: A 799 MET cc_start: 0.8960 (ppp) cc_final: 0.8698 (tmm) REVERT: A 845 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7915 (ptp) outliers start: 22 outliers final: 15 residues processed: 63 average time/residue: 0.1601 time to fit residues: 14.4462 Evaluate side-chains 60 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 CYS Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 946 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 75 optimal weight: 0.0670 chunk 47 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 40.0000 chunk 44 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6057 Z= 0.236 Angle : 0.764 11.574 8226 Z= 0.387 Chirality : 0.046 0.144 974 Planarity : 0.006 0.059 1041 Dihedral : 6.002 38.070 826 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.42 % Favored : 86.68 % Rotamer: Outliers : 2.77 % Allowed : 19.88 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.31), residues: 781 helix: 1.18 (0.26), residues: 399 sheet: -2.65 (0.84), residues: 33 loop : -3.61 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 558 HIS 0.011 0.001 HIS A 473 PHE 0.012 0.002 PHE A 395 TYR 0.017 0.001 TYR A 689 ARG 0.002 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 48 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.9298 (tmm) cc_final: 0.8983 (tmm) REVERT: A 319 MET cc_start: 0.8520 (mpp) cc_final: 0.8209 (mpp) REVERT: A 331 PHE cc_start: 0.8859 (m-80) cc_final: 0.8409 (m-80) REVERT: A 689 TYR cc_start: 0.9247 (p90) cc_final: 0.8805 (p90) REVERT: A 705 MET cc_start: 0.8749 (ppp) cc_final: 0.8497 (ppp) REVERT: A 799 MET cc_start: 0.8972 (ppp) cc_final: 0.8699 (tmm) REVERT: A 845 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7755 (ptp) outliers start: 18 outliers final: 17 residues processed: 61 average time/residue: 0.1446 time to fit residues: 12.7278 Evaluate side-chains 64 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 46 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 946 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.5980 chunk 47 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 72 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6057 Z= 0.208 Angle : 0.746 12.359 8226 Z= 0.379 Chirality : 0.045 0.192 974 Planarity : 0.005 0.058 1041 Dihedral : 5.936 38.350 826 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.68 % Favored : 86.43 % Rotamer: Outliers : 3.39 % Allowed : 19.26 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.31), residues: 781 helix: 1.21 (0.26), residues: 400 sheet: -2.68 (0.71), residues: 41 loop : -3.70 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 558 HIS 0.011 0.001 HIS A 473 PHE 0.013 0.002 PHE A 291 TYR 0.018 0.001 TYR A 689 ARG 0.002 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 47 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.9298 (tmm) cc_final: 0.8946 (tmm) REVERT: A 319 MET cc_start: 0.8494 (mpp) cc_final: 0.8207 (mpp) REVERT: A 331 PHE cc_start: 0.8868 (m-80) cc_final: 0.8413 (m-80) REVERT: A 689 TYR cc_start: 0.9247 (p90) cc_final: 0.8830 (p90) REVERT: A 705 MET cc_start: 0.8682 (ppp) cc_final: 0.8450 (ppp) REVERT: A 799 MET cc_start: 0.8984 (ppp) cc_final: 0.8719 (tmm) REVERT: A 845 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7830 (ptp) outliers start: 22 outliers final: 18 residues processed: 64 average time/residue: 0.1569 time to fit residues: 14.3852 Evaluate side-chains 64 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 45 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 CYS Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 946 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 46 optimal weight: 0.0070 chunk 74 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 837 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6057 Z= 0.240 Angle : 0.793 15.081 8226 Z= 0.398 Chirality : 0.047 0.391 974 Planarity : 0.006 0.067 1041 Dihedral : 5.968 38.675 826 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.68 % Favored : 86.43 % Rotamer: Outliers : 3.54 % Allowed : 19.11 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.30), residues: 781 helix: 1.09 (0.26), residues: 400 sheet: -2.42 (0.84), residues: 23 loop : -3.64 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 558 HIS 0.011 0.001 HIS A 473 PHE 0.012 0.001 PHE A 395 TYR 0.018 0.001 TYR A 689 ARG 0.002 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 46 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LYS cc_start: 0.9773 (mmtm) cc_final: 0.9270 (tppt) REVERT: A 319 MET cc_start: 0.8513 (mpp) cc_final: 0.8217 (mpp) REVERT: A 331 PHE cc_start: 0.8871 (m-80) cc_final: 0.8426 (m-80) REVERT: A 689 TYR cc_start: 0.9272 (p90) cc_final: 0.8843 (p90) REVERT: A 705 MET cc_start: 0.8699 (ppp) cc_final: 0.8482 (ppp) REVERT: A 799 MET cc_start: 0.8974 (ppp) cc_final: 0.8701 (tmm) REVERT: A 845 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7803 (ptp) outliers start: 23 outliers final: 19 residues processed: 63 average time/residue: 0.1487 time to fit residues: 13.6005 Evaluate side-chains 66 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 46 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 CYS Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 949 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 6 optimal weight: 30.0000 chunk 47 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.0570 chunk 65 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6057 Z= 0.191 Angle : 0.774 13.985 8226 Z= 0.383 Chirality : 0.046 0.338 974 Planarity : 0.006 0.074 1041 Dihedral : 5.839 38.954 826 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.29 % Favored : 86.81 % Rotamer: Outliers : 2.47 % Allowed : 20.65 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.31), residues: 781 helix: 1.20 (0.27), residues: 399 sheet: -2.26 (0.83), residues: 23 loop : -3.61 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 323 HIS 0.011 0.001 HIS A 473 PHE 0.010 0.001 PHE A 659 TYR 0.019 0.001 TYR A 689 ARG 0.002 0.000 ARG A 347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.9273 (tmm) cc_final: 0.9069 (tmm) REVERT: A 319 MET cc_start: 0.8455 (mpp) cc_final: 0.8197 (mpp) REVERT: A 331 PHE cc_start: 0.8859 (m-80) cc_final: 0.8490 (m-80) REVERT: A 689 TYR cc_start: 0.9256 (p90) cc_final: 0.8819 (p90) REVERT: A 799 MET cc_start: 0.8991 (ppp) cc_final: 0.8732 (tmm) REVERT: A 845 MET cc_start: 0.8218 (ttm) cc_final: 0.7896 (ptp) outliers start: 16 outliers final: 14 residues processed: 60 average time/residue: 0.1444 time to fit residues: 12.5913 Evaluate side-chains 62 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 CYS Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 949 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 0.0970 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.103706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.063423 restraints weight = 24411.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.065283 restraints weight = 10596.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.066316 restraints weight = 6938.551| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6057 Z= 0.208 Angle : 0.809 21.134 8226 Z= 0.395 Chirality : 0.046 0.303 974 Planarity : 0.006 0.078 1041 Dihedral : 5.788 39.250 826 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.29 % Favored : 86.81 % Rotamer: Outliers : 2.62 % Allowed : 20.18 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.31), residues: 781 helix: 1.28 (0.27), residues: 399 sheet: -2.18 (0.83), residues: 23 loop : -3.57 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 558 HIS 0.012 0.001 HIS A 473 PHE 0.009 0.001 PHE A 395 TYR 0.017 0.001 TYR A 689 ARG 0.002 0.000 ARG A 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1525.00 seconds wall clock time: 27 minutes 58.78 seconds (1678.78 seconds total)