Starting phenix.real_space_refine on Tue Mar 11 14:29:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q73_18202/03_2025/8q73_18202.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q73_18202/03_2025/8q73_18202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q73_18202/03_2025/8q73_18202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q73_18202/03_2025/8q73_18202.map" model { file = "/net/cci-nas-00/data/ceres_data/8q73_18202/03_2025/8q73_18202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q73_18202/03_2025/8q73_18202.cif" } resolution = 3.58 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 3792 2.51 5 N 982 2.21 5 O 1101 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5909 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5909 Classifications: {'peptide': 779} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 742} Time building chain proxies: 4.66, per 1000 atoms: 0.79 Number of scatterers: 5909 At special positions: 0 Unit cell: (80.9998, 93.0636, 144.766, 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 34 16.00 O 1101 8.00 N 982 7.00 C 3792 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 - 3.00 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: 1.57 Conformation dependent library (CDL) restraints added in 1.4 seconds 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 52.2% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 197 through 211 removed outlier: 4.172A pdb=" N ILE A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 264 through 297 removed outlier: 3.548A pdb=" N PHE A 286 " --> pdb=" O TRP A 282 " (cutoff:3.500A) Proline residue: A 289 - end of helix removed outlier: 4.073A pdb=" N SER A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 297 " --> pdb=" O PHE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 Processing helix chain 'A' and resid 317 through 325 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.652A pdb=" N GLN A 330 " --> pdb=" O CYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 348 removed outlier: 3.720A pdb=" N TYR A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N HIS A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A 347 " --> pdb=" O HIS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 377 removed outlier: 3.780A pdb=" N LEU A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 412 removed outlier: 3.539A pdb=" N ALA A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 removed outlier: 4.794A pdb=" N LYS A 416 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 515 removed outlier: 3.743A pdb=" N GLU A 515 " --> pdb=" O VAL A 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 512 through 515' Processing helix chain 'A' and resid 516 through 529 Processing helix chain 'A' and resid 534 through 567 removed outlier: 3.939A pdb=" N LEU A 538 " --> pdb=" O PRO A 534 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) Proline residue: A 548 - end of helix removed outlier: 3.658A pdb=" N THR A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 591 removed outlier: 3.665A pdb=" N LEU A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 620 Processing helix chain 'A' and resid 625 through 632 removed outlier: 3.628A pdb=" N LEU A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 676 Processing helix chain 'A' and resid 680 through 698 Processing helix chain 'A' and resid 731 through 738 Processing helix chain 'A' and resid 743 through 757 removed outlier: 3.906A pdb=" N GLU A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 794 removed outlier: 4.187A pdb=" N SER A 788 " --> pdb=" O GLY A 784 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR A 789 " --> pdb=" O ARG A 785 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 791 " --> pdb=" O ILE A 787 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 815 removed outlier: 3.898A pdb=" N VAL A 815 " --> pdb=" O ILE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 840 removed outlier: 3.525A pdb=" N GLY A 840 " --> pdb=" O LEU A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 859 removed outlier: 3.548A pdb=" N LEU A 856 " --> pdb=" O ASP A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 874 removed outlier: 4.170A pdb=" N ILE A 873 " --> pdb=" O THR A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 913 removed outlier: 4.225A pdb=" N ILE A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 890 " --> pdb=" O GLU A 886 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 894 " --> pdb=" O THR A 890 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 910 " --> pdb=" O TYR A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 942 removed outlier: 3.523A pdb=" N ALA A 942 " --> pdb=" O GLY A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 954 removed outlier: 5.032A pdb=" N VAL A 948 " --> pdb=" O SER A 944 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N VAL A 949 " --> pdb=" O SER A 945 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 310 through 312 removed outlier: 3.518A pdb=" N VAL A 311 " --> pdb=" O MET A 315 " (cutoff:3.500A) removed outlier: 7.024A 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 429 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.571A pdb=" N GLY A 465 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 492 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 484 through 488 removed outlier: 6.229A pdb=" N ASN A 475 " --> pdb=" O ASN A 500 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ASN A 500 " --> pdb=" O ASN A 475 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 621 through 623 removed outlier: 3.781A pdb=" N VAL A 879 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 820 through 821 removed outlier: 8.678A pdb=" N PHE A 821 " --> pdb=" O SER A 797 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N MET A 799 " --> pdb=" O PHE A 821 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE A 638 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 800 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N MET A 845 " --> pdb=" O LEU A 863 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 652 through 655 removed outlier: 6.782A pdb=" N SER A 774 " --> pdb=" O VAL A 654 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 728 through 729 removed outlier: 4.984A pdb=" N VAL A 763 " --> pdb=" O CYS A 770 " (cutoff:3.500A) 281 hydrogen bonds defined for protein. 816 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: 1.86 Time building geometry restraints manager: 1.86 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: 1882 1.34 - 1.46: 844 1.46 - 1.58: 3243 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 6023 Sorted by residual: bond pdb=" N PRO A 457 " pdb=" CD PRO A 457 " ideal model delta sigma weight residual 1.473 1.425 0.048 1.40e-02 5.10e+03 1.17e+01 bond pdb=" CA PRO A 457 " pdb=" CB PRO A 457 " ideal model delta sigma weight residual 1.532 1.569 -0.037 1.34e-02 5.57e+03 7.60e+00 bond pdb=" CG PRO A 457 " pdb=" CD PRO A 457 " ideal model delta sigma weight residual 1.503 1.567 -0.064 3.40e-02 8.65e+02 3.56e+00 bond pdb=" C HIS A 680 " pdb=" N PRO A 681 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.28e-02 6.10e+03 3.21e+00 bond pdb=" C ASP A 825 " pdb=" N PRO A 826 " ideal model delta sigma weight residual 1.333 1.355 -0.021 1.44e-02 4.82e+03 2.21e+00 ... (remaining 6018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 8043 2.88 - 5.76: 116 5.76 - 8.64: 19 8.64 - 11.52: 1 11.52 - 14.40: 1 Bond angle restraints: 8180 Sorted by residual: angle pdb=" N VAL A 594 " pdb=" CA VAL A 594 " pdb=" C VAL A 594 " ideal model delta sigma weight residual 113.71 106.73 6.98 9.50e-01 1.11e+00 5.40e+01 angle pdb=" CA PRO A 457 " pdb=" N PRO A 457 " pdb=" CD PRO A 457 " ideal model delta sigma weight residual 112.00 104.27 7.73 1.40e+00 5.10e-01 3.05e+01 angle pdb=" C GLY A 816 " pdb=" N ILE A 817 " pdb=" CA ILE A 817 " ideal model delta sigma weight residual 121.97 131.34 -9.37 1.80e+00 3.09e-01 2.71e+01 angle pdb=" N LEU A 915 " pdb=" CA LEU A 915 " pdb=" C LEU A 915 " ideal model delta sigma weight residual 114.16 106.62 7.54 1.48e+00 4.57e-01 2.60e+01 angle pdb=" N CYS A 599 " pdb=" CA CYS A 599 " pdb=" C CYS A 599 " ideal model delta sigma weight residual 114.09 106.91 7.18 1.55e+00 4.16e-01 2.15e+01 ... (remaining 8175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 3308 17.80 - 35.60: 264 35.60 - 53.39: 31 53.39 - 71.19: 18 71.19 - 88.99: 11 Dihedral angle restraints: 3632 sinusoidal: 1395 harmonic: 2237 Sorted by residual: dihedral pdb=" CA VAL A 914 " pdb=" C VAL A 914 " pdb=" N LEU A 915 " pdb=" CA LEU A 915 " ideal model delta harmonic sigma weight residual 180.00 145.74 34.26 0 5.00e+00 4.00e-02 4.69e+01 dihedral pdb=" CA SER A 301 " pdb=" C SER A 301 " pdb=" N PRO A 302 " pdb=" CA PRO A 302 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA LYS A 780 " pdb=" C LYS A 780 " pdb=" N PRO A 781 " pdb=" CA PRO A 781 " ideal model delta harmonic sigma weight residual -180.00 -157.76 -22.24 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 3629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 596 0.035 - 0.070: 240 0.070 - 0.105: 95 0.105 - 0.140: 30 0.140 - 0.175: 8 Chirality restraints: 969 Sorted by residual: chirality pdb=" CA VAL A 648 " pdb=" N VAL A 648 " pdb=" C VAL A 648 " pdb=" CB VAL A 648 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA VAL A 474 " pdb=" N VAL A 474 " pdb=" C VAL A 474 " pdb=" CB VAL A 474 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA VAL A 635 " pdb=" N VAL A 635 " pdb=" C VAL A 635 " pdb=" CB VAL A 635 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 966 not shown) Planarity restraints: 1035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 597 " -0.052 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO A 598 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 598 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 598 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 662 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO A 663 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 663 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 663 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 301 " -0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO A 302 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.034 5.00e-02 4.00e+02 ... (remaining 1032 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1093 2.77 - 3.31: 6313 3.31 - 3.84: 9865 3.84 - 4.37: 10963 4.37 - 4.90: 18243 Nonbonded interactions: 46477 Sorted by model distance: nonbonded pdb=" OG SER A 415 " pdb=" OE2 GLU A 419 " model vdw 2.243 3.040 nonbonded pdb=" O ILE A 824 " pdb=" NZ LYS A 829 " model vdw 2.247 3.120 nonbonded pdb=" O LYS A 615 " pdb=" NE2 GLN A 619 " model vdw 2.268 3.120 nonbonded pdb=" O GLY A 784 " pdb=" OG SER A 788 " model vdw 2.272 3.040 nonbonded pdb=" NE2 HIS A 749 " pdb=" OG SER A 774 " model vdw 2.285 3.120 ... (remaining 46472 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 20.310 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 0.064 6023 Z= 0.244 Angle : 0.916 14.404 8180 Z= 0.547 Chirality : 0.047 0.175 969 Planarity : 0.008 0.078 1035 Dihedral : 14.497 88.988 2192 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 1.03 % Allowed : 12.61 % Favored : 86.36 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % 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: -2.53 (0.29), residues: 777 helix: -0.23 (0.27), residues: 378 sheet: -3.91 (0.80), residues: 28 loop : -3.17 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 282 HIS 0.008 0.002 HIS A 749 PHE 0.017 0.001 PHE A 385 TYR 0.013 0.001 TYR A 570 ARG 0.002 0.000 ARG A 896 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 293 PHE cc_start: 0.8617 (m-80) cc_final: 0.8126 (m-80) REVERT: A 299 MET cc_start: 0.8658 (mmt) cc_final: 0.8365 (mmm) REVERT: A 315 MET cc_start: 0.8356 (tpt) cc_final: 0.8044 (tpt) REVERT: A 351 ASN cc_start: 0.7838 (p0) cc_final: 0.7599 (p0) REVERT: A 353 ASP cc_start: 0.7850 (m-30) cc_final: 0.7153 (m-30) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1449 time to fit residues: 19.2328 Evaluate side-chains 60 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 5.9990 chunk 58 optimal weight: 30.0000 chunk 32 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 40.0000 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.100572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.063297 restraints weight = 26900.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.064459 restraints weight = 17126.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.065064 restraints weight = 12929.764| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6023 Z= 0.347 Angle : 0.817 10.017 8180 Z= 0.430 Chirality : 0.048 0.155 969 Planarity : 0.006 0.056 1035 Dihedral : 5.876 32.969 822 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 1.16 % Allowed : 13.51 % Favored : 85.33 % Rotamer: Outliers : 2.48 % Allowed : 8.84 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % 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: -2.42 (0.29), residues: 777 helix: -0.17 (0.26), residues: 384 sheet: -3.45 (0.87), residues: 30 loop : -3.15 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 282 HIS 0.008 0.002 HIS A 749 PHE 0.025 0.002 PHE A 821 TYR 0.022 0.002 TYR A 789 ARG 0.003 0.001 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.9235 (tmm) cc_final: 0.8611 (ppp) REVERT: A 293 PHE cc_start: 0.9014 (m-80) cc_final: 0.8200 (m-80) REVERT: A 299 MET cc_start: 0.8750 (mmt) cc_final: 0.8384 (mmm) REVERT: A 315 MET cc_start: 0.8864 (tpt) cc_final: 0.8575 (tpp) REVERT: A 391 MET cc_start: 0.9298 (ptm) cc_final: 0.8901 (ppp) REVERT: A 838 MET cc_start: 0.8151 (ptm) cc_final: 0.7292 (ppp) REVERT: A 941 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7771 (tpp) outliers start: 16 outliers final: 10 residues processed: 74 average time/residue: 0.1313 time to fit residues: 14.2287 Evaluate side-chains 70 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 941 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 64 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 47 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 32 optimal weight: 30.0000 chunk 31 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** 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 = 0.4183 r_free = 0.4183 target = 0.097326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.059595 restraints weight = 28067.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.060866 restraints weight = 17900.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.061442 restraints weight = 13826.213| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 6023 Z= 0.420 Angle : 0.878 11.388 8180 Z= 0.457 Chirality : 0.049 0.153 969 Planarity : 0.006 0.054 1035 Dihedral : 6.143 27.426 822 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 1.03 % Allowed : 14.16 % Favored : 84.81 % Rotamer: Outliers : 3.57 % Allowed : 13.02 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.62 (0.28), residues: 777 helix: -0.43 (0.25), residues: 377 sheet: -3.64 (0.99), residues: 12 loop : -3.16 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 908 HIS 0.012 0.002 HIS A 749 PHE 0.023 0.003 PHE A 821 TYR 0.019 0.002 TYR A 789 ARG 0.003 0.001 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.9154 (tmm) cc_final: 0.8641 (ppp) REVERT: A 293 PHE cc_start: 0.9039 (m-80) cc_final: 0.8221 (m-80) REVERT: A 299 MET cc_start: 0.8775 (mmt) cc_final: 0.8436 (mmm) REVERT: A 315 MET cc_start: 0.8754 (tpt) cc_final: 0.8493 (tpp) REVERT: A 391 MET cc_start: 0.9379 (ptm) cc_final: 0.9012 (ppp) REVERT: A 610 MET cc_start: 0.9147 (ttm) cc_final: 0.8696 (ttp) REVERT: A 695 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6687 (pm20) REVERT: A 838 MET cc_start: 0.8162 (ptm) cc_final: 0.7592 (ppp) REVERT: A 885 LEU cc_start: 0.9681 (tt) cc_final: 0.9422 (mt) REVERT: A 917 MET cc_start: 0.8181 (ttp) cc_final: 0.7367 (tmm) outliers start: 23 outliers final: 13 residues processed: 70 average time/residue: 0.1379 time to fit residues: 14.1950 Evaluate side-chains 69 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 924 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.099762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.061424 restraints weight = 27912.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.062397 restraints weight = 17926.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.063050 restraints weight = 13489.461| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6023 Z= 0.259 Angle : 0.765 13.196 8180 Z= 0.389 Chirality : 0.046 0.154 969 Planarity : 0.005 0.055 1035 Dihedral : 5.870 30.693 822 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.90 % Allowed : 13.26 % Favored : 85.84 % Rotamer: Outliers : 2.79 % Allowed : 16.43 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % 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: -2.20 (0.29), residues: 777 helix: -0.00 (0.26), residues: 381 sheet: -3.63 (0.99), residues: 12 loop : -3.06 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 323 HIS 0.011 0.002 HIS A 749 PHE 0.015 0.002 PHE A 385 TYR 0.014 0.002 TYR A 789 ARG 0.002 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 PHE cc_start: 0.9010 (m-80) cc_final: 0.8656 (m-80) REVERT: A 299 MET cc_start: 0.8786 (mmt) cc_final: 0.8444 (mmm) REVERT: A 391 MET cc_start: 0.9442 (ptm) cc_final: 0.9078 (ppp) REVERT: A 412 ASP cc_start: 0.9226 (OUTLIER) cc_final: 0.8956 (p0) REVERT: A 610 MET cc_start: 0.9062 (ttm) cc_final: 0.8586 (ttp) outliers start: 18 outliers final: 11 residues processed: 77 average time/residue: 0.1404 time to fit residues: 15.7180 Evaluate side-chains 71 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 924 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 14 optimal weight: 0.0670 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 56 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 619 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.103440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.065391 restraints weight = 27109.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.066355 restraints weight = 16546.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.067039 restraints weight = 12176.808| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6023 Z= 0.169 Angle : 0.748 13.695 8180 Z= 0.366 Chirality : 0.046 0.156 969 Planarity : 0.005 0.057 1035 Dihedral : 5.446 31.442 822 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.90 % Allowed : 11.97 % Favored : 87.13 % Rotamer: Outliers : 1.24 % Allowed : 18.60 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % 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: -1.76 (0.30), residues: 777 helix: 0.50 (0.27), residues: 382 sheet: -3.45 (0.79), residues: 30 loop : -2.93 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 574 HIS 0.010 0.001 HIS A 749 PHE 0.020 0.001 PHE A 291 TYR 0.009 0.001 TYR A 570 ARG 0.004 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.8397 (ptt180) cc_final: 0.8058 (ppt170) REVERT: A 293 PHE cc_start: 0.8977 (m-80) cc_final: 0.8628 (m-80) REVERT: A 299 MET cc_start: 0.8838 (mmt) cc_final: 0.8507 (mmm) REVERT: A 391 MET cc_start: 0.9432 (ptm) cc_final: 0.9064 (ppp) REVERT: A 412 ASP cc_start: 0.9127 (OUTLIER) cc_final: 0.8619 (p0) REVERT: A 610 MET cc_start: 0.9051 (ttm) cc_final: 0.8574 (ttp) REVERT: A 838 MET cc_start: 0.8362 (ppp) cc_final: 0.7944 (ppp) REVERT: A 845 MET cc_start: 0.6051 (ptm) cc_final: 0.5549 (ptt) outliers start: 8 outliers final: 3 residues processed: 73 average time/residue: 0.1319 time to fit residues: 14.1862 Evaluate side-chains 64 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 910 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 20.0000 chunk 71 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 5 optimal weight: 0.0870 chunk 47 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.103389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.065139 restraints weight = 27272.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.066370 restraints weight = 16912.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.067049 restraints weight = 12635.868| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6023 Z= 0.176 Angle : 0.773 16.446 8180 Z= 0.370 Chirality : 0.045 0.154 969 Planarity : 0.005 0.057 1035 Dihedral : 5.253 30.079 822 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.90 % Allowed : 11.33 % Favored : 87.77 % Rotamer: Outliers : 2.79 % Allowed : 18.60 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % 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: -1.64 (0.30), residues: 777 helix: 0.64 (0.27), residues: 380 sheet: -3.52 (0.70), residues: 30 loop : -2.88 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 574 HIS 0.009 0.001 HIS A 749 PHE 0.025 0.001 PHE A 291 TYR 0.026 0.001 TYR A 789 ARG 0.001 0.000 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.9133 (tmm) cc_final: 0.8542 (ppp) REVERT: A 293 PHE cc_start: 0.8984 (m-80) cc_final: 0.8171 (m-80) REVERT: A 299 MET cc_start: 0.8834 (mmt) cc_final: 0.8495 (mmm) REVERT: A 391 MET cc_start: 0.9478 (ptm) cc_final: 0.9097 (ppp) REVERT: A 412 ASP cc_start: 0.9178 (OUTLIER) cc_final: 0.8904 (p0) REVERT: A 610 MET cc_start: 0.9067 (ttm) cc_final: 0.8591 (ttp) REVERT: A 695 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6254 (pm20) REVERT: A 838 MET cc_start: 0.8342 (ppp) cc_final: 0.7934 (ppp) outliers start: 18 outliers final: 9 residues processed: 82 average time/residue: 0.1314 time to fit residues: 15.9958 Evaluate side-chains 70 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 910 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 61 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 12 optimal weight: 0.0570 chunk 28 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 36 optimal weight: 0.0270 chunk 69 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 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 = 0.4247 r_free = 0.4247 target = 0.101700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.063873 restraints weight = 27528.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.064645 restraints weight = 18074.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.065485 restraints weight = 13237.409| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6023 Z= 0.214 Angle : 0.786 13.435 8180 Z= 0.382 Chirality : 0.046 0.190 969 Planarity : 0.005 0.057 1035 Dihedral : 5.242 27.586 822 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.90 % Allowed : 11.58 % Favored : 87.52 % Rotamer: Outliers : 2.33 % Allowed : 19.22 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.55 (0.30), residues: 777 helix: 0.74 (0.27), residues: 375 sheet: -3.54 (0.74), residues: 30 loop : -2.82 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 574 HIS 0.010 0.001 HIS A 749 PHE 0.022 0.002 PHE A 291 TYR 0.012 0.001 TYR A 789 ARG 0.001 0.000 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.9136 (tmm) cc_final: 0.8695 (ppp) REVERT: A 293 PHE cc_start: 0.9016 (m-80) cc_final: 0.8224 (m-80) REVERT: A 299 MET cc_start: 0.8841 (mmt) cc_final: 0.8502 (mmm) REVERT: A 391 MET cc_start: 0.9473 (ptm) cc_final: 0.9103 (ppp) REVERT: A 412 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8937 (p0) REVERT: A 610 MET cc_start: 0.9066 (ttm) cc_final: 0.8585 (ttp) REVERT: A 695 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6320 (pm20) REVERT: A 705 MET cc_start: 0.8718 (ttt) cc_final: 0.8470 (tmm) REVERT: A 838 MET cc_start: 0.8389 (ppp) cc_final: 0.7975 (ppp) REVERT: A 845 MET cc_start: 0.5566 (ptt) cc_final: 0.5135 (ppp) outliers start: 15 outliers final: 10 residues processed: 75 average time/residue: 0.1292 time to fit residues: 14.3610 Evaluate side-chains 69 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 910 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 13 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 0.0270 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.098766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.061285 restraints weight = 26889.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.062223 restraints weight = 17952.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.062798 restraints weight = 13608.098| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6023 Z= 0.316 Angle : 0.812 12.693 8180 Z= 0.409 Chirality : 0.048 0.215 969 Planarity : 0.005 0.057 1035 Dihedral : 5.467 26.145 822 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 1.03 % Allowed : 11.97 % Favored : 87.00 % Rotamer: Outliers : 2.48 % Allowed : 19.84 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.29), residues: 777 helix: 0.41 (0.27), residues: 373 sheet: -3.63 (0.74), residues: 30 loop : -2.86 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 574 HIS 0.009 0.002 HIS A 749 PHE 0.019 0.002 PHE A 385 TYR 0.012 0.002 TYR A 789 ARG 0.003 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 292 MET cc_start: 0.9200 (tmm) cc_final: 0.8747 (ppp) REVERT: A 293 PHE cc_start: 0.9116 (m-80) cc_final: 0.8320 (m-80) REVERT: A 299 MET cc_start: 0.8854 (mmt) cc_final: 0.8506 (mmm) REVERT: A 391 MET cc_start: 0.9450 (ptm) cc_final: 0.9038 (ppp) REVERT: A 412 ASP cc_start: 0.9244 (OUTLIER) cc_final: 0.8973 (p0) REVERT: A 610 MET cc_start: 0.9089 (ttm) cc_final: 0.8624 (ttp) REVERT: A 695 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6202 (pm20) REVERT: A 799 MET cc_start: 0.7762 (ppp) cc_final: 0.7308 (ppp) REVERT: A 817 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.6995 (tp) REVERT: A 845 MET cc_start: 0.5720 (ptt) cc_final: 0.4824 (ppp) REVERT: A 885 LEU cc_start: 0.9646 (tt) cc_final: 0.9399 (mp) outliers start: 16 outliers final: 10 residues processed: 73 average time/residue: 0.1304 time to fit residues: 13.9998 Evaluate side-chains 71 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 924 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.8980 chunk 26 optimal weight: 30.0000 chunk 15 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 42 optimal weight: 0.0980 chunk 33 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.101563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.063969 restraints weight = 27450.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.064506 restraints weight = 18192.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.065256 restraints weight = 13110.116| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6023 Z= 0.197 Angle : 0.782 12.542 8180 Z= 0.380 Chirality : 0.047 0.197 969 Planarity : 0.005 0.057 1035 Dihedral : 5.339 28.165 822 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.90 % Allowed : 11.58 % Favored : 87.52 % Rotamer: Outliers : 2.17 % Allowed : 20.00 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 777 helix: 0.70 (0.27), residues: 374 sheet: -3.65 (0.74), residues: 30 loop : -2.76 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 574 HIS 0.010 0.001 HIS A 749 PHE 0.022 0.001 PHE A 291 TYR 0.012 0.001 TYR A 789 ARG 0.003 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.8299 (ptt180) cc_final: 0.7848 (ptm160) REVERT: A 292 MET cc_start: 0.9140 (tmm) cc_final: 0.8735 (ppp) REVERT: A 293 PHE cc_start: 0.9058 (m-80) cc_final: 0.8265 (m-80) REVERT: A 299 MET cc_start: 0.8859 (mmt) cc_final: 0.8509 (mmm) REVERT: A 391 MET cc_start: 0.9448 (ptm) cc_final: 0.9025 (ppp) REVERT: A 412 ASP cc_start: 0.9146 (OUTLIER) cc_final: 0.8725 (p0) REVERT: A 610 MET cc_start: 0.9054 (ttm) cc_final: 0.8580 (ttp) REVERT: A 705 MET cc_start: 0.8848 (ttt) cc_final: 0.8457 (tmm) REVERT: A 799 MET cc_start: 0.7703 (ppp) cc_final: 0.7302 (ppp) REVERT: A 817 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.7071 (mm) REVERT: A 838 MET cc_start: 0.8403 (ppp) cc_final: 0.8029 (ppp) REVERT: A 845 MET cc_start: 0.5530 (ptt) cc_final: 0.4718 (ppp) REVERT: A 885 LEU cc_start: 0.9621 (tt) cc_final: 0.9400 (mp) REVERT: A 941 MET cc_start: 0.8590 (tpp) cc_final: 0.8110 (tpt) outliers start: 14 outliers final: 10 residues processed: 72 average time/residue: 0.1362 time to fit residues: 14.5153 Evaluate side-chains 68 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 910 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 51 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.099477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.061920 restraints weight = 27247.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.062960 restraints weight = 17488.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.063712 restraints weight = 13238.574| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6023 Z= 0.257 Angle : 0.797 15.053 8180 Z= 0.393 Chirality : 0.047 0.177 969 Planarity : 0.005 0.057 1035 Dihedral : 5.360 26.544 822 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.90 % Allowed : 11.71 % Favored : 87.39 % Rotamer: Outliers : 1.86 % Allowed : 20.47 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.62 (0.30), residues: 777 helix: 0.65 (0.27), residues: 365 sheet: -3.90 (0.86), residues: 22 loop : -2.74 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 574 HIS 0.012 0.001 HIS A 749 PHE 0.015 0.002 PHE A 291 TYR 0.013 0.001 TYR A 789 ARG 0.003 0.000 ARG A 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.9206 (tmm) cc_final: 0.8766 (ppp) REVERT: A 293 PHE cc_start: 0.9093 (m-80) cc_final: 0.8282 (m-80) REVERT: A 299 MET cc_start: 0.8865 (mmt) cc_final: 0.8486 (mmm) REVERT: A 391 MET cc_start: 0.9448 (ptm) cc_final: 0.9034 (ppp) REVERT: A 412 ASP cc_start: 0.9170 (OUTLIER) cc_final: 0.8922 (p0) REVERT: A 610 MET cc_start: 0.9064 (ttm) cc_final: 0.8611 (ttp) REVERT: A 705 MET cc_start: 0.8780 (ttt) cc_final: 0.8234 (tmm) REVERT: A 799 MET cc_start: 0.7882 (ppp) cc_final: 0.7439 (ppp) REVERT: A 817 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7080 (mm) REVERT: A 838 MET cc_start: 0.8426 (ppp) cc_final: 0.8038 (ppp) REVERT: A 845 MET cc_start: 0.5666 (ptt) cc_final: 0.5341 (ppp) REVERT: A 885 LEU cc_start: 0.9630 (tt) cc_final: 0.9397 (mp) outliers start: 12 outliers final: 10 residues processed: 68 average time/residue: 0.1337 time to fit residues: 13.4301 Evaluate side-chains 68 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 910 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 30.0000 chunk 25 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 74 optimal weight: 0.1980 chunk 56 optimal weight: 30.0000 chunk 38 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.101348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.063308 restraints weight = 27992.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.064283 restraints weight = 17668.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.064918 restraints weight = 12985.003| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6023 Z= 0.180 Angle : 0.798 17.164 8180 Z= 0.382 Chirality : 0.047 0.162 969 Planarity : 0.005 0.057 1035 Dihedral : 5.274 27.148 822 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.90 % Allowed : 11.84 % Favored : 87.26 % Rotamer: Outliers : 2.17 % Allowed : 20.31 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.47 (0.31), residues: 777 helix: 0.72 (0.28), residues: 375 sheet: -3.91 (0.85), residues: 22 loop : -2.68 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 574 HIS 0.013 0.001 HIS A 749 PHE 0.009 0.001 PHE A 395 TYR 0.011 0.001 TYR A 789 ARG 0.004 0.000 ARG A 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3221.28 seconds wall clock time: 56 minutes 23.78 seconds (3383.78 seconds total)