Starting phenix.real_space_refine on Tue Mar 3 18:07:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7roz_24610/03_2026/7roz_24610.cif Found real_map, /net/cci-nas-00/data/ceres_data/7roz_24610/03_2026/7roz_24610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7roz_24610/03_2026/7roz_24610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7roz_24610/03_2026/7roz_24610.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7roz_24610/03_2026/7roz_24610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7roz_24610/03_2026/7roz_24610.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 Mg 1 5.21 5 S 47 5.16 5 C 4897 2.51 5 N 1343 2.21 5 O 1486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7774 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 7773 Classifications: {'peptide': 1064} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 38, 'TRANS': 1025} Chain breaks: 8 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 802 Unresolved non-hydrogen angles: 1015 Unresolved non-hydrogen dihedrals: 715 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLU:plan': 20, 'ARG:plan': 17, 'TYR:plan': 17, 'PHE:plan': 15, 'TRP:plan': 5, 'GLN:plan1': 5, 'ASP:plan': 8, 'HIS:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 487 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.69, per 1000 atoms: 0.22 Number of scatterers: 7774 At special positions: 0 Unit cell: (96.216, 102.124, 81.868, 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) S 47 16.00 Mg 1 11.99 O 1486 8.00 N 1343 7.00 C 4897 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: 0.62 Conformation dependent library (CDL) restraints added in 259.5 milliseconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 36.4% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 22 through 34 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 270 through 273 removed outlier: 3.538A pdb=" N ALA A 273 " --> pdb=" O LYS A 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 273' Processing helix chain 'A' and resid 295 through 305 Processing helix chain 'A' and resid 309 through 315 Processing helix chain 'A' and resid 315 through 325 Processing helix chain 'A' and resid 326 through 340 removed outlier: 3.858A pdb=" N GLN A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 409 through 413 removed outlier: 5.768A pdb=" N SER A 413 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 434 removed outlier: 3.501A pdb=" N LEU A 433 " --> pdb=" O PRO A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 461 removed outlier: 3.541A pdb=" N ASN A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 494 through 503 removed outlier: 3.608A pdb=" N ILE A 498 " --> pdb=" O LYS A 494 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 521 removed outlier: 3.826A pdb=" N LEU A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 573 Processing helix chain 'A' and resid 632 through 643 Processing helix chain 'A' and resid 645 through 662 removed outlier: 3.840A pdb=" N PHE A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 665 No H-bonds generated for 'chain 'A' and resid 663 through 665' Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.810A pdb=" N ALA A 669 " --> pdb=" O ASP A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 692 removed outlier: 3.519A pdb=" N GLN A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 720 Processing helix chain 'A' and resid 753 through 759 Processing helix chain 'A' and resid 802 through 807 removed outlier: 3.565A pdb=" N LYS A 806 " --> pdb=" O HIS A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 868 through 882 Processing helix chain 'A' and resid 884 through 897 Processing helix chain 'A' and resid 905 through 921 Processing helix chain 'A' and resid 958 through 969 removed outlier: 3.867A pdb=" N ARG A 962 " --> pdb=" O GLY A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 989 Processing helix chain 'A' and resid 998 through 1017 removed outlier: 4.113A pdb=" N HIS A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU A1008 " --> pdb=" O ASP A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1053 Processing helix chain 'A' and resid 1055 through 1067 Processing helix chain 'A' and resid 1077 through 1089 Processing helix chain 'A' and resid 1101 through 1106 removed outlier: 3.957A pdb=" N VAL A1106 " --> pdb=" O PHE A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1121 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 removed outlier: 3.983A pdb=" N ALA A 57 " --> pdb=" O ILE A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 169 removed outlier: 6.964A pdb=" N ARG A 105 " --> pdb=" O TRP A 135 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP A 135 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP A 107 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG A 133 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE A 109 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU A 127 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 125 removed outlier: 6.176A pdb=" N PHE A 123 " --> pdb=" O VAL A 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 400 removed outlier: 5.339A pdb=" N LEU A 393 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR A 385 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY A 395 " --> pdb=" O ARG A 383 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 383 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE A 415 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLN A 382 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 417 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N TRP A 485 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 467 " --> pdb=" O VAL A 464 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 530 removed outlier: 4.843A pdb=" N LEU A 618 " --> pdb=" O THR A 528 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN A 582 " --> pdb=" O THR A 621 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TRP A 623 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA A 580 " --> pdb=" O TRP A 623 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 593 " --> pdb=" O GLY A 558 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 628 removed outlier: 3.992A pdb=" N MET A 627 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG A 749 " --> pdb=" O CYS A 811 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N CYS A 811 " --> pdb=" O ARG A 749 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS A 734 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 627 through 628 removed outlier: 3.992A pdb=" N MET A 627 " --> pdb=" O ILE A 730 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 939 through 940 removed outlier: 6.219A pdb=" N PHE A 939 " --> pdb=" O TYR A 951 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 339 hydrogen bonds defined for protein. 963 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: 1.48 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2631 1.34 - 1.46: 1298 1.46 - 1.57: 3893 1.57 - 1.69: 1 1.69 - 1.81: 72 Bond restraints: 7895 Sorted by residual: bond pdb=" CB PRO A 940 " pdb=" CG PRO A 940 " ideal model delta sigma weight residual 1.492 1.580 -0.088 5.00e-02 4.00e+02 3.11e+00 bond pdb=" CB GLN A 567 " pdb=" CG GLN A 567 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.79e-01 bond pdb=" C ASN A 784 " pdb=" N PRO A 785 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.75e-01 bond pdb=" CA GLU A 117 " pdb=" CB GLU A 117 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.54e-02 4.22e+03 6.76e-01 bond pdb=" CG LEU A 911 " pdb=" CD2 LEU A 911 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.96e-01 ... (remaining 7890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 10404 1.40 - 2.80: 257 2.80 - 4.20: 39 4.20 - 5.59: 10 5.59 - 6.99: 2 Bond angle restraints: 10712 Sorted by residual: angle pdb=" CA PRO A 940 " pdb=" N PRO A 940 " pdb=" CD PRO A 940 " ideal model delta sigma weight residual 112.00 106.81 5.19 1.40e+00 5.10e-01 1.37e+01 angle pdb=" N LYS A 610 " pdb=" CA LYS A 610 " pdb=" C LYS A 610 " ideal model delta sigma weight residual 114.04 110.14 3.90 1.24e+00 6.50e-01 9.88e+00 angle pdb=" C ASP A 119 " pdb=" N GLU A 120 " pdb=" CA GLU A 120 " ideal model delta sigma weight residual 121.54 127.05 -5.51 1.91e+00 2.74e-01 8.32e+00 angle pdb=" CA GLU A 117 " pdb=" CB GLU A 117 " pdb=" CG GLU A 117 " ideal model delta sigma weight residual 114.10 119.42 -5.32 2.00e+00 2.50e-01 7.07e+00 angle pdb=" C VAL A 956 " pdb=" N PHE A 957 " pdb=" CA PHE A 957 " ideal model delta sigma weight residual 122.61 126.38 -3.77 1.56e+00 4.11e-01 5.85e+00 ... (remaining 10707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 4299 15.78 - 31.55: 361 31.55 - 47.33: 103 47.33 - 63.11: 17 63.11 - 78.88: 7 Dihedral angle restraints: 4787 sinusoidal: 1689 harmonic: 3098 Sorted by residual: dihedral pdb=" CA VAL A 66 " pdb=" C VAL A 66 " pdb=" N LYS A 67 " pdb=" CA LYS A 67 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA PRO A 851 " pdb=" C PRO A 851 " pdb=" N PRO A 852 " pdb=" CA PRO A 852 " ideal model delta harmonic sigma weight residual 180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA SER A 68 " pdb=" C SER A 68 " pdb=" N ARG A 69 " pdb=" CA ARG A 69 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 4784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 843 0.035 - 0.069: 289 0.069 - 0.103: 98 0.103 - 0.138: 33 0.138 - 0.172: 3 Chirality restraints: 1266 Sorted by residual: chirality pdb=" CB ILE A 539 " pdb=" CA ILE A 539 " pdb=" CG1 ILE A 539 " pdb=" CG2 ILE A 539 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CB ILE A 96 " pdb=" CA ILE A 96 " pdb=" CG1 ILE A 96 " pdb=" CG2 ILE A 96 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA GLN A 567 " pdb=" N GLN A 567 " pdb=" C GLN A 567 " pdb=" CB GLN A 567 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1263 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 939 " -0.078 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO A 940 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 940 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 940 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 850 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.28e+00 pdb=" N PRO A 851 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 851 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 851 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 627 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO A 628 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 628 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 628 " -0.035 5.00e-02 4.00e+02 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 82 2.63 - 3.20: 7370 3.20 - 3.77: 12257 3.77 - 4.33: 16872 4.33 - 4.90: 26779 Nonbonded interactions: 63360 Sorted by model distance: nonbonded pdb=" OD1 ASP A 832 " pdb="MG MG A1201 " model vdw 2.064 2.170 nonbonded pdb=" OD2 ASP A 834 " pdb="MG MG A1201 " model vdw 2.108 2.170 nonbonded pdb=" O LYS A 566 " pdb=" NE2 GLN A 570 " model vdw 2.202 3.120 nonbonded pdb=" O ALA A 432 " pdb=" OG1 THR A 448 " model vdw 2.230 3.040 nonbonded pdb=" NH2 ARG A 633 " pdb=" O LYS A 718 " model vdw 2.288 3.120 ... (remaining 63355 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.750 Find NCS groups from input model: 0.030 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 7895 Z= 0.113 Angle : 0.543 6.992 10712 Z= 0.297 Chirality : 0.042 0.172 1266 Planarity : 0.005 0.115 1394 Dihedral : 13.572 78.881 2763 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.26), residues: 1047 helix: 0.52 (0.28), residues: 378 sheet: -2.31 (0.42), residues: 152 loop : -1.78 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 729 TYR 0.015 0.001 TYR A 747 PHE 0.019 0.001 PHE A 251 TRP 0.025 0.001 TRP A 501 HIS 0.004 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7895) covalent geometry : angle 0.54335 (10712) hydrogen bonds : bond 0.19981 ( 325) hydrogen bonds : angle 8.21921 ( 963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.6239 (mtmm) cc_final: 0.5837 (mtmm) REVERT: A 311 PHE cc_start: 0.7238 (t80) cc_final: 0.7036 (t80) REVERT: A 331 LEU cc_start: 0.8136 (mm) cc_final: 0.7929 (mt) REVERT: A 864 ASP cc_start: 0.7488 (p0) cc_final: 0.7227 (p0) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1023 time to fit residues: 24.3487 Evaluate side-chains 102 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS A 538 GLN A 619 ASN A 816 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.108842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.086888 restraints weight = 18365.458| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.56 r_work: 0.3325 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7895 Z= 0.191 Angle : 0.658 11.464 10712 Z= 0.340 Chirality : 0.045 0.162 1266 Planarity : 0.005 0.071 1394 Dihedral : 4.704 23.652 1117 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 1.31 % Allowed : 11.04 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.26), residues: 1047 helix: 0.56 (0.27), residues: 384 sheet: -2.10 (0.43), residues: 148 loop : -1.65 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 937 TYR 0.017 0.002 TYR A 799 PHE 0.019 0.002 PHE A 837 TRP 0.010 0.001 TRP A 501 HIS 0.004 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 7895) covalent geometry : angle 0.65752 (10712) hydrogen bonds : bond 0.04062 ( 325) hydrogen bonds : angle 5.89528 ( 963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8248 (m-30) cc_final: 0.7785 (p0) REVERT: A 58 ARG cc_start: 0.6990 (mtm-85) cc_final: 0.6752 (mtt180) REVERT: A 92 TYR cc_start: 0.6005 (t80) cc_final: 0.4763 (t80) REVERT: A 331 LEU cc_start: 0.8858 (mm) cc_final: 0.8560 (mm) REVERT: A 864 ASP cc_start: 0.8766 (p0) cc_final: 0.8500 (p0) REVERT: A 923 LYS cc_start: 0.9017 (mttm) cc_final: 0.8651 (tttt) outliers start: 10 outliers final: 5 residues processed: 107 average time/residue: 0.0848 time to fit residues: 12.5079 Evaluate side-chains 87 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 567 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 88 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.108615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.086729 restraints weight = 18324.593| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.56 r_work: 0.3327 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7895 Z= 0.155 Angle : 0.607 11.423 10712 Z= 0.312 Chirality : 0.044 0.198 1266 Planarity : 0.004 0.057 1394 Dihedral : 4.567 23.018 1117 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.97 % Allowed : 12.22 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.26), residues: 1047 helix: 0.61 (0.27), residues: 387 sheet: -2.15 (0.42), residues: 141 loop : -1.72 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 526 TYR 0.012 0.001 TYR A 808 PHE 0.019 0.002 PHE A 876 TRP 0.007 0.001 TRP A 501 HIS 0.014 0.001 HIS A 865 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 7895) covalent geometry : angle 0.60685 (10712) hydrogen bonds : bond 0.03695 ( 325) hydrogen bonds : angle 5.65887 ( 963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.7133 (mtm-85) cc_final: 0.6926 (mtt180) REVERT: A 92 TYR cc_start: 0.6114 (t80) cc_final: 0.4832 (t80) REVERT: A 251 PHE cc_start: 0.7253 (t80) cc_final: 0.7020 (t80) REVERT: A 331 LEU cc_start: 0.8877 (mm) cc_final: 0.8585 (mm) REVERT: A 377 ASN cc_start: 0.9050 (t0) cc_final: 0.8844 (t0) REVERT: A 725 VAL cc_start: 0.9119 (OUTLIER) cc_final: 0.8919 (m) REVERT: A 738 MET cc_start: 0.8911 (ptp) cc_final: 0.8653 (ptp) outliers start: 15 outliers final: 8 residues processed: 96 average time/residue: 0.0706 time to fit residues: 9.9278 Evaluate side-chains 84 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 763 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 0.0040 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.108261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.086251 restraints weight = 18658.523| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.60 r_work: 0.3317 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7895 Z= 0.146 Angle : 0.575 10.300 10712 Z= 0.296 Chirality : 0.042 0.217 1266 Planarity : 0.004 0.050 1394 Dihedral : 4.449 22.285 1117 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.10 % Allowed : 13.93 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.26), residues: 1047 helix: 0.80 (0.27), residues: 381 sheet: -2.20 (0.41), residues: 141 loop : -1.66 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 532 TYR 0.012 0.001 TYR A 808 PHE 0.025 0.002 PHE A 837 TRP 0.007 0.001 TRP A 501 HIS 0.004 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7895) covalent geometry : angle 0.57486 (10712) hydrogen bonds : bond 0.03364 ( 325) hydrogen bonds : angle 5.44184 ( 963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8204 (ttt) cc_final: 0.7974 (ttm) REVERT: A 251 PHE cc_start: 0.7111 (t80) cc_final: 0.6879 (t80) REVERT: A 331 LEU cc_start: 0.8905 (mm) cc_final: 0.8610 (mm) REVERT: A 689 MET cc_start: 0.9255 (ptm) cc_final: 0.8965 (ptm) REVERT: A 738 MET cc_start: 0.8802 (ptp) cc_final: 0.8589 (ptp) outliers start: 16 outliers final: 11 residues processed: 94 average time/residue: 0.0713 time to fit residues: 9.7334 Evaluate side-chains 87 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 763 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 57 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 10 optimal weight: 0.2980 chunk 88 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 0.0470 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 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 = 0.3851 r_free = 0.3851 target = 0.108757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.087003 restraints weight = 18498.524| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.57 r_work: 0.3334 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7895 Z= 0.123 Angle : 0.562 11.556 10712 Z= 0.288 Chirality : 0.042 0.216 1266 Planarity : 0.004 0.047 1394 Dihedral : 4.365 21.846 1117 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.37 % Allowed : 14.59 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.26), residues: 1047 helix: 0.85 (0.27), residues: 386 sheet: -2.14 (0.41), residues: 141 loop : -1.62 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 532 TYR 0.014 0.001 TYR A 92 PHE 0.019 0.001 PHE A 837 TRP 0.006 0.001 TRP A 501 HIS 0.003 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7895) covalent geometry : angle 0.56190 (10712) hydrogen bonds : bond 0.03159 ( 325) hydrogen bonds : angle 5.27756 ( 963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.6145 (t80) cc_final: 0.5015 (t80) REVERT: A 251 PHE cc_start: 0.7015 (t80) cc_final: 0.6806 (t80) REVERT: A 331 LEU cc_start: 0.8854 (mm) cc_final: 0.8554 (mm) REVERT: A 689 MET cc_start: 0.9247 (ptm) cc_final: 0.8951 (ptm) REVERT: A 738 MET cc_start: 0.8689 (ptp) cc_final: 0.8487 (ptp) REVERT: A 880 MET cc_start: 0.8731 (mtt) cc_final: 0.8467 (mtt) outliers start: 18 outliers final: 10 residues processed: 94 average time/residue: 0.0781 time to fit residues: 10.4537 Evaluate side-chains 89 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 577 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 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 = 0.3825 r_free = 0.3825 target = 0.107234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.085363 restraints weight = 18624.005| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.58 r_work: 0.3299 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7895 Z= 0.161 Angle : 0.576 11.754 10712 Z= 0.297 Chirality : 0.042 0.210 1266 Planarity : 0.004 0.044 1394 Dihedral : 4.412 22.900 1117 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.37 % Allowed : 15.11 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.26), residues: 1047 helix: 0.90 (0.27), residues: 386 sheet: -2.14 (0.38), residues: 157 loop : -1.64 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 532 TYR 0.012 0.001 TYR A 808 PHE 0.017 0.001 PHE A 837 TRP 0.007 0.001 TRP A 501 HIS 0.004 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 7895) covalent geometry : angle 0.57567 (10712) hydrogen bonds : bond 0.03270 ( 325) hydrogen bonds : angle 5.29145 ( 963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.6063 (t80) cc_final: 0.5853 (t80) REVERT: A 331 LEU cc_start: 0.8902 (mm) cc_final: 0.8611 (mm) REVERT: A 547 ASP cc_start: 0.8247 (t0) cc_final: 0.8020 (t0) REVERT: A 634 GLU cc_start: 0.8241 (pm20) cc_final: 0.7940 (pm20) REVERT: A 692 GLN cc_start: 0.8462 (pp30) cc_final: 0.8123 (pp30) REVERT: A 738 MET cc_start: 0.8782 (ptp) cc_final: 0.8565 (ptp) outliers start: 18 outliers final: 13 residues processed: 91 average time/residue: 0.0647 time to fit residues: 8.7259 Evaluate side-chains 92 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 763 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS A 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.104608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.082924 restraints weight = 18631.417| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.53 r_work: 0.3243 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7895 Z= 0.230 Angle : 0.640 13.341 10712 Z= 0.330 Chirality : 0.044 0.209 1266 Planarity : 0.004 0.041 1394 Dihedral : 4.735 25.659 1117 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 2.37 % Allowed : 15.51 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.26), residues: 1047 helix: 0.82 (0.27), residues: 384 sheet: -2.34 (0.39), residues: 136 loop : -1.76 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 532 TYR 0.013 0.001 TYR A 808 PHE 0.030 0.002 PHE A 251 TRP 0.011 0.001 TRP A 501 HIS 0.005 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 7895) covalent geometry : angle 0.64034 (10712) hydrogen bonds : bond 0.03625 ( 325) hydrogen bonds : angle 5.54381 ( 963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8579 (m-30) cc_final: 0.8087 (p0) REVERT: A 92 TYR cc_start: 0.6068 (t80) cc_final: 0.5655 (t80) REVERT: A 331 LEU cc_start: 0.8986 (mm) cc_final: 0.8702 (mm) REVERT: A 547 ASP cc_start: 0.8432 (t0) cc_final: 0.8146 (t0) REVERT: A 634 GLU cc_start: 0.8304 (pm20) cc_final: 0.7980 (pm20) REVERT: A 692 GLN cc_start: 0.8493 (pp30) cc_final: 0.8176 (pp30) REVERT: A 738 MET cc_start: 0.8947 (ptp) cc_final: 0.8671 (ptp) outliers start: 18 outliers final: 12 residues processed: 98 average time/residue: 0.0722 time to fit residues: 10.3028 Evaluate side-chains 90 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 774 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 29 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 26 optimal weight: 0.0270 chunk 41 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.107246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.085916 restraints weight = 18783.427| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.56 r_work: 0.3310 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7895 Z= 0.124 Angle : 0.603 13.816 10712 Z= 0.305 Chirality : 0.042 0.205 1266 Planarity : 0.004 0.040 1394 Dihedral : 4.477 23.022 1117 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 1.84 % Allowed : 17.21 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.26), residues: 1047 helix: 1.11 (0.27), residues: 380 sheet: -2.14 (0.37), residues: 157 loop : -1.63 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 729 TYR 0.016 0.001 TYR A 92 PHE 0.022 0.001 PHE A 29 TRP 0.010 0.001 TRP A 623 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7895) covalent geometry : angle 0.60350 (10712) hydrogen bonds : bond 0.03053 ( 325) hydrogen bonds : angle 5.21351 ( 963) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8061 (p0) REVERT: A 331 LEU cc_start: 0.8956 (mm) cc_final: 0.8691 (mm) REVERT: A 547 ASP cc_start: 0.8400 (t0) cc_final: 0.8073 (t0) REVERT: A 634 GLU cc_start: 0.8236 (pm20) cc_final: 0.7902 (pm20) REVERT: A 692 GLN cc_start: 0.8409 (pp30) cc_final: 0.8083 (pp30) REVERT: A 920 ASP cc_start: 0.8406 (t0) cc_final: 0.8121 (t0) outliers start: 14 outliers final: 10 residues processed: 89 average time/residue: 0.0617 time to fit residues: 8.1935 Evaluate side-chains 89 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 652 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 70 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 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 = 0.3811 r_free = 0.3811 target = 0.106508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.085107 restraints weight = 18718.833| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.54 r_work: 0.3295 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7895 Z= 0.150 Angle : 0.611 14.353 10712 Z= 0.308 Chirality : 0.043 0.237 1266 Planarity : 0.004 0.040 1394 Dihedral : 4.466 22.945 1117 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.10 % Allowed : 16.95 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.26), residues: 1047 helix: 1.13 (0.27), residues: 380 sheet: -2.13 (0.37), residues: 157 loop : -1.62 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 9 TYR 0.011 0.001 TYR A 385 PHE 0.019 0.002 PHE A 505 TRP 0.011 0.001 TRP A 501 HIS 0.003 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 7895) covalent geometry : angle 0.61115 (10712) hydrogen bonds : bond 0.03089 ( 325) hydrogen bonds : angle 5.17922 ( 963) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8070 (p0) REVERT: A 602 LEU cc_start: 0.8101 (tp) cc_final: 0.7889 (tp) REVERT: A 634 GLU cc_start: 0.8245 (pm20) cc_final: 0.7916 (pm20) REVERT: A 692 GLN cc_start: 0.8404 (pp30) cc_final: 0.8110 (pp30) REVERT: A 920 ASP cc_start: 0.8398 (t0) cc_final: 0.8110 (t0) outliers start: 16 outliers final: 12 residues processed: 91 average time/residue: 0.0674 time to fit residues: 9.1210 Evaluate side-chains 90 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 774 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 50 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 0.0270 chunk 105 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 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 = 0.3822 r_free = 0.3822 target = 0.107180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.085952 restraints weight = 18692.016| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.56 r_work: 0.3314 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7895 Z= 0.132 Angle : 0.624 14.416 10712 Z= 0.312 Chirality : 0.044 0.224 1266 Planarity : 0.004 0.040 1394 Dihedral : 4.468 22.644 1117 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.23 % Allowed : 16.69 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.26), residues: 1047 helix: 1.13 (0.27), residues: 378 sheet: -2.13 (0.37), residues: 157 loop : -1.64 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 58 TYR 0.011 0.001 TYR A 808 PHE 0.020 0.002 PHE A 505 TRP 0.011 0.001 TRP A 501 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7895) covalent geometry : angle 0.62429 (10712) hydrogen bonds : bond 0.03078 ( 325) hydrogen bonds : angle 5.15125 ( 963) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8529 (m-30) cc_final: 0.8048 (p0) REVERT: A 634 GLU cc_start: 0.8223 (pm20) cc_final: 0.7911 (pm20) REVERT: A 692 GLN cc_start: 0.8387 (pp30) cc_final: 0.8077 (pp30) REVERT: A 920 ASP cc_start: 0.8402 (t0) cc_final: 0.8124 (t0) outliers start: 17 outliers final: 12 residues processed: 90 average time/residue: 0.0664 time to fit residues: 8.8544 Evaluate side-chains 86 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 774 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 54 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 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 = 0.3819 r_free = 0.3819 target = 0.107091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.085875 restraints weight = 18634.799| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.53 r_work: 0.3313 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7895 Z= 0.137 Angle : 0.607 14.513 10712 Z= 0.307 Chirality : 0.044 0.236 1266 Planarity : 0.004 0.040 1394 Dihedral : 4.455 22.499 1117 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 1.84 % Allowed : 17.48 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.26), residues: 1047 helix: 1.20 (0.27), residues: 379 sheet: -2.14 (0.38), residues: 147 loop : -1.68 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 9 TYR 0.032 0.001 TYR A 92 PHE 0.021 0.001 PHE A 505 TRP 0.012 0.001 TRP A 623 HIS 0.003 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7895) covalent geometry : angle 0.60673 (10712) hydrogen bonds : bond 0.03001 ( 325) hydrogen bonds : angle 5.05916 ( 963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1627.12 seconds wall clock time: 28 minutes 38.09 seconds (1718.09 seconds total)