Starting phenix.real_space_refine on Sat Dec 28 05:38:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7roz_24610/12_2024/7roz_24610.cif Found real_map, /net/cci-nas-00/data/ceres_data/7roz_24610/12_2024/7roz_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7roz_24610/12_2024/7roz_24610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7roz_24610/12_2024/7roz_24610.map" model { file = "/net/cci-nas-00/data/ceres_data/7roz_24610/12_2024/7roz_24610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7roz_24610/12_2024/7roz_24610.cif" } resolution = 3.1 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= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 17, 'ASN:plan1': 3, 'TRP:plan': 5, 'ASP:plan': 8, 'PHE:plan': 15, 'GLU:plan': 20, 'ARG:plan': 17} 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: 7.45, per 1000 atoms: 0.96 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: 2.23 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.03 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: 3.81 Time building geometry restraints manager: 2.52 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: 2.000 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.960 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.100 ------------------------------------------------------------------------------- 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= 0.162 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 : 11.67 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.26), 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 TRP 0.025 0.001 TRP A 501 HIS 0.004 0.001 HIS A 304 PHE 0.019 0.001 PHE A 251 TYR 0.015 0.001 TYR A 747 ARG 0.008 0.001 ARG A 729 *********************** 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 : 0.860 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: 0.2476 time to fit residues: 58.7840 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 : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 83 optimal weight: 0.1980 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 0.0040 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 7.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7895 Z= 0.199 Angle : 0.628 11.374 10712 Z= 0.324 Chirality : 0.043 0.157 1266 Planarity : 0.005 0.073 1394 Dihedral : 4.533 22.495 1117 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.79 % Allowed : 10.91 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.26), residues: 1047 helix: 0.53 (0.27), residues: 388 sheet: -2.08 (0.44), residues: 141 loop : -1.59 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 501 HIS 0.005 0.001 HIS A 33 PHE 0.021 0.001 PHE A 837 TYR 0.016 0.001 TYR A 799 ARG 0.006 0.001 ARG A 937 *********************** 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 116 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.804 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: symmetry clash REVERT: A 331 LEU cc_start: 0.8216 (mm) cc_final: 0.7992 (mt) REVERT: A 864 ASP cc_start: 0.7399 (p0) cc_final: 0.7167 (p0) outliers start: 6 outliers final: 2 residues processed: 115 average time/residue: 0.2115 time to fit residues: 33.3603 Evaluate side-chains 91 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 53 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS A 816 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3107 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= 0.290 Angle : 0.624 9.196 10712 Z= 0.322 Chirality : 0.044 0.189 1266 Planarity : 0.004 0.058 1394 Dihedral : 4.595 23.652 1117 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 1.97 % Allowed : 11.83 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.36 (0.26), residues: 1047 helix: 0.57 (0.27), residues: 387 sheet: -2.10 (0.42), residues: 148 loop : -1.69 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 501 HIS 0.005 0.001 HIS A 822 PHE 0.016 0.002 PHE A 876 TYR 0.014 0.001 TYR A 808 ARG 0.006 0.001 ARG A 499 *********************** 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 102 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 99 average time/residue: 0.2058 time to fit residues: 29.3067 Evaluate side-chains 82 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 763 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7895 Z= 0.302 Angle : 0.623 10.757 10712 Z= 0.323 Chirality : 0.044 0.215 1266 Planarity : 0.004 0.050 1394 Dihedral : 4.653 24.501 1117 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.97 % Allowed : 14.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.26), residues: 1047 helix: 0.55 (0.26), residues: 387 sheet: -2.39 (0.40), residues: 138 loop : -1.71 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 501 HIS 0.005 0.001 HIS A 822 PHE 0.022 0.002 PHE A 837 TYR 0.014 0.001 TYR A 808 ARG 0.006 0.001 ARG A 532 *********************** 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 94 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 91 average time/residue: 0.1651 time to fit residues: 22.1236 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 : 0.759 ------------------------------------------------------------------------------- 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 138 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 331 LEU 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 58 optimal weight: 8.9990 chunk 1 optimal weight: 0.0970 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 87 optimal weight: 0.0470 chunk 70 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 25 optimal weight: 0.0050 chunk 34 optimal weight: 4.9990 overall best weight: 0.3692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7895 Z= 0.171 Angle : 0.565 10.607 10712 Z= 0.292 Chirality : 0.042 0.206 1266 Planarity : 0.004 0.047 1394 Dihedral : 4.467 21.827 1117 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.23 % Allowed : 14.45 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.31 (0.26), residues: 1047 helix: 0.66 (0.27), residues: 387 sheet: -2.13 (0.40), residues: 148 loop : -1.68 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 485 HIS 0.002 0.001 HIS A 84 PHE 0.019 0.001 PHE A 837 TYR 0.014 0.001 TYR A 293 ARG 0.004 0.000 ARG A 532 *********************** 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 99 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 724 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8777 (tp) outliers start: 17 outliers final: 10 residues processed: 94 average time/residue: 0.1760 time to fit residues: 24.1597 Evaluate side-chains 84 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 95 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 724 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.1980 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 98 optimal weight: 0.0170 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7895 Z= 0.211 Angle : 0.568 11.876 10712 Z= 0.293 Chirality : 0.043 0.218 1266 Planarity : 0.004 0.044 1394 Dihedral : 4.471 22.466 1117 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.10 % Allowed : 15.24 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.27 (0.26), residues: 1047 helix: 0.76 (0.27), residues: 387 sheet: -2.24 (0.39), residues: 153 loop : -1.66 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 501 HIS 0.003 0.001 HIS A 822 PHE 0.017 0.001 PHE A 837 TYR 0.029 0.001 TYR A 92 ARG 0.003 0.000 ARG A 532 *********************** 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 88 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 724 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8812 (tp) outliers start: 16 outliers final: 12 residues processed: 83 average time/residue: 0.1855 time to fit residues: 22.4834 Evaluate side-chains 82 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 331 LEU 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 724 LEU Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 774 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** A 915 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3967 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= 0.225 Angle : 0.579 12.614 10712 Z= 0.299 Chirality : 0.043 0.231 1266 Planarity : 0.004 0.042 1394 Dihedral : 4.510 23.010 1117 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.10 % Allowed : 14.98 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.25 (0.26), residues: 1047 helix: 0.80 (0.27), residues: 387 sheet: -2.14 (0.40), residues: 148 loop : -1.71 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 501 HIS 0.003 0.001 HIS A 822 PHE 0.037 0.002 PHE A 251 TYR 0.013 0.001 TYR A 92 ARG 0.002 0.000 ARG A 506 *********************** 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 85 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 724 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8812 (tp) outliers start: 16 outliers final: 12 residues processed: 82 average time/residue: 0.1865 time to fit residues: 22.2123 Evaluate side-chains 82 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 278 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 724 LEU 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 30 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 64 optimal weight: 0.0570 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7895 Z= 0.224 Angle : 0.584 13.756 10712 Z= 0.298 Chirality : 0.043 0.227 1266 Planarity : 0.004 0.041 1394 Dihedral : 4.510 22.967 1117 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.23 % Allowed : 15.51 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.21 (0.26), residues: 1047 helix: 0.84 (0.27), residues: 387 sheet: -2.15 (0.40), residues: 148 loop : -1.69 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 501 HIS 0.003 0.001 HIS A 822 PHE 0.017 0.001 PHE A 957 TYR 0.017 0.001 TYR A 92 ARG 0.002 0.000 ARG A 729 *********************** 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 87 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 724 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8817 (tp) outliers start: 17 outliers final: 12 residues processed: 83 average time/residue: 0.1899 time to fit residues: 23.2732 Evaluate side-chains 79 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 331 LEU 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 724 LEU Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 774 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.0050 chunk 74 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7895 Z= 0.219 Angle : 0.604 13.746 10712 Z= 0.308 Chirality : 0.044 0.230 1266 Planarity : 0.004 0.041 1394 Dihedral : 4.533 22.906 1117 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.71 % Allowed : 16.43 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.17 (0.26), residues: 1047 helix: 0.94 (0.27), residues: 382 sheet: -2.23 (0.38), residues: 151 loop : -1.66 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 501 HIS 0.003 0.001 HIS A 822 PHE 0.045 0.002 PHE A 251 TYR 0.032 0.001 TYR A 92 ARG 0.008 0.000 ARG A 9 *********************** 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 82 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 724 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8821 (tp) outliers start: 13 outliers final: 12 residues processed: 79 average time/residue: 0.1878 time to fit residues: 21.7470 Evaluate side-chains 81 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 331 LEU 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 724 LEU Chi-restraints excluded: chain A residue 763 SER 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 61 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 0.0670 chunk 105 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4295 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= 0.197 Angle : 0.600 14.360 10712 Z= 0.306 Chirality : 0.043 0.224 1266 Planarity : 0.004 0.041 1394 Dihedral : 4.487 22.383 1117 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.84 % Allowed : 16.03 % 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 (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: -1.00 (0.26), residues: 1047 helix: 1.10 (0.27), residues: 377 sheet: -2.08 (0.39), residues: 146 loop : -1.58 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 501 HIS 0.003 0.001 HIS A 33 PHE 0.019 0.001 PHE A 29 TYR 0.011 0.001 TYR A 808 ARG 0.003 0.000 ARG A 9 ********************** 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 88 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 724 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8785 (tp) outliers start: 14 outliers final: 12 residues processed: 84 average time/residue: 0.1776 time to fit residues: 21.8988 Evaluate side-chains 81 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 331 LEU 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 724 LEU Chi-restraints excluded: chain A residue 763 SER 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 25 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 0.0370 chunk 84 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- 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** A 340 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.107234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.085875 restraints weight = 18291.973| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.47 r_work: 0.3313 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7895 Z= 0.212 Angle : 0.608 14.573 10712 Z= 0.309 Chirality : 0.044 0.233 1266 Planarity : 0.004 0.041 1394 Dihedral : 4.542 22.477 1117 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 1.58 % Allowed : 16.95 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.99 (0.26), residues: 1047 helix: 1.11 (0.27), residues: 377 sheet: -2.04 (0.39), residues: 146 loop : -1.59 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 501 HIS 0.003 0.001 HIS A 822 PHE 0.020 0.001 PHE A 29 TYR 0.020 0.001 TYR A 92 ARG 0.003 0.000 ARG A 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1877.96 seconds wall clock time: 35 minutes 12.52 seconds (2112.52 seconds total)