Starting phenix.real_space_refine on Wed Feb 12 23:39:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n70_24214/02_2025/7n70_24214_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n70_24214/02_2025/7n70_24214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n70_24214/02_2025/7n70_24214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n70_24214/02_2025/7n70_24214.map" model { file = "/net/cci-nas-00/data/ceres_data/7n70_24214/02_2025/7n70_24214_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n70_24214/02_2025/7n70_24214_trim.cif" } resolution = 2.8 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= 0.015 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 49 5.16 5 Be 1 3.05 5 C 5158 2.51 5 N 1340 2.21 5 O 1401 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7953 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7900 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 959} Chain breaks: 6 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {' MG': 1, 'BEF': 1, 'LMT': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.47, per 1000 atoms: 0.69 Number of scatterers: 7953 At special positions: 0 Unit cell: (85.634, 102.943, 134.828, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 49 16.00 Mg 1 11.99 F 3 9.00 O 1401 8.00 N 1340 7.00 C 5158 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 990.2 milliseconds 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 51.6% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 59 through 68 removed outlier: 3.526A pdb=" N LEU A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.941A pdb=" N GLY A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 200 through 212 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 233 through 249 removed outlier: 3.995A pdb=" N GLY A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 238 " --> pdb=" O PRO A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 283 removed outlier: 4.172A pdb=" N CYS A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 393 through 396 removed outlier: 3.843A pdb=" N CYS A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 396' Processing helix chain 'A' and resid 397 through 405 Processing helix chain 'A' and resid 417 through 445 removed outlier: 3.673A pdb=" N LYS A 422 " --> pdb=" O LYS A 418 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 423 " --> pdb=" O HIS A 419 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 458 through 464 Processing helix chain 'A' and resid 467 through 486 Processing helix chain 'A' and resid 492 through 502 removed outlier: 4.098A pdb=" N ASN A 497 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 502 " --> pdb=" O GLY A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 566 through 577 Processing helix chain 'A' and resid 651 through 656 Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 695 through 700 removed outlier: 3.593A pdb=" N GLN A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 709 removed outlier: 3.706A pdb=" N VAL A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 737 removed outlier: 3.991A pdb=" N VAL A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 760 Processing helix chain 'A' and resid 821 through 832 removed outlier: 3.547A pdb=" N LYS A 830 " --> pdb=" O GLY A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 842 Processing helix chain 'A' and resid 850 through 864 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 877 through 884 Processing helix chain 'A' and resid 909 through 949 removed outlier: 3.533A pdb=" N MET A 913 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 964 Processing helix chain 'A' and resid 965 through 973 Processing helix chain 'A' and resid 974 through 976 No H-bonds generated for 'chain 'A' and resid 974 through 976' Processing helix chain 'A' and resid 993 through 1019 Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.667A pdb=" N PHE A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A1057 " --> pdb=" O TYR A1053 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A1060 " --> pdb=" O LEU A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1072 Processing helix chain 'A' and resid 1073 through 1093 Processing helix chain 'A' and resid 1108 through 1145 Proline residue: A1138 - end of helix Processing helix chain 'A' and resid 1152 through 1164 Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 79 removed outlier: 3.813A pdb=" N GLU A 91 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 5.228A pdb=" N ARG A 159 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 176 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 303 removed outlier: 4.555A pdb=" N CYS A 291 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N CYS A 312 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL A 386 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASP A 325 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 320 through 321 removed outlier: 6.398A pdb=" N MET A 334 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA A 378 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU A 332 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 490 removed outlier: 6.274A pdb=" N GLY A 887 " --> pdb=" O PHE A 901 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER A 903 " --> pdb=" O GLY A 887 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER A 889 " --> pdb=" O SER A 903 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL A 868 " --> pdb=" O VAL A 886 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ILE A 888 " --> pdb=" O VAL A 868 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N MET A 870 " --> pdb=" O ILE A 888 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N THR A 844 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR A 844 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU A 818 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N PHE A 846 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU A 820 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N HIS A 767 " --> pdb=" O HIS A 817 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ALA A 819 " --> pdb=" O HIS A 767 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE A 769 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 783 " --> pdb=" O THR A 774 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 530 through 531 removed outlier: 7.131A pdb=" N GLY A 517 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 722 " --> pdb=" O GLY A 517 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 718 " --> pdb=" O MET A 521 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL A 523 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU A 716 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU A 714 " --> pdb=" O PRO A 525 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N LYS A 527 " --> pdb=" O SER A 712 " (cutoff:3.500A) removed outlier: 13.360A pdb=" N SER A 712 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU A 713 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER A 687 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 715 " --> pdb=" O LEU A 685 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG A 631 " --> pdb=" O PRO A 624 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER A 633 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ARG A 622 " --> pdb=" O SER A 633 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL A 635 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 588 " --> pdb=" O VAL A 619 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 559 444 hydrogen bonds defined for protein. 1257 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: 3.76 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2321 1.33 - 1.46: 1236 1.46 - 1.58: 4498 1.58 - 1.70: 4 1.70 - 1.82: 73 Bond restraints: 8132 Sorted by residual: bond pdb=" CAV Y01 A1203 " pdb=" CBC Y01 A1203 " ideal model delta sigma weight residual 1.523 1.619 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" CG PRO A 689 " pdb=" CD PRO A 689 " ideal model delta sigma weight residual 1.503 1.347 0.156 3.40e-02 8.65e+02 2.10e+01 bond pdb=" F2 BEF A1201 " pdb="BE BEF A1201 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" CAY Y01 A1203 " pdb=" OAW Y01 A1203 " ideal model delta sigma weight residual 1.332 1.412 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" CAM Y01 A1203 " pdb=" CAY Y01 A1203 " ideal model delta sigma weight residual 1.505 1.577 -0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 8127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 10983 2.90 - 5.81: 88 5.81 - 8.71: 18 8.71 - 11.62: 4 11.62 - 14.52: 3 Bond angle restraints: 11096 Sorted by residual: angle pdb=" N PRO A 689 " pdb=" CD PRO A 689 " pdb=" CG PRO A 689 " ideal model delta sigma weight residual 103.20 92.24 10.96 1.50e+00 4.44e-01 5.34e+01 angle pdb=" CA PRO A 689 " pdb=" N PRO A 689 " pdb=" CD PRO A 689 " ideal model delta sigma weight residual 112.00 104.44 7.56 1.40e+00 5.10e-01 2.92e+01 angle pdb=" CAM Y01 A1203 " pdb=" CAY Y01 A1203 " pdb=" OAW Y01 A1203 " ideal model delta sigma weight residual 111.19 125.71 -14.52 3.00e+00 1.11e-01 2.34e+01 angle pdb=" CAZ Y01 A1203 " pdb=" CAV Y01 A1203 " pdb=" CBC Y01 A1203 " ideal model delta sigma weight residual 111.19 124.87 -13.68 3.00e+00 1.11e-01 2.08e+01 angle pdb=" N TYR A 935 " pdb=" CA TYR A 935 " pdb=" C TYR A 935 " ideal model delta sigma weight residual 111.11 116.35 -5.24 1.20e+00 6.94e-01 1.90e+01 ... (remaining 11091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 4415 15.25 - 30.50: 381 30.50 - 45.74: 109 45.74 - 60.99: 25 60.99 - 76.24: 9 Dihedral angle restraints: 4939 sinusoidal: 1957 harmonic: 2982 Sorted by residual: dihedral pdb=" CA PHE A 507 " pdb=" C PHE A 507 " pdb=" N ASP A 508 " pdb=" CA ASP A 508 " ideal model delta harmonic sigma weight residual 180.00 162.91 17.09 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ALA A 551 " pdb=" C ALA A 551 " pdb=" N THR A 552 " pdb=" CA THR A 552 " ideal model delta harmonic sigma weight residual -180.00 -163.34 -16.66 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CB MET A 932 " pdb=" CG MET A 932 " pdb=" SD MET A 932 " pdb=" CE MET A 932 " ideal model delta sinusoidal sigma weight residual 180.00 122.08 57.92 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 4936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1220 0.079 - 0.159: 105 0.159 - 0.238: 1 0.238 - 0.318: 1 0.318 - 0.397: 3 Chirality restraints: 1330 Sorted by residual: chirality pdb=" CBG Y01 A1203 " pdb=" CAQ Y01 A1203 " pdb=" CBD Y01 A1203 " pdb=" CBI Y01 A1203 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA TYR A 935 " pdb=" N TYR A 935 " pdb=" C TYR A 935 " pdb=" CB TYR A 935 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CBH Y01 A1203 " pdb=" CAT Y01 A1203 " pdb=" CAZ Y01 A1203 " pdb=" CBF Y01 A1203 " both_signs ideal model delta sigma weight residual False -2.85 -2.53 -0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 1327 not shown) Planarity restraints: 1390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 688 " -0.066 5.00e-02 4.00e+02 9.54e-02 1.46e+01 pdb=" N PRO A 689 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 689 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 689 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1064 " -0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO A1065 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A1065 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A1065 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 962 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C ASP A 962 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP A 962 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 963 " -0.012 2.00e-02 2.50e+03 ... (remaining 1387 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 107 2.67 - 3.23: 7435 3.23 - 3.78: 12428 3.78 - 4.34: 17321 4.34 - 4.90: 29466 Nonbonded interactions: 66757 Sorted by model distance: nonbonded pdb=" OD2 ASP A 508 " pdb="MG MG A1202 " model vdw 2.109 2.170 nonbonded pdb=" OD2 ASP A 508 " pdb=" F1 BEF A1201 " model vdw 2.135 2.990 nonbonded pdb=" F1 BEF A1201 " pdb="MG MG A1202 " model vdw 2.152 2.120 nonbonded pdb=" O THR A 510 " pdb="MG MG A1202 " model vdw 2.165 2.170 nonbonded pdb=" OG SER A 633 " pdb=" OE2 GLU A 708 " model vdw 2.175 3.040 ... (remaining 66752 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: 2.780 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.430 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.005 0.156 8132 Z= 0.312 Angle : 0.726 14.519 11096 Z= 0.346 Chirality : 0.046 0.397 1330 Planarity : 0.005 0.095 1390 Dihedral : 13.221 76.240 3013 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.27 (0.27), residues: 1018 helix: 1.16 (0.24), residues: 487 sheet: -1.29 (0.41), residues: 142 loop : -0.36 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1023 HIS 0.003 0.001 HIS A 554 PHE 0.031 0.002 PHE A 103 TYR 0.021 0.001 TYR A 935 ARG 0.006 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.870 Fit side-chains REVERT: A 67 TRP cc_start: 0.7759 (t60) cc_final: 0.7444 (t60) REVERT: A 220 VAL cc_start: 0.8215 (t) cc_final: 0.7906 (p) REVERT: A 418 LYS cc_start: 0.7901 (ptmt) cc_final: 0.7671 (ptpt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 1.2452 time to fit residues: 143.1354 Evaluate side-chains 66 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A 721 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.104560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.080873 restraints weight = 14132.159| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.83 r_work: 0.2916 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8132 Z= 0.234 Angle : 0.588 7.369 11096 Z= 0.282 Chirality : 0.043 0.137 1330 Planarity : 0.005 0.056 1390 Dihedral : 5.189 55.657 1191 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.08 % Allowed : 8.07 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.80 (0.27), residues: 1018 helix: 1.39 (0.24), residues: 490 sheet: -0.75 (0.42), residues: 138 loop : 0.06 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 71 HIS 0.003 0.001 HIS A 554 PHE 0.013 0.001 PHE A1154 TYR 0.012 0.001 TYR A 161 ARG 0.010 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.856 Fit side-chains REVERT: A 45 TRP cc_start: 0.7612 (p-90) cc_final: 0.7171 (m-90) REVERT: A 67 TRP cc_start: 0.8442 (t60) cc_final: 0.7901 (t60) REVERT: A 220 VAL cc_start: 0.8201 (t) cc_final: 0.7900 (p) REVERT: A 418 LYS cc_start: 0.8120 (ptmt) cc_final: 0.7351 (ptpt) REVERT: A 849 MET cc_start: 0.9036 (tpt) cc_final: 0.8522 (tpt) REVERT: A 941 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.8030 (mp) REVERT: A 1096 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7255 (tm) outliers start: 18 outliers final: 9 residues processed: 76 average time/residue: 1.1132 time to fit residues: 91.1308 Evaluate side-chains 70 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1096 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.103529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.081017 restraints weight = 14330.356| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.69 r_work: 0.2923 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8132 Z= 0.220 Angle : 0.553 6.915 11096 Z= 0.265 Chirality : 0.042 0.134 1330 Planarity : 0.004 0.037 1390 Dihedral : 4.896 52.345 1191 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.42 % Allowed : 9.80 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.05 (0.27), residues: 1018 helix: 1.59 (0.24), residues: 490 sheet: -0.54 (0.43), residues: 138 loop : 0.16 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 578 HIS 0.003 0.001 HIS A 554 PHE 0.012 0.001 PHE A1154 TYR 0.012 0.001 TYR A 161 ARG 0.006 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.845 Fit side-chains REVERT: A 45 TRP cc_start: 0.7610 (p-90) cc_final: 0.7172 (m-10) REVERT: A 67 TRP cc_start: 0.8415 (t60) cc_final: 0.7870 (t60) REVERT: A 220 VAL cc_start: 0.8345 (t) cc_final: 0.8072 (p) REVERT: A 418 LYS cc_start: 0.8227 (ptmt) cc_final: 0.7412 (ptpt) REVERT: A 632 MET cc_start: 0.7681 (ptm) cc_final: 0.7389 (ptp) REVERT: A 662 GLU cc_start: 0.9112 (pm20) cc_final: 0.8903 (pm20) REVERT: A 941 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8053 (mp) REVERT: A 1096 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7329 (tm) outliers start: 21 outliers final: 8 residues processed: 82 average time/residue: 1.0054 time to fit residues: 89.5963 Evaluate side-chains 72 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1096 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 55 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.102391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.079715 restraints weight = 14193.706| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.73 r_work: 0.2894 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8132 Z= 0.269 Angle : 0.591 10.033 11096 Z= 0.274 Chirality : 0.043 0.206 1330 Planarity : 0.004 0.037 1390 Dihedral : 4.795 47.544 1191 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.19 % Allowed : 11.65 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.10 (0.27), residues: 1018 helix: 1.61 (0.24), residues: 491 sheet: -0.45 (0.43), residues: 137 loop : 0.18 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 100 HIS 0.003 0.001 HIS A 408 PHE 0.013 0.001 PHE A1154 TYR 0.014 0.001 TYR A 161 ARG 0.004 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.846 Fit side-chains REVERT: A 45 TRP cc_start: 0.7628 (p-90) cc_final: 0.7193 (m-10) REVERT: A 67 TRP cc_start: 0.8418 (t60) cc_final: 0.7900 (t60) REVERT: A 220 VAL cc_start: 0.8451 (t) cc_final: 0.8217 (p) REVERT: A 418 LYS cc_start: 0.8270 (ptmt) cc_final: 0.7433 (ptpt) REVERT: A 673 GLN cc_start: 0.8402 (tp40) cc_final: 0.7992 (tp-100) REVERT: A 941 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8073 (mp) REVERT: A 1096 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7360 (tm) outliers start: 19 outliers final: 10 residues processed: 75 average time/residue: 1.0887 time to fit residues: 88.1142 Evaluate side-chains 75 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 905 MET Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1124 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 2 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 57 optimal weight: 0.0270 chunk 59 optimal weight: 0.4980 chunk 94 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 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.104694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.081468 restraints weight = 14172.884| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.80 r_work: 0.2932 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8132 Z= 0.176 Angle : 0.536 7.550 11096 Z= 0.252 Chirality : 0.041 0.156 1330 Planarity : 0.004 0.037 1390 Dihedral : 4.527 43.337 1191 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.31 % Allowed : 13.03 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 (0.27), residues: 1018 helix: 1.81 (0.24), residues: 491 sheet: -0.36 (0.43), residues: 137 loop : 0.34 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.004 0.000 HIS A 408 PHE 0.010 0.001 PHE A1154 TYR 0.010 0.001 TYR A 931 ARG 0.003 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 45 TRP cc_start: 0.7623 (p-90) cc_final: 0.7160 (m-10) REVERT: A 220 VAL cc_start: 0.8431 (t) cc_final: 0.8179 (p) REVERT: A 347 VAL cc_start: 0.8607 (t) cc_final: 0.8298 (m) REVERT: A 418 LYS cc_start: 0.8311 (ptmt) cc_final: 0.7474 (ptpt) REVERT: A 662 GLU cc_start: 0.9098 (pm20) cc_final: 0.8886 (pm20) REVERT: A 673 GLN cc_start: 0.8392 (tp40) cc_final: 0.8011 (tp-100) REVERT: A 941 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8078 (mp) REVERT: A 1096 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7390 (tm) outliers start: 20 outliers final: 6 residues processed: 82 average time/residue: 1.0851 time to fit residues: 95.9341 Evaluate side-chains 72 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1096 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN A 408 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.104195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.081822 restraints weight = 14222.271| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.72 r_work: 0.2937 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8132 Z= 0.176 Angle : 0.534 8.891 11096 Z= 0.251 Chirality : 0.041 0.182 1330 Planarity : 0.004 0.037 1390 Dihedral : 4.345 38.781 1191 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.08 % Allowed : 13.38 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.52 (0.27), residues: 1018 helix: 1.89 (0.24), residues: 491 sheet: -0.13 (0.42), residues: 138 loop : 0.44 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 170 HIS 0.004 0.000 HIS A 408 PHE 0.010 0.001 PHE A1154 TYR 0.012 0.001 TYR A 161 ARG 0.005 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.838 Fit side-chains REVERT: A 45 TRP cc_start: 0.7611 (p-90) cc_final: 0.7163 (m-10) REVERT: A 67 TRP cc_start: 0.8448 (t60) cc_final: 0.7936 (t60) REVERT: A 220 VAL cc_start: 0.8453 (t) cc_final: 0.8199 (p) REVERT: A 418 LYS cc_start: 0.8337 (ptmt) cc_final: 0.7481 (ptpt) REVERT: A 673 GLN cc_start: 0.8390 (tp40) cc_final: 0.7997 (tp-100) REVERT: A 941 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.8076 (mp) REVERT: A 1096 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7399 (tm) outliers start: 18 outliers final: 11 residues processed: 78 average time/residue: 1.1237 time to fit residues: 94.2425 Evaluate side-chains 77 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1096 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 20 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 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 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.103613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.081300 restraints weight = 14288.574| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.70 r_work: 0.2935 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8132 Z= 0.206 Angle : 0.545 9.163 11096 Z= 0.258 Chirality : 0.041 0.176 1330 Planarity : 0.004 0.035 1390 Dihedral : 4.264 34.156 1191 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.42 % Allowed : 13.38 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.27), residues: 1018 helix: 1.89 (0.24), residues: 491 sheet: -0.06 (0.43), residues: 138 loop : 0.48 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 100 HIS 0.003 0.001 HIS A 408 PHE 0.011 0.001 PHE A1154 TYR 0.013 0.001 TYR A 161 ARG 0.004 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.893 Fit side-chains REVERT: A 45 TRP cc_start: 0.7625 (p-90) cc_final: 0.7161 (m-10) REVERT: A 67 TRP cc_start: 0.8450 (t60) cc_final: 0.7937 (t60) REVERT: A 220 VAL cc_start: 0.8493 (t) cc_final: 0.8237 (p) REVERT: A 418 LYS cc_start: 0.8363 (ptmt) cc_final: 0.7497 (ptpt) REVERT: A 673 GLN cc_start: 0.8410 (tp40) cc_final: 0.8016 (tp-100) REVERT: A 834 LYS cc_start: 0.8178 (pmtt) cc_final: 0.7932 (mmtm) REVERT: A 941 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8104 (mp) REVERT: A 1096 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7563 (tm) outliers start: 21 outliers final: 12 residues processed: 79 average time/residue: 1.1129 time to fit residues: 94.5735 Evaluate side-chains 76 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1096 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 48 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 101 optimal weight: 0.0670 chunk 80 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 29 optimal weight: 0.0980 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.105029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.082852 restraints weight = 14314.270| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.70 r_work: 0.2960 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8132 Z= 0.156 Angle : 0.519 9.385 11096 Z= 0.246 Chirality : 0.040 0.158 1330 Planarity : 0.004 0.036 1390 Dihedral : 4.069 27.142 1191 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.31 % Allowed : 14.07 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.76 (0.27), residues: 1018 helix: 2.16 (0.24), residues: 478 sheet: 0.10 (0.43), residues: 139 loop : 0.48 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.004 0.000 HIS A 408 PHE 0.009 0.001 PHE A1154 TYR 0.010 0.001 TYR A 161 ARG 0.004 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.901 Fit side-chains REVERT: A 45 TRP cc_start: 0.7615 (p-90) cc_final: 0.7151 (m-10) REVERT: A 67 TRP cc_start: 0.8446 (t60) cc_final: 0.7898 (t60) REVERT: A 220 VAL cc_start: 0.8484 (t) cc_final: 0.8232 (p) REVERT: A 418 LYS cc_start: 0.8371 (ptmt) cc_final: 0.7550 (mttp) REVERT: A 673 GLN cc_start: 0.8425 (tp40) cc_final: 0.8039 (tp-100) REVERT: A 785 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7768 (pm20) REVERT: A 834 LYS cc_start: 0.8126 (pmtt) cc_final: 0.7906 (mmtm) REVERT: A 941 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8080 (mp) REVERT: A 1096 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7541 (tm) REVERT: A 1134 ASP cc_start: 0.8102 (m-30) cc_final: 0.7818 (m-30) outliers start: 20 outliers final: 9 residues processed: 87 average time/residue: 1.0178 time to fit residues: 95.7130 Evaluate side-chains 80 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1096 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 95 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.103646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.081290 restraints weight = 14574.079| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.73 r_work: 0.2931 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8132 Z= 0.207 Angle : 0.548 9.660 11096 Z= 0.258 Chirality : 0.041 0.151 1330 Planarity : 0.004 0.035 1390 Dihedral : 4.068 23.776 1191 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.85 % Allowed : 15.11 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.65 (0.27), residues: 1018 helix: 1.99 (0.24), residues: 485 sheet: 0.04 (0.42), residues: 143 loop : 0.51 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 100 HIS 0.003 0.001 HIS A 408 PHE 0.011 0.001 PHE A1154 TYR 0.012 0.001 TYR A 161 ARG 0.004 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 45 TRP cc_start: 0.7613 (p-90) cc_final: 0.7159 (m-10) REVERT: A 220 VAL cc_start: 0.8543 (t) cc_final: 0.8302 (p) REVERT: A 418 LYS cc_start: 0.8394 (ptmt) cc_final: 0.7567 (mttp) REVERT: A 673 GLN cc_start: 0.8436 (tp40) cc_final: 0.8049 (tp-100) REVERT: A 785 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7824 (pm20) REVERT: A 834 LYS cc_start: 0.8194 (pmtt) cc_final: 0.7954 (mmtm) REVERT: A 941 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8123 (mp) REVERT: A 1096 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7602 (tm) outliers start: 16 outliers final: 10 residues processed: 77 average time/residue: 1.1893 time to fit residues: 98.5075 Evaluate side-chains 78 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1096 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.102579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.080098 restraints weight = 14191.784| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.71 r_work: 0.2905 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8132 Z= 0.262 Angle : 0.568 9.663 11096 Z= 0.268 Chirality : 0.042 0.148 1330 Planarity : 0.004 0.034 1390 Dihedral : 4.181 21.186 1191 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.85 % Allowed : 14.99 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.57 (0.27), residues: 1018 helix: 1.94 (0.24), residues: 483 sheet: 0.03 (0.42), residues: 142 loop : 0.44 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 100 HIS 0.003 0.001 HIS A 554 PHE 0.012 0.001 PHE A1154 TYR 0.014 0.001 TYR A 161 ARG 0.005 0.000 ARG A 455 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 45 TRP cc_start: 0.7588 (p-90) cc_final: 0.7167 (m-10) REVERT: A 418 LYS cc_start: 0.8324 (ptmt) cc_final: 0.7474 (ptpt) REVERT: A 673 GLN cc_start: 0.8419 (tp40) cc_final: 0.8033 (tp-100) REVERT: A 785 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7785 (pm20) REVERT: A 941 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8066 (mp) REVERT: A 1096 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7599 (tm) REVERT: A 1128 MET cc_start: 0.7555 (mtt) cc_final: 0.7347 (mtp) outliers start: 16 outliers final: 10 residues processed: 73 average time/residue: 1.1363 time to fit residues: 89.2339 Evaluate side-chains 76 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 873 ASP Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1025 VAL Chi-restraints excluded: chain A residue 1096 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 62 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 35 optimal weight: 0.0470 chunk 71 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.103800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.081466 restraints weight = 14436.868| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.74 r_work: 0.2927 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8132 Z= 0.189 Angle : 0.540 9.472 11096 Z= 0.255 Chirality : 0.041 0.176 1330 Planarity : 0.004 0.036 1390 Dihedral : 4.078 19.054 1191 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.85 % Allowed : 15.34 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.66 (0.27), residues: 1018 helix: 1.98 (0.24), residues: 485 sheet: 0.01 (0.41), residues: 147 loop : 0.58 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 170 HIS 0.003 0.001 HIS A 408 PHE 0.011 0.001 PHE A1123 TYR 0.012 0.001 TYR A 161 ARG 0.005 0.000 ARG A 455 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4714.71 seconds wall clock time: 84 minutes 25.63 seconds (5065.63 seconds total)