Starting phenix.real_space_refine on Tue Nov 14 07:18:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n70_24214/11_2023/7n70_24214_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n70_24214/11_2023/7n70_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n70_24214/11_2023/7n70_24214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n70_24214/11_2023/7n70_24214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n70_24214/11_2023/7n70_24214_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n70_24214/11_2023/7n70_24214_trim.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 7953 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 7953 Unusual residues: {' MG': 1, 'BEF': 1, 'LMT': 1, 'Y01': 1} Classifications: {'peptide': 1032, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 959, None: 4} Not linked: pdbres="PRO A1168 " pdbres="BEF A1201 " Not linked: pdbres="BEF A1201 " pdbres=" MG A1202 " Not linked: pdbres=" MG A1202 " pdbres="Y01 A1203 " Not linked: pdbres="Y01 A1203 " pdbres="LMT A1204 " Chain breaks: 6 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Time building chain proxies: 4.92, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 0.99 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: 3.14 Time building geometry restraints manager: 3.54 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: 92.24 - 100.61: 16 100.61 - 108.98: 618 108.98 - 117.34: 5400 117.34 - 125.71: 4917 125.71 - 134.08: 145 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: 4369 15.25 - 30.50: 372 30.50 - 45.74: 108 45.74 - 60.99: 23 60.99 - 76.24: 9 Dihedral angle restraints: 4881 sinusoidal: 1899 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 4878 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 2.390 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 2.440 ... (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: 1.310 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: 7.070 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 26.680 Find NCS groups from input model: 0.220 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: 0.000 Load rotamer database and sin/cos tables:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.080 ------------------------------------------------------------------------------- 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 : 13.209 76.240 2955 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.959 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 1.2011 time to fit residues: 138.0336 Evaluate side-chains 66 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2986 ------------------------------------------------------------------------------- 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: 0.9980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8132 Z= 0.292 Angle : 0.598 7.143 11096 Z= 0.288 Chirality : 0.043 0.136 1330 Planarity : 0.005 0.055 1390 Dihedral : 5.105 56.429 1133 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.19 % Allowed : 8.42 % Favored : 89.39 % 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: 0.73 (0.27), residues: 1018 helix: 1.39 (0.24), residues: 490 sheet: -0.82 (0.42), residues: 138 loop : -0.05 (0.33), residues: 390 *********************** 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 90 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 71 time to evaluate : 0.946 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 78 average time/residue: 1.0321 time to fit residues: 86.9970 Evaluate side-chains 68 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.4243 time to fit residues: 3.2827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 93 optimal weight: 0.0970 chunk 101 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 179 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8132 Z= 0.160 Angle : 0.531 6.803 11096 Z= 0.252 Chirality : 0.041 0.130 1330 Planarity : 0.004 0.039 1390 Dihedral : 4.759 53.389 1133 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.08 % Allowed : 10.27 % Favored : 87.66 % 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: 1.12 (0.27), residues: 1018 helix: 1.71 (0.24), residues: 490 sheet: -0.50 (0.43), residues: 138 loop : 0.09 (0.33), residues: 390 *********************** 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 88 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 1.287 Fit side-chains outliers start: 18 outliers final: 6 residues processed: 80 average time/residue: 1.0358 time to fit residues: 89.8468 Evaluate side-chains 67 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.942 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.1625 time to fit residues: 2.1680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 44 optimal weight: 0.0170 chunk 62 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 89 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8132 Z= 0.165 Angle : 0.540 8.860 11096 Z= 0.251 Chirality : 0.041 0.218 1330 Planarity : 0.004 0.038 1390 Dihedral : 4.535 49.462 1133 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.42 % Allowed : 11.19 % Favored : 86.39 % 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: 1.32 (0.27), residues: 1018 helix: 1.86 (0.24), residues: 484 sheet: -0.35 (0.43), residues: 138 loop : 0.22 (0.33), residues: 396 *********************** 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 92 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 71 time to evaluate : 0.923 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 81 average time/residue: 1.0547 time to fit residues: 92.2127 Evaluate side-chains 70 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.3999 time to fit residues: 3.0832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 25 optimal weight: 0.2980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8132 Z= 0.243 Angle : 0.566 8.047 11096 Z= 0.263 Chirality : 0.042 0.154 1330 Planarity : 0.004 0.037 1390 Dihedral : 4.483 43.489 1133 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.08 % Allowed : 12.34 % Favored : 85.58 % 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: 1.86 (0.24), residues: 490 sheet: -0.27 (0.43), residues: 138 loop : 0.24 (0.33), residues: 390 *********************** 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 85 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 67 time to evaluate : 0.998 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 81 average time/residue: 1.0759 time to fit residues: 94.2356 Evaluate side-chains 67 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.1120 time to fit residues: 1.7252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 52 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8132 Z= 0.191 Angle : 0.534 8.244 11096 Z= 0.251 Chirality : 0.041 0.178 1330 Planarity : 0.004 0.037 1390 Dihedral : 4.324 40.448 1133 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.85 % Allowed : 14.07 % Favored : 84.08 % 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: 1.97 (0.24), residues: 484 sheet: -0.06 (0.43), residues: 139 loop : 0.33 (0.33), residues: 395 *********************** 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 82 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.996 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 77 average time/residue: 1.0247 time to fit residues: 85.5099 Evaluate side-chains 67 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.949 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.1454 time to fit residues: 2.4970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8132 Z= 0.198 Angle : 0.539 8.994 11096 Z= 0.251 Chirality : 0.041 0.163 1330 Planarity : 0.004 0.036 1390 Dihedral : 4.199 36.111 1133 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.61 % Allowed : 14.53 % Favored : 83.85 % 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: 1.58 (0.27), residues: 1018 helix: 2.00 (0.24), residues: 483 sheet: 0.02 (0.42), residues: 139 loop : 0.37 (0.33), residues: 396 *********************** 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 77 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.874 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 73 average time/residue: 1.0204 time to fit residues: 80.7334 Evaluate side-chains 67 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.919 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1293 time to fit residues: 1.6982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 95 optimal weight: 0.0770 overall best weight: 0.5940 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8132 Z= 0.179 Angle : 0.527 9.316 11096 Z= 0.246 Chirality : 0.041 0.151 1330 Planarity : 0.004 0.036 1390 Dihedral : 4.041 31.010 1133 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.61 % Allowed : 14.76 % 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: 1.66 (0.27), residues: 1018 helix: 2.04 (0.24), residues: 483 sheet: 0.08 (0.42), residues: 139 loop : 0.44 (0.33), residues: 396 *********************** 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 80 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 0.754 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 78 average time/residue: 0.8795 time to fit residues: 74.7719 Evaluate side-chains 73 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.1221 time to fit residues: 1.4705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 60 optimal weight: 0.0980 chunk 97 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 179 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8132 Z= 0.177 Angle : 0.538 9.538 11096 Z= 0.250 Chirality : 0.041 0.174 1330 Planarity : 0.004 0.035 1390 Dihedral : 3.962 26.684 1133 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.50 % Allowed : 15.80 % Favored : 82.70 % 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: 1.71 (0.27), residues: 1018 helix: 2.05 (0.24), residues: 483 sheet: 0.13 (0.42), residues: 139 loop : 0.49 (0.33), residues: 396 *********************** 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 79 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.967 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 76 average time/residue: 1.0366 time to fit residues: 85.5548 Evaluate side-chains 72 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.1913 time to fit residues: 1.7407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 0.0980 chunk 94 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 179 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8132 Z= 0.347 Angle : 0.600 9.580 11096 Z= 0.283 Chirality : 0.044 0.170 1330 Planarity : 0.004 0.034 1390 Dihedral : 4.241 26.136 1133 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.27 % Allowed : 16.15 % Favored : 82.58 % 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: 1.41 (0.27), residues: 1018 helix: 1.78 (0.24), residues: 489 sheet: -0.02 (0.43), residues: 144 loop : 0.36 (0.34), residues: 385 ********************** 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 74 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.964 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 72 average time/residue: 0.9895 time to fit residues: 77.6469 Evaluate side-chains 67 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.957 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.2876 time to fit residues: 1.6772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 15 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 179 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.081708 restraints weight = 14077.498| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.66 r_work: 0.2936 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2070 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= 0.170 Angle : 0.535 9.236 11096 Z= 0.251 Chirality : 0.041 0.173 1330 Planarity : 0.004 0.034 1390 Dihedral : 3.996 23.299 1133 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.15 % Allowed : 16.15 % Favored : 82.70 % 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: 1.63 (0.28), residues: 1018 helix: 1.96 (0.24), residues: 490 sheet: -0.00 (0.42), residues: 148 loop : 0.52 (0.35), residues: 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2518.73 seconds wall clock time: 45 minutes 49.26 seconds (2749.26 seconds total)