Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 19:07:16 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op5_13013/12_2021/7op5_13013_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op5_13013/12_2021/7op5_13013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op5_13013/12_2021/7op5_13013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op5_13013/12_2021/7op5_13013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op5_13013/12_2021/7op5_13013_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op5_13013/12_2021/7op5_13013_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 8554 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8554 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2, 'peptide': 1076} Link IDs: {'PTRANS': 50, 'TRANS': 1025, None: 2} Not linked: pdbres="LYS A1385 " pdbres="BEF A1401 " Not linked: pdbres="BEF A1401 " pdbres=" MG A1402 " Chain breaks: 9 Time building chain proxies: 5.58, per 1000 atoms: 0.65 Number of scatterers: 8554 At special positions: 0 Unit cell: (79.8136, 91.7585, 144.425, 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 53 16.00 Mg 1 11.99 F 3 9.00 O 1526 8.00 N 1426 7.00 C 5544 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 Amimo 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=0, symmetry=0 Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.6 seconds 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 9 sheets defined 40.7% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 242 through 250 removed outlier: 4.085A pdb=" N TRP A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 259 Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 395 through 410 removed outlier: 4.080A pdb=" N ALA A 398 " --> pdb=" O PRO A 395 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A 399 " --> pdb=" O PHE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 445 removed outlier: 3.748A pdb=" N ALA A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N MET A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 No H-bonds generated for 'chain 'A' and resid 499 through 502' Processing helix chain 'A' and resid 530 through 535 Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 570 through 579 removed outlier: 3.852A pdb=" N LEU A 574 " --> pdb=" O THR A 570 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A 575 " --> pdb=" O ARG A 571 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 579 " --> pdb=" O VAL A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 617 removed outlier: 3.553A pdb=" N LEU A 605 " --> pdb=" O CYS A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 624 Processing helix chain 'A' and resid 626 through 635 removed outlier: 4.690A pdb=" N LEU A 631 " --> pdb=" O ARG A 627 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 658 removed outlier: 3.663A pdb=" N ALA A 651 " --> pdb=" O GLY A 647 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG A 654 " --> pdb=" O PHE A 650 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 673 removed outlier: 3.502A pdb=" N VAL A 668 " --> pdb=" O PRO A 665 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 669 " --> pdb=" O GLN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 717 removed outlier: 4.048A pdb=" N TRP A 717 " --> pdb=" O ASP A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 758 removed outlier: 3.866A pdb=" N VAL A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 783 removed outlier: 4.362A pdb=" N LYS A 778 " --> pdb=" O PRO A 774 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 871 Proline residue: A 869 - end of helix No H-bonds generated for 'chain 'A' and resid 865 through 871' Processing helix chain 'A' and resid 881 through 889 Processing helix chain 'A' and resid 910 through 913 No H-bonds generated for 'chain 'A' and resid 910 through 913' Processing helix chain 'A' and resid 916 through 919 No H-bonds generated for 'chain 'A' and resid 916 through 919' Processing helix chain 'A' and resid 939 through 948 Processing helix chain 'A' and resid 964 through 971 Processing helix chain 'A' and resid 1045 through 1051 Processing helix chain 'A' and resid 1057 through 1064 Processing helix chain 'A' and resid 1073 through 1085 Processing helix chain 'A' and resid 1097 through 1105 removed outlier: 5.373A pdb=" N ALA A1101 " --> pdb=" O ASN A1098 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A1102 " --> pdb=" O ASP A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1120 No H-bonds generated for 'chain 'A' and resid 1118 through 1120' Processing helix chain 'A' and resid 1133 through 1166 removed outlier: 3.997A pdb=" N SER A1158 " --> pdb=" O MET A1154 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1185 Processing helix chain 'A' and resid 1188 through 1196 removed outlier: 4.296A pdb=" N SER A1196 " --> pdb=" O ALA A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1242 removed outlier: 4.053A pdb=" N MET A1231 " --> pdb=" O PHE A1227 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN A1242 " --> pdb=" O VAL A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1280 removed outlier: 3.752A pdb=" N SER A1270 " --> pdb=" O LEU A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1313 Processing helix chain 'A' and resid 1317 through 1322 Processing helix chain 'A' and resid 1330 through 1352 removed outlier: 3.626A pdb=" N ILE A1337 " --> pdb=" O LYS A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1367 Processing helix chain 'A' and resid 1379 through 1382 No H-bonds generated for 'chain 'A' and resid 1379 through 1382' Processing sheet with id= A, first strand: chain 'A' and resid 206 through 208 Processing sheet with id= B, first strand: chain 'A' and resid 322 through 325 removed outlier: 3.778A pdb=" N LYS A 338 " --> pdb=" O HIS A 333 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 450 through 455 Processing sheet with id= D, first strand: chain 'A' and resid 508 through 511 removed outlier: 3.753A pdb=" N CYS A 494 " --> pdb=" O LYS A 510 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN A 497 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LEU A 543 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 660 through 662 Processing sheet with id= F, first strand: chain 'A' and resid 952 through 955 removed outlier: 3.537A pdb=" N VAL A 954 " --> pdb=" O MET A 677 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 691 through 697 removed outlier: 7.191A pdb=" N ILE A 930 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE A 695 " --> pdb=" O PHE A 928 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE A 928 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL A 697 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL A 926 " --> pdb=" O VAL A 697 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N CYS A 898 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE A 928 " --> pdb=" O ILE A 896 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE A 896 " --> pdb=" O PHE A 928 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A 834 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG A 850 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 832 " --> pdb=" O ARG A 850 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1037 through 1039 removed outlier: 6.505A pdb=" N HIS A 979 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LYS A 996 " --> pdb=" O ILE A 986 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.810A pdb=" N ASP A 486 " --> pdb=" O ARG A 564 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG A 564 " --> pdb=" O ASP A 486 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU A 488 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL A 562 " --> pdb=" O LEU A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id= I 315 hydrogen bonds defined for protein. 858 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: 2.78 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2683 1.34 - 1.46: 1647 1.46 - 1.58: 4348 1.58 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 8755 Sorted by residual: bond pdb=" F2 BEF A1401 " pdb="BE BEF A1401 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" F3 BEF A1401 " pdb="BE BEF A1401 " ideal model delta sigma weight residual 1.476 1.545 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" F1 BEF A1401 " pdb="BE BEF A1401 " ideal model delta sigma weight residual 1.476 1.533 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" N LYS A 582 " pdb=" CA LYS A 582 " ideal model delta sigma weight residual 1.458 1.504 -0.046 1.90e-02 2.77e+03 5.91e+00 bond pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 1.457 1.479 -0.021 1.29e-02 6.01e+03 2.73e+00 ... (remaining 8750 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.77: 264 106.77 - 113.58: 4814 113.58 - 120.39: 3426 120.39 - 127.21: 3282 127.21 - 134.02: 100 Bond angle restraints: 11886 Sorted by residual: angle pdb=" C ASP A 378 " pdb=" N VAL A 379 " pdb=" CA VAL A 379 " ideal model delta sigma weight residual 121.97 126.35 -4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" F2 BEF A1401 " pdb="BE BEF A1401 " pdb=" F3 BEF A1401 " ideal model delta sigma weight residual 119.96 107.39 12.57 3.00e+00 1.11e-01 1.75e+01 angle pdb=" N SER A 487 " pdb=" CA SER A 487 " pdb=" C SER A 487 " ideal model delta sigma weight residual 108.34 113.44 -5.10 1.31e+00 5.83e-01 1.51e+01 angle pdb=" C GLY A 863 " pdb=" N SER A 864 " pdb=" CA SER A 864 " ideal model delta sigma weight residual 121.27 133.97 -12.70 3.40e+00 8.65e-02 1.39e+01 angle pdb=" F1 BEF A1401 " pdb="BE BEF A1401 " pdb=" F3 BEF A1401 " ideal model delta sigma weight residual 120.12 109.69 10.43 3.00e+00 1.11e-01 1.21e+01 ... (remaining 11881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 4586 16.26 - 32.52: 504 32.52 - 48.78: 91 48.78 - 65.04: 12 65.04 - 81.30: 3 Dihedral angle restraints: 5196 sinusoidal: 2051 harmonic: 3145 Sorted by residual: dihedral pdb=" CA GLU A 381 " pdb=" C GLU A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta harmonic sigma weight residual -180.00 -152.57 -27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA PRO A 581 " pdb=" C PRO A 581 " pdb=" N LYS A 582 " pdb=" CA LYS A 582 " ideal model delta harmonic sigma weight residual 180.00 157.80 22.20 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA LEU A1354 " pdb=" C LEU A1354 " pdb=" N PHE A1355 " pdb=" CA PHE A1355 " ideal model delta harmonic sigma weight residual -180.00 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 825 0.034 - 0.068: 355 0.068 - 0.102: 124 0.102 - 0.136: 47 0.136 - 0.171: 9 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CB ILE A 282 " pdb=" CA ILE A 282 " pdb=" CG1 ILE A 282 " pdb=" CG2 ILE A 282 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CB ILE A1232 " pdb=" CA ILE A1232 " pdb=" CG1 ILE A1232 " pdb=" CG2 ILE A1232 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA GLU A 781 " pdb=" N GLU A 781 " pdb=" C GLU A 781 " pdb=" CB GLU A 781 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 1357 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 581 " -0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C PRO A 581 " 0.070 2.00e-02 2.50e+03 pdb=" O PRO A 581 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS A 582 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 785 " 0.022 2.00e-02 2.50e+03 1.65e-02 6.77e+00 pdb=" CG TRP A 785 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 785 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 785 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 785 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 785 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 785 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 785 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 785 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 785 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 233 " -0.017 2.00e-02 2.50e+03 1.55e-02 4.78e+00 pdb=" CG TYR A 233 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 233 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 233 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 233 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 233 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 233 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 233 " 0.000 2.00e-02 2.50e+03 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 54 2.53 - 3.12: 6673 3.12 - 3.72: 12572 3.72 - 4.31: 16442 4.31 - 4.90: 27738 Nonbonded interactions: 63479 Sorted by model distance: nonbonded pdb=" F2 BEF A1401 " pdb="MG MG A1402 " model vdw 1.940 2.120 nonbonded pdb=" O ASP A 680 " pdb=" OG1 THR A 684 " model vdw 2.180 2.440 nonbonded pdb=" F1 BEF A1401 " pdb="MG MG A1402 " model vdw 2.232 2.120 nonbonded pdb=" OG1 THR A1253 " pdb=" O LYS A1255 " model vdw 2.248 2.440 nonbonded pdb=" OH TYR A 332 " pdb=" OD1 ASP A 337 " model vdw 2.255 2.440 ... (remaining 63474 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 53 5.16 5 Be 1 3.05 5 C 5544 2.51 5 N 1426 2.21 5 O 1526 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Write .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: 7.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 42.710 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.170 Process input model: 28.680 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.210 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 81.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 8755 Z= 0.249 Angle : 0.716 12.696 11886 Z= 0.391 Chirality : 0.046 0.171 1360 Planarity : 0.005 0.047 1485 Dihedral : 13.583 81.295 3158 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.25), residues: 1056 helix: 0.30 (0.25), residues: 434 sheet: -1.87 (0.41), residues: 171 loop : -2.22 (0.27), residues: 451 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.071 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2399 time to fit residues: 44.5325 Evaluate side-chains 102 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.155 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 0.0370 chunk 45 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 8755 Z= 0.189 Angle : 0.568 7.480 11886 Z= 0.298 Chirality : 0.043 0.144 1360 Planarity : 0.004 0.064 1485 Dihedral : 4.965 24.718 1171 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.26), residues: 1056 helix: 0.68 (0.25), residues: 434 sheet: -1.55 (0.42), residues: 162 loop : -2.26 (0.27), residues: 460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.040 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 121 average time/residue: 0.2033 time to fit residues: 34.8564 Evaluate side-chains 113 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0878 time to fit residues: 2.8809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.0040 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 8755 Z= 0.245 Angle : 0.569 6.990 11886 Z= 0.300 Chirality : 0.044 0.148 1360 Planarity : 0.005 0.101 1485 Dihedral : 4.973 21.629 1171 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.26), residues: 1056 helix: 0.64 (0.25), residues: 428 sheet: -1.40 (0.43), residues: 160 loop : -2.20 (0.27), residues: 468 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 1.080 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 110 average time/residue: 0.2061 time to fit residues: 32.0974 Evaluate side-chains 105 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 0.964 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0887 time to fit residues: 1.8516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 chunk 92 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8755 Z= 0.173 Angle : 0.521 6.990 11886 Z= 0.272 Chirality : 0.042 0.147 1360 Planarity : 0.005 0.100 1485 Dihedral : 4.673 20.327 1171 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.26), residues: 1056 helix: 0.79 (0.25), residues: 432 sheet: -1.28 (0.43), residues: 160 loop : -2.23 (0.26), residues: 464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 123 average time/residue: 0.2029 time to fit residues: 35.6673 Evaluate side-chains 112 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0935 time to fit residues: 2.3800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.4980 chunk 58 optimal weight: 0.0050 chunk 1 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 0.0170 chunk 88 optimal weight: 0.5980 chunk 71 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.3232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 8755 Z= 0.156 Angle : 0.518 7.321 11886 Z= 0.271 Chirality : 0.042 0.165 1360 Planarity : 0.005 0.104 1485 Dihedral : 4.422 19.777 1171 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.26), residues: 1056 helix: 1.04 (0.26), residues: 433 sheet: -1.13 (0.43), residues: 158 loop : -2.06 (0.27), residues: 465 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 1.059 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 121 average time/residue: 0.2140 time to fit residues: 36.8635 Evaluate side-chains 116 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 1.062 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1007 time to fit residues: 2.5356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 8755 Z= 0.202 Angle : 0.531 6.457 11886 Z= 0.277 Chirality : 0.042 0.160 1360 Planarity : 0.005 0.109 1485 Dihedral : 4.473 18.654 1171 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.26), residues: 1056 helix: 0.97 (0.26), residues: 432 sheet: -1.19 (0.42), residues: 162 loop : -2.01 (0.27), residues: 462 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 118 average time/residue: 0.1989 time to fit residues: 33.8856 Evaluate side-chains 110 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1020 time to fit residues: 2.1715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.6980 chunk 58 optimal weight: 0.0970 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 8755 Z= 0.205 Angle : 0.539 6.718 11886 Z= 0.280 Chirality : 0.042 0.171 1360 Planarity : 0.005 0.116 1485 Dihedral : 4.473 18.351 1171 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.26), residues: 1056 helix: 0.98 (0.26), residues: 432 sheet: -1.17 (0.42), residues: 162 loop : -2.01 (0.27), residues: 462 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 0.967 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 111 average time/residue: 0.1982 time to fit residues: 31.8501 Evaluate side-chains 105 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0881 time to fit residues: 2.1264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.0010 chunk 50 optimal weight: 0.4980 chunk 9 optimal weight: 0.0870 chunk 81 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1324 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.095 8755 Z= 0.183 Angle : 0.539 10.341 11886 Z= 0.280 Chirality : 0.041 0.180 1360 Planarity : 0.006 0.151 1485 Dihedral : 4.324 18.601 1171 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.26), residues: 1056 helix: 1.11 (0.26), residues: 432 sheet: -1.12 (0.42), residues: 162 loop : -1.92 (0.27), residues: 462 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 1.070 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 111 average time/residue: 0.2013 time to fit residues: 32.2179 Evaluate side-chains 107 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 1.031 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1071 time to fit residues: 1.9766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 98 optimal weight: 0.0010 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 0.0040 chunk 86 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.100 8755 Z= 0.178 Angle : 0.540 9.709 11886 Z= 0.279 Chirality : 0.041 0.188 1360 Planarity : 0.006 0.134 1485 Dihedral : 4.210 18.431 1171 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.26), residues: 1056 helix: 1.24 (0.26), residues: 427 sheet: -1.05 (0.42), residues: 162 loop : -1.87 (0.27), residues: 467 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 113 average time/residue: 0.2094 time to fit residues: 33.9198 Evaluate side-chains 107 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1046 time to fit residues: 2.0371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 10.0000 chunk 48 optimal weight: 0.2980 chunk 70 optimal weight: 0.4980 chunk 106 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.129 8755 Z= 0.207 Angle : 0.559 11.189 11886 Z= 0.292 Chirality : 0.042 0.185 1360 Planarity : 0.006 0.143 1485 Dihedral : 4.316 19.521 1171 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.26), residues: 1056 helix: 1.21 (0.26), residues: 425 sheet: -1.07 (0.42), residues: 164 loop : -1.81 (0.27), residues: 467 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.094 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 105 average time/residue: 0.2911 time to fit residues: 45.7849 Evaluate side-chains 104 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1283 time to fit residues: 1.7695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 12 optimal weight: 0.0570 chunk 23 optimal weight: 0.0470 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.170186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.141267 restraints weight = 12979.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.143995 restraints weight = 9113.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.145882 restraints weight = 7201.058| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.132 8755 Z= 0.168 Angle : 0.547 12.076 11886 Z= 0.283 Chirality : 0.041 0.198 1360 Planarity : 0.006 0.138 1485 Dihedral : 4.151 19.758 1171 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.26), residues: 1056 helix: 1.48 (0.26), residues: 419 sheet: -0.96 (0.43), residues: 162 loop : -1.72 (0.27), residues: 475 =============================================================================== Job complete usr+sys time: 2131.00 seconds wall clock time: 39 minutes 26.78 seconds (2366.78 seconds total)