Starting phenix.real_space_refine on Sun Apr 7 20:07:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7way_32389/04_2024/7way_32389.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7way_32389/04_2024/7way_32389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7way_32389/04_2024/7way_32389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7way_32389/04_2024/7way_32389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7way_32389/04_2024/7way_32389.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7way_32389/04_2024/7way_32389.pdb" } resolution = 2.9 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 175 5.49 5 S 28 5.16 5 C 6630 2.51 5 N 2041 2.21 5 O 2579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 246": "OD1" <-> "OD2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11453 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 674 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "C" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 547 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2446 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 55, 'rna3p_pyr': 48} Link IDs: {'rna2p': 12, 'rna3p': 102} Chain breaks: 1 Chain: "A" Number of atoms: 7786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 7786 Classifications: {'peptide': 960} Link IDs: {'PTRANS': 37, 'TRANS': 922} Chain breaks: 2 Time building chain proxies: 6.74, per 1000 atoms: 0.59 Number of scatterers: 11453 At special positions: 0 Unit cell: (100.58, 141.94, 125.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 175 15.00 O 2579 8.00 N 2041 7.00 C 6630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=0, symmetry=0 Time building additional restraints: 4.74 Conformation dependent library (CDL) restraints added in 1.6 seconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 49.6% alpha, 22.4% beta 61 base pairs and 103 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 60 through 92 Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 221 through 272 removed outlier: 3.644A pdb=" N VAL A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 309 Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.689A pdb=" N LYS A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 371 through 378 removed outlier: 4.135A pdb=" N GLN A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 394 through 411 Processing helix chain 'A' and resid 413 through 443 removed outlier: 3.532A pdb=" N VAL A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 466 Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 472 through 493 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 510 through 513 Processing helix chain 'A' and resid 589 through 596 Processing helix chain 'A' and resid 697 through 717 Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 725 through 750 Processing helix chain 'A' and resid 770 through 774 Processing helix chain 'A' and resid 775 through 790 removed outlier: 3.550A pdb=" N MET A 779 " --> pdb=" O GLN A 775 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 796 Processing helix chain 'A' and resid 818 through 829 Processing helix chain 'A' and resid 866 through 876 removed outlier: 3.981A pdb=" N GLU A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 885 Processing helix chain 'A' and resid 886 through 901 Processing helix chain 'A' and resid 921 through 936 removed outlier: 3.594A pdb=" N ALA A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 949 removed outlier: 3.518A pdb=" N THR A 949 " --> pdb=" O GLN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 973 removed outlier: 3.887A pdb=" N PHE A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 502 through 506 removed outlier: 3.643A pdb=" N GLY A 614 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR A 638 " --> pdb=" O ALA A 612 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY A 614 " --> pdb=" O ALA A 636 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA A 636 " --> pdb=" O GLY A 614 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL A 616 " --> pdb=" O PHE A 634 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE A 634 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU A 618 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA A 632 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR A 620 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU A 630 " --> pdb=" O THR A 620 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR A 622 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN A 628 " --> pdb=" O TYR A 622 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU A 633 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 502 through 506 removed outlier: 3.643A pdb=" N GLY A 614 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR A 638 " --> pdb=" O ALA A 612 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY A 614 " --> pdb=" O ALA A 636 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA A 636 " --> pdb=" O GLY A 614 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL A 616 " --> pdb=" O PHE A 634 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE A 634 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU A 618 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA A 632 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR A 620 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU A 630 " --> pdb=" O THR A 620 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR A 622 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN A 628 " --> pdb=" O TYR A 622 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU A 633 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 13.056A pdb=" N CYS A 515 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N ASN A 561 " --> pdb=" O CYS A 515 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE A 517 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL A 559 " --> pdb=" O PHE A 517 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE A 556 " --> pdb=" O VAL A 572 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 117 removed outlier: 4.365A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL A 139 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE A 128 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL A 139 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N SER A 126 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 114 through 117 removed outlier: 4.365A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL A 139 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N THR A 153 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR A 155 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 691 through 694 removed outlier: 4.520A pdb=" N ALA A 756 " --> pdb=" O ILE A 658 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ARG A 660 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 Processing sheet with id=AA8, first strand: chain 'A' and resid 830 through 832 removed outlier: 3.747A pdb=" N THR A 838 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 850 through 855 Processing sheet with id=AB1, first strand: chain 'A' and resid 909 through 911 447 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 151 hydrogen bonds 290 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 103 stacking parallelities Total time for adding SS restraints: 6.35 Time building geometry restraints manager: 5.16 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: 2340 1.33 - 1.45: 3480 1.45 - 1.57: 5834 1.57 - 1.69: 346 1.69 - 1.81: 41 Bond restraints: 12041 Sorted by residual: bond pdb=" CG LEU A 894 " pdb=" CD2 LEU A 894 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.30e+00 bond pdb=" N ASN A 528 " pdb=" CA ASN A 528 " ideal model delta sigma weight residual 1.453 1.466 -0.012 1.22e-02 6.72e+03 1.02e+00 bond pdb=" CA ILE A 108 " pdb=" CB ILE A 108 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 9.61e-01 bond pdb=" N TYR A 530 " pdb=" CA TYR A 530 " ideal model delta sigma weight residual 1.455 1.467 -0.012 1.29e-02 6.01e+03 9.27e-01 bond pdb=" O4' DA B 24 " pdb=" C1' DA B 24 " ideal model delta sigma weight residual 1.414 1.397 0.017 2.00e-02 2.50e+03 7.00e-01 ... (remaining 12036 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.49: 909 105.49 - 112.62: 6570 112.62 - 119.75: 4058 119.75 - 126.87: 4996 126.87 - 134.00: 505 Bond angle restraints: 17038 Sorted by residual: angle pdb=" N VAL A 524 " pdb=" CA VAL A 524 " pdb=" C VAL A 524 " ideal model delta sigma weight residual 112.96 109.33 3.63 1.00e+00 1.00e+00 1.32e+01 angle pdb=" N ASN A 107 " pdb=" CA ASN A 107 " pdb=" C ASN A 107 " ideal model delta sigma weight residual 114.75 110.90 3.85 1.26e+00 6.30e-01 9.34e+00 angle pdb=" CA LEU A 894 " pdb=" CB LEU A 894 " pdb=" CG LEU A 894 " ideal model delta sigma weight residual 116.30 126.80 -10.50 3.50e+00 8.16e-02 8.99e+00 angle pdb=" N LEU A 529 " pdb=" CA LEU A 529 " pdb=" C LEU A 529 " ideal model delta sigma weight residual 108.13 113.01 -4.88 1.72e+00 3.38e-01 8.03e+00 angle pdb=" CA TYR A 530 " pdb=" CB TYR A 530 " pdb=" CG TYR A 530 " ideal model delta sigma weight residual 113.90 118.58 -4.68 1.80e+00 3.09e-01 6.76e+00 ... (remaining 17033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.00: 6651 32.00 - 64.00: 557 64.00 - 96.01: 57 96.01 - 128.01: 0 128.01 - 160.01: 2 Dihedral angle restraints: 7267 sinusoidal: 4465 harmonic: 2802 Sorted by residual: dihedral pdb=" O4' U D 17 " pdb=" C1' U D 17 " pdb=" N1 U D 17 " pdb=" C2 U D 17 " ideal model delta sinusoidal sigma weight residual 232.00 90.82 141.18 1 1.70e+01 3.46e-03 5.91e+01 dihedral pdb=" CA ARG A 443 " pdb=" C ARG A 443 " pdb=" N SER A 444 " pdb=" CA SER A 444 " ideal model delta harmonic sigma weight residual -180.00 -154.38 -25.62 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA LEU A 527 " pdb=" C LEU A 527 " pdb=" N ASN A 528 " pdb=" CA ASN A 528 " ideal model delta harmonic sigma weight residual 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 7264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1760 0.057 - 0.115: 179 0.115 - 0.172: 21 0.172 - 0.229: 0 0.229 - 0.286: 1 Chirality restraints: 1961 Sorted by residual: chirality pdb=" CG LEU A 529 " pdb=" CB LEU A 529 " pdb=" CD1 LEU A 529 " pdb=" CD2 LEU A 529 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C3' C D 40 " pdb=" C4' C D 40 " pdb=" O3' C D 40 " pdb=" C2' C D 40 " both_signs ideal model delta sigma weight residual False -2.48 -2.33 -0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" C1' C D 19 " pdb=" O4' C D 19 " pdb=" C2' C D 19 " pdb=" N1 C D 19 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1958 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D 56 " -0.024 2.00e-02 2.50e+03 1.08e-02 3.18e+00 pdb=" N9 A D 56 " 0.024 2.00e-02 2.50e+03 pdb=" C8 A D 56 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A D 56 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A D 56 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A D 56 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A D 56 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A D 56 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A D 56 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A D 56 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A D 56 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 38 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 39 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 529 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.36e+00 pdb=" C LEU A 529 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU A 529 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR A 530 " -0.009 2.00e-02 2.50e+03 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 592 2.72 - 3.26: 10071 3.26 - 3.81: 19637 3.81 - 4.35: 24195 4.35 - 4.90: 37246 Nonbonded interactions: 91741 Sorted by model distance: nonbonded pdb=" OG1 THR A 816 " pdb=" NE2 GLN A 963 " model vdw 2.172 2.520 nonbonded pdb=" OG1 THR A 38 " pdb=" OD1 ASP A 40 " model vdw 2.190 2.440 nonbonded pdb=" O2' C D 40 " pdb=" OP1 U D 41 " model vdw 2.209 2.440 nonbonded pdb=" O HIS A 173 " pdb=" OG1 THR A 183 " model vdw 2.224 2.440 nonbonded pdb=" OD1 ASP A 865 " pdb=" OG SER A 867 " model vdw 2.233 2.440 ... (remaining 91736 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: 0.820 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: 3.480 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 38.510 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 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 0.038 12041 Z= 0.216 Angle : 0.542 10.496 17038 Z= 0.297 Chirality : 0.036 0.286 1961 Planarity : 0.004 0.043 1543 Dihedral : 19.589 160.010 5457 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.28), residues: 954 helix: 2.23 (0.25), residues: 430 sheet: -0.08 (0.43), residues: 139 loop : -0.28 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 519 HIS 0.005 0.001 HIS A 251 PHE 0.008 0.001 PHE A 543 TYR 0.019 0.001 TYR A 776 ARG 0.006 0.000 ARG A 956 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.002 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 54 average time/residue: 1.6134 time to fit residues: 94.1026 Evaluate side-chains 35 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.0570 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 0.0060 overall best weight: 1.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN A 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12041 Z= 0.191 Angle : 0.513 7.232 17038 Z= 0.278 Chirality : 0.035 0.190 1961 Planarity : 0.004 0.042 1543 Dihedral : 21.705 160.468 3449 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.60 % Allowed : 5.01 % Favored : 94.40 % 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: 1.49 (0.28), residues: 954 helix: 2.37 (0.25), residues: 440 sheet: -0.01 (0.43), residues: 138 loop : -0.26 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 86 HIS 0.007 0.001 HIS A 251 PHE 0.010 0.001 PHE A 517 TYR 0.022 0.001 TYR A 372 ARG 0.004 0.000 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 1.080 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 40 average time/residue: 1.5617 time to fit residues: 67.9405 Evaluate side-chains 37 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 28 optimal weight: 0.0570 chunk 101 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN A 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12041 Z= 0.176 Angle : 0.488 7.172 17038 Z= 0.266 Chirality : 0.034 0.151 1961 Planarity : 0.004 0.043 1543 Dihedral : 21.620 159.992 3449 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.72 % Allowed : 6.44 % Favored : 92.85 % 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: 1.59 (0.28), residues: 954 helix: 2.47 (0.25), residues: 442 sheet: 0.02 (0.42), residues: 138 loop : -0.23 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 86 HIS 0.007 0.001 HIS A 251 PHE 0.009 0.001 PHE A 517 TYR 0.016 0.001 TYR A 85 ARG 0.007 0.000 ARG A 824 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.962 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 46 average time/residue: 1.4080 time to fit residues: 70.6675 Evaluate side-chains 40 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 780 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 48 optimal weight: 0.2980 chunk 68 optimal weight: 0.0270 chunk 102 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 0.3980 chunk 29 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.1240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12041 Z= 0.151 Angle : 0.483 8.843 17038 Z= 0.259 Chirality : 0.034 0.227 1961 Planarity : 0.003 0.043 1543 Dihedral : 21.615 160.277 3449 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.07 % Allowed : 7.99 % Favored : 90.94 % 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: 1.72 (0.28), residues: 954 helix: 2.58 (0.25), residues: 442 sheet: 0.18 (0.43), residues: 140 loop : -0.22 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 86 HIS 0.005 0.001 HIS A 251 PHE 0.007 0.001 PHE A 543 TYR 0.022 0.001 TYR A 372 ARG 0.004 0.000 ARG A 956 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 1.084 Fit side-chains REVERT: A 195 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7623 (m-30) outliers start: 9 outliers final: 3 residues processed: 47 average time/residue: 1.3686 time to fit residues: 70.4381 Evaluate side-chains 43 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 780 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12041 Z= 0.166 Angle : 0.491 8.654 17038 Z= 0.263 Chirality : 0.034 0.201 1961 Planarity : 0.003 0.043 1543 Dihedral : 21.532 160.233 3447 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.83 % Allowed : 9.06 % Favored : 90.11 % 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: 1.76 (0.28), residues: 954 helix: 2.60 (0.25), residues: 442 sheet: 0.14 (0.43), residues: 140 loop : -0.16 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 86 HIS 0.005 0.001 HIS A 251 PHE 0.007 0.001 PHE A 543 TYR 0.014 0.001 TYR A 853 ARG 0.005 0.000 ARG A 956 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.968 Fit side-chains REVERT: A 195 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7618 (m-30) outliers start: 7 outliers final: 3 residues processed: 44 average time/residue: 1.4124 time to fit residues: 68.1125 Evaluate side-chains 40 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 780 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12041 Z= 0.152 Angle : 0.500 13.779 17038 Z= 0.262 Chirality : 0.034 0.177 1961 Planarity : 0.003 0.042 1543 Dihedral : 21.516 160.230 3447 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.83 % Allowed : 9.42 % Favored : 89.75 % 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: 1.81 (0.28), residues: 954 helix: 2.63 (0.25), residues: 442 sheet: 0.22 (0.42), residues: 150 loop : -0.14 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 86 HIS 0.004 0.001 HIS A 251 PHE 0.007 0.001 PHE A 543 TYR 0.025 0.001 TYR A 372 ARG 0.005 0.000 ARG A 956 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 1.059 Fit side-chains REVERT: A 195 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: A 486 TRP cc_start: 0.7343 (m-10) cc_final: 0.7115 (m-10) outliers start: 7 outliers final: 3 residues processed: 43 average time/residue: 1.4263 time to fit residues: 66.8691 Evaluate side-chains 43 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 780 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 40.0000 chunk 61 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN A 907 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12041 Z= 0.222 Angle : 0.533 13.670 17038 Z= 0.281 Chirality : 0.035 0.191 1961 Planarity : 0.004 0.042 1543 Dihedral : 21.520 159.835 3447 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.48 % Allowed : 10.01 % Favored : 89.51 % 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: 1.70 (0.28), residues: 954 helix: 2.55 (0.25), residues: 441 sheet: 0.00 (0.43), residues: 138 loop : -0.12 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 86 HIS 0.007 0.001 HIS A 251 PHE 0.008 0.001 PHE A 543 TYR 0.015 0.001 TYR A 85 ARG 0.005 0.000 ARG A 956 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 1.038 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 45 average time/residue: 1.5926 time to fit residues: 77.4319 Evaluate side-chains 44 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 780 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 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 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12041 Z= 0.191 Angle : 0.527 15.430 17038 Z= 0.276 Chirality : 0.035 0.175 1961 Planarity : 0.004 0.047 1543 Dihedral : 21.513 159.939 3447 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.60 % Allowed : 11.20 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.28), residues: 954 helix: 2.56 (0.25), residues: 442 sheet: 0.20 (0.43), residues: 150 loop : -0.12 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 486 HIS 0.005 0.001 HIS A 251 PHE 0.008 0.001 PHE A 543 TYR 0.024 0.001 TYR A 372 ARG 0.007 0.000 ARG A 956 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 1.091 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 44 average time/residue: 1.4668 time to fit residues: 70.4318 Evaluate side-chains 43 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 780 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 0.0770 chunk 106 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12041 Z= 0.139 Angle : 0.517 16.102 17038 Z= 0.271 Chirality : 0.034 0.150 1961 Planarity : 0.004 0.044 1543 Dihedral : 21.525 159.792 3447 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.83 % Allowed : 10.85 % Favored : 88.32 % 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: 1.83 (0.28), residues: 954 helix: 2.60 (0.25), residues: 442 sheet: 0.24 (0.43), residues: 150 loop : -0.08 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 486 HIS 0.004 0.001 HIS A 251 PHE 0.007 0.001 PHE A 509 TYR 0.013 0.001 TYR A 244 ARG 0.008 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.994 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 45 average time/residue: 1.5200 time to fit residues: 74.2869 Evaluate side-chains 45 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 780 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 68 optimal weight: 0.0970 chunk 54 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 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 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12041 Z= 0.149 Angle : 0.518 15.715 17038 Z= 0.268 Chirality : 0.034 0.153 1961 Planarity : 0.003 0.043 1543 Dihedral : 21.502 160.056 3447 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.48 % Allowed : 11.56 % Favored : 87.96 % 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: 1.90 (0.28), residues: 954 helix: 2.65 (0.25), residues: 442 sheet: 0.28 (0.43), residues: 150 loop : -0.02 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 486 HIS 0.003 0.001 HIS A 251 PHE 0.007 0.001 PHE A 543 TYR 0.026 0.001 TYR A 372 ARG 0.008 0.000 ARG A 956 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 1.083 Fit side-chains REVERT: A 111 ARG cc_start: 0.6596 (tpp-160) cc_final: 0.5999 (tpp-160) outliers start: 4 outliers final: 3 residues processed: 42 average time/residue: 1.5630 time to fit residues: 71.2324 Evaluate side-chains 42 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 780 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 10.0000 chunk 81 optimal weight: 0.0030 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 11 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.113194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.078401 restraints weight = 22245.564| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.43 r_work: 0.2833 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12041 Z= 0.177 Angle : 0.522 15.711 17038 Z= 0.273 Chirality : 0.034 0.162 1961 Planarity : 0.004 0.042 1543 Dihedral : 21.494 159.882 3447 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.48 % Allowed : 11.44 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.88 (0.28), residues: 954 helix: 2.64 (0.25), residues: 442 sheet: 0.16 (0.43), residues: 148 loop : 0.01 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 486 HIS 0.005 0.001 HIS A 251 PHE 0.007 0.001 PHE A 543 TYR 0.014 0.001 TYR A 85 ARG 0.008 0.000 ARG A 956 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2683.04 seconds wall clock time: 49 minutes 42.29 seconds (2982.29 seconds total)