Starting phenix.real_space_refine (version: dev) on Thu May 12 21:44:45 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/05_2022/7ozu_13135_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/05_2022/7ozu_13135.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/05_2022/7ozu_13135_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/05_2022/7ozu_13135_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/05_2022/7ozu_13135_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/05_2022/7ozu_13135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/05_2022/7ozu_13135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/05_2022/7ozu_13135_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/05_2022/7ozu_13135_updated.pdb" } resolution = 3.3 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= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 8408 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6565 Classifications: {'peptide': 814} Link IDs: {'PTRANS': 26, 'TRANS': 786, 'PCIS': 1} Chain breaks: 3 Chain: "B" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 109, 'PCIS': 1} Chain: "C" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 478 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "P" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 212 Classifications: {'RNA': 10} Modifications used: {'rna3p_pyr': 5, 'rna2p_pur': 1, 'rna3p_pur': 4} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 12} Modifications used: {'rna3p_pyr': 4, 'rna3p_pur': 7, 'rna3p': 1} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1692 SG CYS A 301 47.629 66.446 35.948 1.00 75.77 S ATOM 1733 SG CYS A 306 47.619 65.877 32.167 1.00 71.14 S ATOM 1765 SG CYS A 310 50.645 65.595 34.602 1.00 65.59 S ATOM 3132 SG CYS A 487 29.807 62.600 44.981 1.00 68.93 S ATOM 4385 SG CYS A 645 28.884 62.549 41.352 1.00 75.15 S ATOM 4391 SG CYS A 646 31.664 64.707 42.888 1.00 71.21 S Time building chain proxies: 5.09, per 1000 atoms: 0.61 Number of scatterers: 8408 At special positions: 0 Unit cell: (90.906, 94.242, 98.412, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 57 16.00 P 22 15.00 O 1638 8.00 N 1405 7.00 C 5284 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: 3.72 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 306 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 310 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 301 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 487 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 646 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 645 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 642 " Number of angles added : 6 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 7 sheets defined 48.0% alpha, 9.8% beta 7 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 154 through 158 removed outlier: 4.064A pdb=" N ASN A 158 " --> pdb=" O ASP A 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 158' Processing helix chain 'A' and resid 169 through 199 removed outlier: 4.074A pdb=" N TYR A 175 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 247 Proline residue: A 243 - end of helix removed outlier: 3.812A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.267A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 317 removed outlier: 3.693A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.609A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.746A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 3.726A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 562 through 581 removed outlier: 5.757A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 718 through 731 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 796 through 798 No H-bonds generated for 'chain 'A' and resid 796 through 798' Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 847 through 850 Processing helix chain 'A' and resid 853 through 865 removed outlier: 3.869A pdb=" N GLU A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 871 Processing helix chain 'A' and resid 875 through 895 removed outlier: 3.916A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 915 Processing helix chain 'A' and resid 918 through 925 removed outlier: 3.853A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 97 Processing helix chain 'B' and resid 100 through 109 removed outlier: 4.042A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.735A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 2 through 20 Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 26 through 41 Processing helix chain 'C' and resid 45 through 61 Processing sheet with id= A, first strand: chain 'A' and resid 32 through 38 Processing sheet with id= B, first strand: chain 'A' and resid 330 through 335 Processing sheet with id= C, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= D, first strand: chain 'A' and resid 556 through 559 removed outlier: 5.938A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 800 through 802 removed outlier: 4.120A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 816 through 822 Processing sheet with id= G, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.061A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1330 1.31 - 1.43: 2520 1.43 - 1.56: 4659 1.56 - 1.68: 46 1.68 - 1.81: 87 Bond restraints: 8642 Sorted by residual: bond pdb=" O4' 7OK T 9 " pdb=" C1' 7OK T 9 " ideal model delta sigma weight residual 1.412 1.626 -0.214 1.50e-02 4.44e+03 2.03e+02 bond pdb=" C2' 7OK T 9 " pdb=" C1' 7OK T 9 " ideal model delta sigma weight residual 1.529 1.346 0.183 1.50e-02 4.44e+03 1.50e+02 bond pdb=" C4' 7OK T 9 " pdb=" O4' 7OK T 9 " ideal model delta sigma weight residual 1.451 1.299 0.152 1.50e-02 4.44e+03 1.03e+02 bond pdb=" C4 7OK T 9 " pdb=" N4 7OK T 9 " ideal model delta sigma weight residual 1.241 1.439 -0.198 2.00e-02 2.50e+03 9.84e+01 bond pdb=" C2 7OK T 9 " pdb=" N3 7OK T 9 " ideal model delta sigma weight residual 1.500 1.329 0.171 2.00e-02 2.50e+03 7.28e+01 ... (remaining 8637 not shown) Histogram of bond angle deviations from ideal: 92.05 - 100.44: 7 100.44 - 108.83: 635 108.83 - 117.22: 5515 117.22 - 125.60: 5493 125.60 - 133.99: 181 Bond angle restraints: 11831 Sorted by residual: angle pdb=" O3' 7OK T 9 " pdb=" P A T 10 " pdb=" O5' A T 10 " ideal model delta sigma weight residual 104.00 92.05 11.95 1.50e+00 4.44e-01 6.34e+01 angle pdb=" C2' 7OK T 9 " pdb=" C1' 7OK T 9 " pdb=" N1 7OK T 9 " ideal model delta sigma weight residual 112.00 122.08 -10.08 1.50e+00 4.44e-01 4.52e+01 angle pdb=" O4' 7OK T 9 " pdb=" C1' 7OK T 9 " pdb=" N1 7OK T 9 " ideal model delta sigma weight residual 108.50 100.57 7.93 1.50e+00 4.44e-01 2.79e+01 angle pdb=" O3' 7OK T 9 " pdb=" P A T 10 " pdb=" OP2 A T 10 " ideal model delta sigma weight residual 108.00 119.56 -11.56 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C5' 7OK T 9 " pdb=" C4' 7OK T 9 " pdb=" C3' 7OK T 9 " ideal model delta sigma weight residual 116.00 110.24 5.76 1.50e+00 4.44e-01 1.48e+01 ... (remaining 11826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 4624 17.03 - 34.06: 378 34.06 - 51.09: 47 51.09 - 68.12: 14 68.12 - 85.15: 6 Dihedral angle restraints: 5069 sinusoidal: 2129 harmonic: 2940 Sorted by residual: dihedral pdb=" CA LEU A 758 " pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA PHE A 571 " pdb=" C PHE A 571 " pdb=" N HIS A 572 " pdb=" CA HIS A 572 " ideal model delta harmonic sigma weight residual 180.00 -162.96 -17.04 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA TRP A 290 " pdb=" C TRP A 290 " pdb=" N ASP A 291 " pdb=" CA ASP A 291 " ideal model delta harmonic sigma weight residual -180.00 -163.53 -16.47 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 5066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1268 0.084 - 0.168: 74 0.168 - 0.252: 0 0.252 - 0.336: 0 0.336 - 0.420: 1 Chirality restraints: 1343 Sorted by residual: chirality pdb=" C2' 7OK T 9 " pdb=" C3' 7OK T 9 " pdb=" O2' 7OK T 9 " pdb=" C1' 7OK T 9 " both_signs ideal model delta sigma weight residual False -2.75 -2.33 -0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CA ASN A 138 " pdb=" N ASN A 138 " pdb=" C ASN A 138 " pdb=" CB ASN A 138 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE A 757 " pdb=" N ILE A 757 " pdb=" C ILE A 757 " pdb=" CB ILE A 757 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 1340 not shown) Planarity restraints: 1425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 7OK T 9 " -0.081 2.00e-02 2.50e+03 1.18e-01 3.48e+02 pdb=" N1 7OK T 9 " -0.008 2.00e-02 2.50e+03 pdb=" C2 7OK T 9 " -0.016 2.00e-02 2.50e+03 pdb=" O2 7OK T 9 " -0.068 2.00e-02 2.50e+03 pdb=" N3 7OK T 9 " 0.040 2.00e-02 2.50e+03 pdb=" C4 7OK T 9 " 0.099 2.00e-02 2.50e+03 pdb=" N4 7OK T 9 " 0.160 2.00e-02 2.50e+03 pdb=" C5 7OK T 9 " 0.105 2.00e-02 2.50e+03 pdb=" C6 7OK T 9 " 0.048 2.00e-02 2.50e+03 pdb=" OAC 7OK T 9 " -0.278 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 926 " 0.042 5.00e-02 4.00e+02 6.54e-02 6.85e+00 pdb=" N PRO A 927 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 927 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 927 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 758 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" C LEU A 758 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU A 758 " -0.014 2.00e-02 2.50e+03 pdb=" N SER A 759 " -0.012 2.00e-02 2.50e+03 ... (remaining 1422 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1177 2.75 - 3.29: 8132 3.29 - 3.83: 14217 3.83 - 4.36: 17446 4.36 - 4.90: 29370 Nonbonded interactions: 70342 Sorted by model distance: nonbonded pdb=" OD2 ASP A 260 " pdb=" OG1 THR A 262 " model vdw 2.218 2.440 nonbonded pdb=" NZ LYS A 426 " pdb=" OE1 GLN A 886 " model vdw 2.220 2.520 nonbonded pdb=" OG SER A 343 " pdb=" OD2 ASP A 377 " model vdw 2.226 2.440 nonbonded pdb=" OG1 THR A 206 " pdb=" OD1 ASN A 209 " model vdw 2.234 2.440 nonbonded pdb=" OG SER A 318 " pdb=" O ARG A 349 " model vdw 2.241 2.440 ... (remaining 70337 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 22 5.49 5 S 57 5.16 5 C 5284 2.51 5 N 1405 2.21 5 O 1638 1.98 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 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: 0.540 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: 3.720 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.060 Process input model: 30.630 Find NCS groups from input model: 0.220 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 : 0.007 0.214 8642 Z= 0.443 Angle : 0.522 11.948 11831 Z= 0.284 Chirality : 0.041 0.420 1343 Planarity : 0.005 0.118 1425 Dihedral : 12.438 85.155 3171 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.39 (0.26), residues: 979 helix: 0.69 (0.25), residues: 459 sheet: -0.09 (0.52), residues: 96 loop : 0.02 (0.29), residues: 424 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.972 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2330 time to fit residues: 37.1831 Evaluate side-chains 91 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 8642 Z= 0.318 Angle : 0.523 6.298 11831 Z= 0.274 Chirality : 0.042 0.142 1343 Planarity : 0.004 0.043 1425 Dihedral : 5.896 51.800 1333 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.34 (0.26), residues: 979 helix: 0.69 (0.24), residues: 459 sheet: -0.14 (0.51), residues: 96 loop : -0.05 (0.29), residues: 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.862 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 98 average time/residue: 0.1829 time to fit residues: 25.6931 Evaluate side-chains 97 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.916 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0739 time to fit residues: 1.8640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 8642 Z= 0.250 Angle : 0.471 6.054 11831 Z= 0.249 Chirality : 0.040 0.144 1343 Planarity : 0.004 0.044 1425 Dihedral : 6.016 54.598 1333 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.48 (0.26), residues: 979 helix: 0.81 (0.24), residues: 460 sheet: 0.16 (0.56), residues: 85 loop : -0.04 (0.28), residues: 434 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.927 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 102 average time/residue: 0.1883 time to fit residues: 27.5741 Evaluate side-chains 105 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0851 time to fit residues: 2.7229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.0870 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 0.0980 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8642 Z= 0.162 Angle : 0.429 5.786 11831 Z= 0.225 Chirality : 0.038 0.139 1343 Planarity : 0.003 0.045 1425 Dihedral : 6.123 64.820 1333 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.66 (0.26), residues: 979 helix: 0.96 (0.24), residues: 462 sheet: 0.28 (0.57), residues: 83 loop : 0.04 (0.29), residues: 434 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.948 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 106 average time/residue: 0.1890 time to fit residues: 28.8302 Evaluate side-chains 100 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0822 time to fit residues: 2.1816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 492 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.069 8642 Z= 0.530 Angle : 0.617 6.238 11831 Z= 0.327 Chirality : 0.046 0.156 1343 Planarity : 0.004 0.050 1425 Dihedral : 6.506 65.223 1333 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.05 (0.26), residues: 979 helix: 0.39 (0.24), residues: 466 sheet: -0.40 (0.50), residues: 98 loop : -0.26 (0.29), residues: 415 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 0.890 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 110 average time/residue: 0.2056 time to fit residues: 32.0147 Evaluate side-chains 106 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0824 time to fit residues: 2.1210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 8642 Z= 0.253 Angle : 0.478 5.891 11831 Z= 0.254 Chirality : 0.040 0.141 1343 Planarity : 0.004 0.054 1425 Dihedral : 6.360 70.876 1333 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 979 helix: 0.65 (0.24), residues: 463 sheet: -0.11 (0.60), residues: 73 loop : -0.14 (0.28), residues: 443 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.949 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 102 average time/residue: 0.2000 time to fit residues: 28.9389 Evaluate side-chains 100 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0792 time to fit residues: 1.8708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8642 Z= 0.213 Angle : 0.458 5.917 11831 Z= 0.242 Chirality : 0.039 0.141 1343 Planarity : 0.004 0.052 1425 Dihedral : 6.326 76.501 1333 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.43 (0.26), residues: 979 helix: 0.81 (0.25), residues: 458 sheet: -0.12 (0.60), residues: 75 loop : -0.06 (0.28), residues: 446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.927 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 102 average time/residue: 0.2017 time to fit residues: 29.2694 Evaluate side-chains 100 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0807 time to fit residues: 1.5711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 0.0000 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 8642 Z= 0.143 Angle : 0.431 7.098 11831 Z= 0.226 Chirality : 0.038 0.135 1343 Planarity : 0.003 0.051 1425 Dihedral : 6.274 80.344 1333 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.57 (0.26), residues: 979 helix: 0.90 (0.25), residues: 463 sheet: -0.08 (0.60), residues: 75 loop : 0.05 (0.29), residues: 441 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 1.008 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 104 average time/residue: 0.2033 time to fit residues: 29.9831 Evaluate side-chains 103 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0782 time to fit residues: 1.8422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 57 optimal weight: 0.2980 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.059 8642 Z= 0.424 Angle : 0.567 6.217 11831 Z= 0.301 Chirality : 0.044 0.151 1343 Planarity : 0.004 0.052 1425 Dihedral : 6.494 78.616 1333 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.14 (0.26), residues: 979 helix: 0.58 (0.24), residues: 464 sheet: -0.00 (0.55), residues: 85 loop : -0.30 (0.28), residues: 430 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 1.220 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 105 average time/residue: 0.2017 time to fit residues: 30.7854 Evaluate side-chains 104 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.984 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0945 time to fit residues: 1.8304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.0570 chunk 24 optimal weight: 0.8980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 8642 Z= 0.149 Angle : 0.445 6.752 11831 Z= 0.234 Chirality : 0.038 0.128 1343 Planarity : 0.003 0.063 1425 Dihedral : 6.364 82.764 1333 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.46 (0.26), residues: 979 helix: 0.83 (0.24), residues: 463 sheet: -0.05 (0.61), residues: 75 loop : -0.06 (0.28), residues: 441 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.945 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1974 time to fit residues: 28.3149 Evaluate side-chains 96 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.918 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.135957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.111374 restraints weight = 9459.965| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.32 r_work: 0.3211 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work: 0.3175 rms_B_bonded: 1.40 restraints_weight: 0.1250 r_work: 0.3149 rms_B_bonded: 1.70 restraints_weight: 0.0625 r_work: 0.3114 rms_B_bonded: 2.17 restraints_weight: 0.0312 r_work: 0.3065 rms_B_bonded: 2.89 restraints_weight: 0.0156 r_work: 0.2993 rms_B_bonded: 4.04 restraints_weight: 0.0078 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8642 Z= 0.201 Angle : 0.466 6.699 11831 Z= 0.244 Chirality : 0.039 0.140 1343 Planarity : 0.004 0.061 1425 Dihedral : 6.335 82.932 1333 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.46 (0.26), residues: 979 helix: 0.85 (0.24), residues: 463 sheet: -0.11 (0.60), residues: 75 loop : -0.08 (0.28), residues: 441 =============================================================================== Job complete usr+sys time: 1622.69 seconds wall clock time: 30 minutes 28.85 seconds (1828.85 seconds total)