Starting phenix.real_space_refine on Tue Feb 11 22:01:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mfe_23814/02_2025/7mfe_23814.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mfe_23814/02_2025/7mfe_23814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mfe_23814/02_2025/7mfe_23814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mfe_23814/02_2025/7mfe_23814.map" model { file = "/net/cci-nas-00/data/ceres_data/7mfe_23814/02_2025/7mfe_23814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mfe_23814/02_2025/7mfe_23814.cif" } resolution = 4.07 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= 0.001 sd= 0.007 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 41 5.16 5 C 4333 2.51 5 N 1184 2.21 5 O 1282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6844 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3291 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 390} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1785 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1766 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 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 673 SG CYS A 248 50.552 27.800 52.225 1.00 14.22 S ATOM 808 SG CYS A 264 42.464 38.382 45.422 1.00 19.76 S Time building chain proxies: 4.84, per 1000 atoms: 0.71 Number of scatterers: 6844 At special positions: 0 Unit cell: (99.752, 74.14, 111.884, 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 41 16.00 P 2 15.00 O 1282 8.00 N 1184 7.00 C 4333 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" ND1 HIS A 269 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 248 " pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" ND1 HIS A 235 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 264 " 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1644 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 6 sheets defined 60.4% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 178 through 188 removed outlier: 4.045A pdb=" N ALA A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N MET A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ARG A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 removed outlier: 4.407A pdb=" N TRP A 216 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 506 removed outlier: 3.918A pdb=" N GLN A 496 " --> pdb=" O PRO A 492 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 504 " --> pdb=" O ASN A 500 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 543 removed outlier: 3.807A pdb=" N ILE A 543 " --> pdb=" O HIS A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 570 removed outlier: 3.916A pdb=" N LEU A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 554 " --> pdb=" O MET A 550 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 627 removed outlier: 5.491A pdb=" N MET A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 652 removed outlier: 3.609A pdb=" N GLU A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 672 removed outlier: 3.606A pdb=" N ILE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 671 " --> pdb=" O PHE A 667 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY A 672 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 681 removed outlier: 3.692A pdb=" N LYS A 680 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 removed outlier: 3.576A pdb=" N ALA A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 720 removed outlier: 3.610A pdb=" N ILE A 714 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 725 removed outlier: 3.799A pdb=" N ILE A 724 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N HIS A 725 " --> pdb=" O PRO A 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 721 through 725' Processing helix chain 'C' and resid 3 through 16 removed outlier: 3.909A pdb=" N ALA C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.543A pdb=" N SER C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 68 removed outlier: 3.995A pdb=" N LEU C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 64 " --> pdb=" O ARG C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 104 Processing helix chain 'C' and resid 111 through 131 removed outlier: 3.600A pdb=" N TYR C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 137 Processing helix chain 'C' and resid 138 through 160 removed outlier: 3.640A pdb=" N GLN C 144 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 180 removed outlier: 3.633A pdb=" N LEU C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 198 Processing helix chain 'C' and resid 210 through 230 removed outlier: 4.233A pdb=" N SER C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG C 222 " --> pdb=" O MET C 218 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 15 removed outlier: 3.573A pdb=" N ALA B 10 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 31 removed outlier: 3.535A pdb=" N GLU B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 67 removed outlier: 3.535A pdb=" N SER B 45 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 55 " --> pdb=" O VAL B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 104 removed outlier: 4.305A pdb=" N VAL B 97 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 133 removed outlier: 3.573A pdb=" N GLY B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 160 removed outlier: 3.881A pdb=" N LYS B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 181 Processing helix chain 'B' and resid 184 through 203 Processing helix chain 'B' and resid 207 through 230 removed outlier: 4.006A pdb=" N LYS B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASP B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 160 removed outlier: 3.520A pdb=" N VAL A 169 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL A 159 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 167 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 208 removed outlier: 4.204A pdb=" N VAL A 197 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR A 198 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N HIS A 223 " --> pdb=" O TYR A 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 241 removed outlier: 3.782A pdb=" N GLY A 258 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 458 through 462 removed outlier: 5.120A pdb=" N LYS A 473 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 479 through 483 removed outlier: 6.214A pdb=" N GLN A 530 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE A 516 " --> pdb=" O GLN A 530 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 582 through 585 removed outlier: 4.155A pdb=" N THR A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 1071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2248 1.34 - 1.46: 1537 1.46 - 1.58: 3103 1.58 - 1.70: 8 1.70 - 1.82: 65 Bond restraints: 6961 Sorted by residual: bond pdb=" N VAL B 97 " pdb=" CA VAL B 97 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.21e-02 6.83e+03 7.76e+00 bond pdb=" N LEU B 98 " pdb=" CA LEU B 98 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.21e-02 6.83e+03 7.39e+00 bond pdb=" N CYS B 94 " pdb=" CA CYS B 94 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.30e-02 5.92e+03 7.18e+00 bond pdb=" N SER B 99 " pdb=" CA SER B 99 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.45e+00 bond pdb=" N ASN B 95 " pdb=" CA ASN B 95 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.33e-02 5.65e+03 5.17e+00 ... (remaining 6956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 9037 1.37 - 2.74: 285 2.74 - 4.11: 45 4.11 - 5.47: 15 5.47 - 6.84: 3 Bond angle restraints: 9385 Sorted by residual: angle pdb=" N ASP B 96 " pdb=" CA ASP B 96 " pdb=" C ASP B 96 " ideal model delta sigma weight residual 111.07 105.23 5.84 1.07e+00 8.73e-01 2.98e+01 angle pdb=" N CYS B 94 " pdb=" CA CYS B 94 " pdb=" C CYS B 94 " ideal model delta sigma weight residual 113.55 108.64 4.91 1.26e+00 6.30e-01 1.52e+01 angle pdb=" N ASN B 95 " pdb=" CA ASN B 95 " pdb=" C ASN B 95 " ideal model delta sigma weight residual 112.54 107.85 4.69 1.22e+00 6.72e-01 1.48e+01 angle pdb=" CA VAL B 97 " pdb=" C VAL B 97 " pdb=" O VAL B 97 " ideal model delta sigma weight residual 120.85 117.20 3.65 1.06e+00 8.90e-01 1.19e+01 angle pdb=" N LEU B 100 " pdb=" CA LEU B 100 " pdb=" C LEU B 100 " ideal model delta sigma weight residual 111.28 107.75 3.53 1.09e+00 8.42e-01 1.05e+01 ... (remaining 9380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3782 17.94 - 35.88: 384 35.88 - 53.82: 63 53.82 - 71.76: 19 71.76 - 89.69: 8 Dihedral angle restraints: 4256 sinusoidal: 1730 harmonic: 2526 Sorted by residual: dihedral pdb=" CA GLU C 209 " pdb=" C GLU C 209 " pdb=" N SER C 210 " pdb=" CA SER C 210 " ideal model delta harmonic sigma weight residual -180.00 -154.10 -25.90 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA MET A 620 " pdb=" C MET A 620 " pdb=" N ALA A 621 " pdb=" CA ALA A 621 " ideal model delta harmonic sigma weight residual -180.00 -158.09 -21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA GLN C 15 " pdb=" C GLN C 15 " pdb=" N ALA C 16 " pdb=" CA ALA C 16 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 4253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 832 0.045 - 0.090: 173 0.090 - 0.134: 36 0.134 - 0.179: 2 0.179 - 0.224: 2 Chirality restraints: 1045 Sorted by residual: chirality pdb=" CA LEU B 100 " pdb=" N LEU B 100 " pdb=" C LEU B 100 " pdb=" CB LEU B 100 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ASP B 96 " pdb=" N ASP B 96 " pdb=" C ASP B 96 " pdb=" CB ASP B 96 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA CYS B 94 " pdb=" N CYS B 94 " pdb=" C CYS B 94 " pdb=" CB CYS B 94 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.96e-01 ... (remaining 1042 not shown) Planarity restraints: 1198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 191 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO A 192 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 621 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.52e+00 pdb=" N PRO A 622 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 622 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 622 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 707 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.04e+00 pdb=" N PRO A 708 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 708 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 708 " 0.028 5.00e-02 4.00e+02 ... (remaining 1195 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 2 2.09 - 2.79: 1688 2.79 - 3.49: 10045 3.49 - 4.20: 15255 4.20 - 4.90: 26734 Nonbonded interactions: 53724 Sorted by model distance: nonbonded pdb=" ND2 ASN A 163 " pdb=" O SER A 679 " model vdw 1.387 3.120 nonbonded pdb=" O TYR A 647 " pdb=" OG1 THR A 651 " model vdw 2.044 3.040 nonbonded pdb=" O PHE A 268 " pdb=" NE2 GLN A 270 " model vdw 2.155 3.120 nonbonded pdb=" OG1 THR C 163 " pdb=" OE2 GLU C 209 " model vdw 2.155 3.040 nonbonded pdb=" CD2 HIS A 235 " pdb="ZN ZN A 902 " model vdw 2.168 1.960 ... (remaining 53719 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name CE )) or resid 4 through 67 or (resid 68 \ and (name N or name CA or name C or name O or name CB )) or resid 69 or resid 7 \ 3 through 74 or (resid 75 and (name N or name CA or name C or name O or name CB \ or name CG )) or (resid 76 and (name N or name CA or name C or name O or name CB \ )) or resid 77 through 102 or (resid 103 and (name N or name CA or name C or na \ me O or name CB or name CG )) or resid 104 through 138 or (resid 139 and (name N \ or name CA or name C or name O or name CB or name CG )) or resid 140 through 15 \ 7 or (resid 158 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE )) or resid 159 through 230)) selection = (chain 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG )) or resid 6 through 102 or (resid 103 and (name \ N or name CA or name C or name O or name CB or name CG )) or resid 104 through \ 133 or (resid 137 and (name N or name CA or name C or name O or name CB )) or re \ sid 138 through 156 or (resid 157 through 158 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name CE )) or resid 159 through 207 \ or (resid 208 through 209 and (name N or name CA or name C or name O or name CB \ )) or resid 210 through 211 or (resid 212 and (name N or name CA or name C or n \ ame O or name CB )) or resid 213 through 229 or (resid 230 and (name N or name C \ A or name C or name O or name CB )))) } 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 group one per residue 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: 0.180 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.810 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 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 : 0.002 0.035 6961 Z= 0.163 Angle : 0.592 6.843 9385 Z= 0.353 Chirality : 0.039 0.224 1045 Planarity : 0.004 0.055 1198 Dihedral : 15.258 89.694 2612 Min Nonbonded Distance : 1.387 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.41 % Allowed : 0.27 % Favored : 99.31 % 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: -2.56 (0.28), residues: 833 helix: -0.73 (0.24), residues: 457 sheet: -3.50 (1.08), residues: 18 loop : -2.92 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 228 HIS 0.007 0.001 HIS A 542 PHE 0.022 0.002 PHE B 117 TYR 0.021 0.002 TYR A 266 ARG 0.004 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 164 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 190 LEU cc_start: 0.8438 (mt) cc_final: 0.8101 (mt) REVERT: A 254 LEU cc_start: 0.6824 (tp) cc_final: 0.6526 (tp) REVERT: C 160 MET cc_start: 0.6214 (tpt) cc_final: 0.5870 (tpt) outliers start: 3 outliers final: 1 residues processed: 166 average time/residue: 0.1806 time to fit residues: 39.9677 Evaluate side-chains 125 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN A 585 HIS C 42 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.179969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.157505 restraints weight = 9768.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.159243 restraints weight = 7439.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.161432 restraints weight = 6347.026| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6961 Z= 0.190 Angle : 0.636 8.084 9385 Z= 0.340 Chirality : 0.042 0.143 1045 Planarity : 0.005 0.055 1198 Dihedral : 5.487 45.193 938 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % 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: 833 helix: 0.27 (0.23), residues: 464 sheet: -3.19 (0.83), residues: 28 loop : -2.62 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 228 HIS 0.008 0.002 HIS A 235 PHE 0.026 0.002 PHE B 174 TYR 0.025 0.002 TYR C 125 ARG 0.005 0.001 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.801 Fit side-chains REVERT: A 190 LEU cc_start: 0.8194 (mt) cc_final: 0.7713 (mt) REVERT: A 254 LEU cc_start: 0.6777 (tp) cc_final: 0.6488 (tp) REVERT: A 564 MET cc_start: 0.7284 (ttm) cc_final: 0.6995 (mtt) REVERT: C 223 ASP cc_start: 0.7233 (p0) cc_final: 0.7027 (p0) REVERT: B 155 ILE cc_start: 0.8002 (tp) cc_final: 0.7624 (tp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1762 time to fit residues: 35.6823 Evaluate side-chains 115 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 11 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 59 optimal weight: 0.0670 chunk 77 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 overall best weight: 2.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN B 108 ASN B 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.177351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.155780 restraints weight = 9977.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.156394 restraints weight = 7574.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.157948 restraints weight = 6981.215| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6961 Z= 0.241 Angle : 0.655 9.935 9385 Z= 0.342 Chirality : 0.042 0.152 1045 Planarity : 0.005 0.055 1198 Dihedral : 5.589 41.819 938 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % 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: -1.45 (0.28), residues: 833 helix: 0.28 (0.23), residues: 467 sheet: -3.17 (0.79), residues: 28 loop : -2.60 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 59 HIS 0.004 0.001 HIS A 568 PHE 0.045 0.003 PHE C 174 TYR 0.021 0.002 TYR C 125 ARG 0.005 0.001 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 LEU cc_start: 0.8206 (mt) cc_final: 0.7770 (mt) REVERT: A 498 PHE cc_start: 0.6278 (m-10) cc_final: 0.6015 (t80) REVERT: A 689 MET cc_start: 0.6254 (ttm) cc_final: 0.6042 (ttm) REVERT: C 56 ARG cc_start: 0.7301 (mtp180) cc_final: 0.7088 (mtp-110) REVERT: C 223 ASP cc_start: 0.7380 (p0) cc_final: 0.7125 (p0) REVERT: B 59 TRP cc_start: 0.6116 (t60) cc_final: 0.5779 (t60) REVERT: B 149 TYR cc_start: 0.7218 (m-80) cc_final: 0.6492 (m-80) REVERT: B 191 LEU cc_start: 0.7063 (mt) cc_final: 0.6843 (mt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1789 time to fit residues: 36.3473 Evaluate side-chains 113 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 71 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 27 optimal weight: 0.0670 chunk 40 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 chunk 21 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS A 494 GLN C 42 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN B 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.182018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.159413 restraints weight = 9865.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.160174 restraints weight = 7754.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.162689 restraints weight = 7092.466| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6961 Z= 0.168 Angle : 0.588 9.602 9385 Z= 0.308 Chirality : 0.040 0.150 1045 Planarity : 0.004 0.054 1198 Dihedral : 5.170 38.886 938 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: -1.01 (0.29), residues: 833 helix: 0.64 (0.24), residues: 467 sheet: -3.15 (0.78), residues: 28 loop : -2.39 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 59 HIS 0.008 0.001 HIS A 477 PHE 0.053 0.002 PHE C 174 TYR 0.014 0.002 TYR A 472 ARG 0.004 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 MET cc_start: 0.5094 (mtt) cc_final: 0.4743 (mmm) REVERT: C 223 ASP cc_start: 0.7290 (p0) cc_final: 0.7079 (p0) REVERT: B 41 ARG cc_start: 0.6857 (ttp80) cc_final: 0.6379 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1870 time to fit residues: 38.3340 Evaluate side-chains 111 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 19 optimal weight: 0.0470 chunk 8 optimal weight: 6.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN A 494 GLN C 42 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.177563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.156899 restraints weight = 9995.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.157842 restraints weight = 9124.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.159654 restraints weight = 8534.806| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6961 Z= 0.238 Angle : 0.656 10.845 9385 Z= 0.338 Chirality : 0.041 0.154 1045 Planarity : 0.005 0.056 1198 Dihedral : 5.425 42.269 938 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.29), residues: 833 helix: 0.65 (0.24), residues: 467 sheet: -2.66 (0.86), residues: 28 loop : -2.40 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 59 HIS 0.003 0.001 HIS A 568 PHE 0.048 0.003 PHE C 174 TYR 0.025 0.002 TYR C 82 ARG 0.007 0.001 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 83 ARG cc_start: 0.6858 (ttp-110) cc_final: 0.5623 (ttp80) REVERT: C 223 ASP cc_start: 0.7279 (p0) cc_final: 0.7032 (p0) REVERT: B 41 ARG cc_start: 0.6708 (ttp80) cc_final: 0.6458 (ttt-90) REVERT: B 131 GLU cc_start: 0.7089 (pp20) cc_final: 0.6880 (pt0) REVERT: B 149 TYR cc_start: 0.7098 (m-80) cc_final: 0.6450 (m-80) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1915 time to fit residues: 36.5426 Evaluate side-chains 113 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN B 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.177764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.155434 restraints weight = 9995.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.156329 restraints weight = 8027.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.158720 restraints weight = 7141.550| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6961 Z= 0.220 Angle : 0.645 11.143 9385 Z= 0.335 Chirality : 0.041 0.171 1045 Planarity : 0.004 0.054 1198 Dihedral : 5.375 40.439 938 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.14 % Allowed : 2.19 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.29), residues: 833 helix: 0.64 (0.24), residues: 468 sheet: -2.40 (0.86), residues: 28 loop : -2.33 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 59 HIS 0.006 0.001 HIS A 568 PHE 0.049 0.003 PHE C 174 TYR 0.022 0.002 TYR C 82 ARG 0.005 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 ARG cc_start: 0.7346 (mtp-110) cc_final: 0.7053 (mtp-110) REVERT: C 223 ASP cc_start: 0.7346 (p0) cc_final: 0.7063 (p0) REVERT: B 41 ARG cc_start: 0.6620 (ttp80) cc_final: 0.6153 (ttt-90) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.1826 time to fit residues: 37.3885 Evaluate side-chains 116 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 HIS C 42 ASN B 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.178836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.157869 restraints weight = 10004.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.157507 restraints weight = 8413.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.160027 restraints weight = 7479.963| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6961 Z= 0.215 Angle : 0.651 11.407 9385 Z= 0.338 Chirality : 0.041 0.173 1045 Planarity : 0.004 0.056 1198 Dihedral : 5.405 41.904 938 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.27 % Allowed : 2.19 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.29), residues: 833 helix: 0.67 (0.24), residues: 465 sheet: -2.17 (0.86), residues: 28 loop : -2.36 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 59 HIS 0.006 0.001 HIS A 568 PHE 0.045 0.002 PHE C 174 TYR 0.026 0.002 TYR C 82 ARG 0.005 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 223 ASP cc_start: 0.7372 (p0) cc_final: 0.7105 (p0) REVERT: B 41 ARG cc_start: 0.6456 (ttp80) cc_final: 0.6095 (ttt-90) REVERT: B 126 TYR cc_start: 0.8086 (m-10) cc_final: 0.7411 (m-80) outliers start: 2 outliers final: 0 residues processed: 143 average time/residue: 0.1839 time to fit residues: 35.5800 Evaluate side-chains 117 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 38 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 60 optimal weight: 0.0370 chunk 27 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 HIS A 494 GLN C 42 ASN B 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.180548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.158453 restraints weight = 9945.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.159094 restraints weight = 8476.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.160698 restraints weight = 8293.053| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6961 Z= 0.185 Angle : 0.660 16.292 9385 Z= 0.337 Chirality : 0.042 0.188 1045 Planarity : 0.004 0.053 1198 Dihedral : 5.190 40.306 938 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.27 % Allowed : 0.96 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.29), residues: 833 helix: 0.83 (0.24), residues: 466 sheet: -2.18 (0.85), residues: 28 loop : -2.24 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 59 HIS 0.005 0.001 HIS A 370 PHE 0.041 0.002 PHE C 174 TYR 0.028 0.002 TYR C 82 ARG 0.004 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 223 ASP cc_start: 0.7440 (p0) cc_final: 0.7203 (p0) REVERT: B 41 ARG cc_start: 0.6618 (ttp80) cc_final: 0.6135 (ttt-90) REVERT: B 131 GLU cc_start: 0.7046 (pp20) cc_final: 0.6672 (pt0) outliers start: 2 outliers final: 0 residues processed: 144 average time/residue: 0.1795 time to fit residues: 35.3044 Evaluate side-chains 111 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN C 42 ASN B 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.180295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.160072 restraints weight = 10021.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.160331 restraints weight = 9615.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.161914 restraints weight = 8794.585| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6961 Z= 0.196 Angle : 0.639 11.800 9385 Z= 0.330 Chirality : 0.042 0.192 1045 Planarity : 0.004 0.054 1198 Dihedral : 5.194 40.848 938 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.14 % Allowed : 0.69 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.29), residues: 833 helix: 0.94 (0.24), residues: 467 sheet: -2.10 (0.91), residues: 28 loop : -2.23 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 59 HIS 0.006 0.001 HIS A 568 PHE 0.045 0.002 PHE C 174 TYR 0.023 0.002 TYR C 82 ARG 0.004 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 223 ASP cc_start: 0.7292 (p0) cc_final: 0.7042 (p0) REVERT: B 40 GLU cc_start: 0.6846 (pm20) cc_final: 0.6220 (pp20) REVERT: B 41 ARG cc_start: 0.6738 (ttp80) cc_final: 0.6322 (ttt-90) REVERT: B 126 TYR cc_start: 0.7976 (m-10) cc_final: 0.7310 (m-80) REVERT: B 131 GLU cc_start: 0.7145 (pp20) cc_final: 0.6915 (pt0) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.1850 time to fit residues: 36.6786 Evaluate side-chains 120 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN A 512 ASN ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.181450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.161250 restraints weight = 10012.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.161813 restraints weight = 9435.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.163773 restraints weight = 8244.644| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6961 Z= 0.182 Angle : 0.637 11.712 9385 Z= 0.327 Chirality : 0.041 0.200 1045 Planarity : 0.004 0.054 1198 Dihedral : 5.127 40.191 938 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.29), residues: 833 helix: 0.97 (0.24), residues: 467 sheet: -2.02 (0.89), residues: 28 loop : -2.16 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 59 HIS 0.005 0.001 HIS A 568 PHE 0.041 0.002 PHE C 174 TYR 0.023 0.002 TYR C 125 ARG 0.004 0.000 ARG A 506 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 LEU cc_start: 0.6697 (tp) cc_final: 0.6347 (tp) REVERT: C 83 ARG cc_start: 0.6341 (ttp-110) cc_final: 0.5390 (ttp80) REVERT: C 223 ASP cc_start: 0.7366 (p0) cc_final: 0.7052 (p0) REVERT: B 40 GLU cc_start: 0.6796 (pm20) cc_final: 0.6281 (pp20) REVERT: B 41 ARG cc_start: 0.6588 (ttp80) cc_final: 0.5988 (ttp80) REVERT: B 118 TYR cc_start: 0.6444 (m-80) cc_final: 0.6057 (m-80) REVERT: B 126 TYR cc_start: 0.8006 (m-10) cc_final: 0.7090 (m-80) REVERT: B 131 GLU cc_start: 0.7250 (pp20) cc_final: 0.7000 (pt0) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2153 time to fit residues: 43.2358 Evaluate side-chains 123 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 HIS A 494 GLN C 42 ASN B 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.182674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.160508 restraints weight = 10000.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.161763 restraints weight = 8334.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.163473 restraints weight = 7915.730| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6961 Z= 0.186 Angle : 0.629 11.907 9385 Z= 0.327 Chirality : 0.041 0.191 1045 Planarity : 0.004 0.053 1198 Dihedral : 5.015 39.380 938 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.27 % Allowed : 0.55 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.29), residues: 833 helix: 1.08 (0.24), residues: 469 sheet: -1.80 (0.94), residues: 28 loop : -2.13 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 59 HIS 0.005 0.001 HIS A 370 PHE 0.036 0.002 PHE C 174 TYR 0.030 0.002 TYR C 125 ARG 0.007 0.000 ARG C 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1837.31 seconds wall clock time: 34 minutes 5.39 seconds (2045.39 seconds total)