Starting phenix.real_space_refine on Sun Jun 8 12:09:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ge6_51291/06_2025/9ge6_51291.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ge6_51291/06_2025/9ge6_51291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ge6_51291/06_2025/9ge6_51291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ge6_51291/06_2025/9ge6_51291.map" model { file = "/net/cci-nas-00/data/ceres_data/9ge6_51291/06_2025/9ge6_51291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ge6_51291/06_2025/9ge6_51291.cif" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 6162 2.51 5 N 1700 2.21 5 O 1742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9646 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6254 Classifications: {'peptide': 799} Link IDs: {'PCIS': 3, 'PTRANS': 40, 'TRANS': 755} Chain: "B" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1696 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "C" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1696 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 6, 'TRANS': 217} Time building chain proxies: 6.05, per 1000 atoms: 0.63 Number of scatterers: 9646 At special positions: 0 Unit cell: (126.085, 111.055, 108.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1742 8.00 N 1700 7.00 C 6162 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: 2.56 Conformation dependent library (CDL) restraints added in 1.2 seconds 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2284 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 6 sheets defined 56.3% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 Processing helix chain 'A' and resid 12 through 50 Processing helix chain 'A' and resid 64 through 74 removed outlier: 3.956A pdb=" N LEU A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 177 through 185 removed outlier: 3.821A pdb=" N GLY A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 231 through 280 removed outlier: 3.800A pdb=" N ARG A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASP A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 321 Processing helix chain 'A' and resid 334 through 361 removed outlier: 5.711A pdb=" N ARG A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Proline residue: A 355 - end of helix Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 378 through 399 Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 401 through 432 Processing helix chain 'A' and resid 436 through 448 Processing helix chain 'A' and resid 449 through 483 Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 501 through 512 removed outlier: 3.533A pdb=" N LEU A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 583 Processing helix chain 'A' and resid 645 through 655 Processing helix chain 'A' and resid 662 through 702 Processing helix chain 'A' and resid 703 through 718 Processing helix chain 'A' and resid 720 through 757 Processing helix chain 'A' and resid 766 through 793 removed outlier: 3.541A pdb=" N TRP A 770 " --> pdb=" O ASP A 766 " (cutoff:3.500A) Proline residue: A 774 - end of helix Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.933A pdb=" N LEU A 798 " --> pdb=" O GLY A 795 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 799 " --> pdb=" O LYS A 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 795 through 799' Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.576A pdb=" N HIS B 21 " --> pdb=" O GLN B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 57 Processing helix chain 'B' and resid 78 through 89 Processing helix chain 'B' and resid 104 through 117 Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 119 through 134 Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 148 through 163 removed outlier: 4.660A pdb=" N GLY B 163 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 195 removed outlier: 3.776A pdb=" N GLU B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 213 removed outlier: 3.547A pdb=" N CYS B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 78 through 89 Processing helix chain 'C' and resid 104 through 116 Proline residue: C 112 - end of helix Processing helix chain 'C' and resid 119 through 134 Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.942A pdb=" N LEU C 140 " --> pdb=" O GLY C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 147 Processing helix chain 'C' and resid 148 through 163 removed outlier: 4.771A pdb=" N GLY C 163 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 removed outlier: 4.362A pdb=" N ASN C 176 " --> pdb=" O PRO C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 197 Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.146A pdb=" N ALA C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 59 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 55 through 59 current: chain 'A' and resid 94 through 102 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 94 through 102 current: chain 'A' and resid 149 through 159 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 492 through 495 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 492 through 495 current: chain 'A' and resid 533 through 534 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 533 through 534 current: chain 'A' and resid 599 through 608 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 16 removed outlier: 6.452A pdb=" N LEU B 12 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR B 27 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS B 14 " --> pdb=" O ILE B 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 93 removed outlier: 6.386A pdb=" N GLY B 91 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASP B 171 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 93 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR B 38 " --> pdb=" O ARG B 215 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU B 217 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA B 40 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU B 219 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL B 42 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 23 through 33 removed outlier: 5.957A pdb=" N LYS C 14 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR C 27 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU C 12 " --> pdb=" O THR C 27 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL C 29 " --> pdb=" O HIS C 10 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS C 10 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C 31 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU C 8 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL C 9 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N SER C 68 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N HIS C 11 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU C 66 " --> pdb=" O HIS C 11 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 93 removed outlier: 6.426A pdb=" N GLY C 91 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ASP C 171 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL C 93 " --> pdb=" O ASP C 171 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1554 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 2.98 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: 3217 1.34 - 1.46: 1484 1.46 - 1.58: 5051 1.58 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 9826 Sorted by residual: bond pdb=" CB MET A 51 " pdb=" CG MET A 51 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" CA LEU A 280 " pdb=" C LEU A 280 " ideal model delta sigma weight residual 1.523 1.500 0.024 1.80e-02 3.09e+03 1.74e+00 bond pdb=" CB GLN A 456 " pdb=" CG GLN A 456 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.53e+00 bond pdb=" CG1 ILE A 17 " pdb=" CD1 ILE A 17 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.43e+00 bond pdb=" CG GLN A 456 " pdb=" CD GLN A 456 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.06e+00 ... (remaining 9821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 12982 1.75 - 3.50: 275 3.50 - 5.26: 61 5.26 - 7.01: 13 7.01 - 8.76: 3 Bond angle restraints: 13334 Sorted by residual: angle pdb=" C VAL B 220 " pdb=" N ASN B 221 " pdb=" CA ASN B 221 " ideal model delta sigma weight residual 121.54 128.29 -6.75 1.91e+00 2.74e-01 1.25e+01 angle pdb=" CA MET A 176 " pdb=" CB MET A 176 " pdb=" CG MET A 176 " ideal model delta sigma weight residual 114.10 119.97 -5.87 2.00e+00 2.50e-01 8.63e+00 angle pdb=" C SER B 96 " pdb=" N PHE B 97 " pdb=" CA PHE B 97 " ideal model delta sigma weight residual 121.54 126.81 -5.27 1.91e+00 2.74e-01 7.60e+00 angle pdb=" C LYS C 88 " pdb=" N HIS C 89 " pdb=" CA HIS C 89 " ideal model delta sigma weight residual 122.15 114.52 7.63 2.83e+00 1.25e-01 7.27e+00 angle pdb=" C MET A 176 " pdb=" CA MET A 176 " pdb=" CB MET A 176 " ideal model delta sigma weight residual 110.43 114.89 -4.46 1.68e+00 3.54e-01 7.06e+00 ... (remaining 13329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 5289 16.29 - 32.59: 520 32.59 - 48.88: 82 48.88 - 65.18: 13 65.18 - 81.47: 12 Dihedral angle restraints: 5916 sinusoidal: 2376 harmonic: 3540 Sorted by residual: dihedral pdb=" CA GLU A 49 " pdb=" C GLU A 49 " pdb=" N PHE A 50 " pdb=" CA PHE A 50 " ideal model delta harmonic sigma weight residual 180.00 144.40 35.60 0 5.00e+00 4.00e-02 5.07e+01 dihedral pdb=" CA PHE B 97 " pdb=" C PHE B 97 " pdb=" N MET B 98 " pdb=" CA MET B 98 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA SER B 96 " pdb=" C SER B 96 " pdb=" N PHE B 97 " pdb=" CA PHE B 97 " ideal model delta harmonic sigma weight residual 180.00 163.24 16.76 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 5913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1085 0.037 - 0.073: 313 0.073 - 0.110: 129 0.110 - 0.147: 18 0.147 - 0.183: 4 Chirality restraints: 1549 Sorted by residual: chirality pdb=" CA PHE B 97 " pdb=" N PHE B 97 " pdb=" C PHE B 97 " pdb=" CB PHE B 97 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA GLU A 49 " pdb=" N GLU A 49 " pdb=" C GLU A 49 " pdb=" CB GLU A 49 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA LEU C 111 " pdb=" N LEU C 111 " pdb=" C LEU C 111 " pdb=" CB LEU C 111 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 1546 not shown) Planarity restraints: 1711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 473 " 0.014 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C LEU A 473 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU A 473 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG A 474 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 50 " 0.014 2.00e-02 2.50e+03 1.83e-02 5.89e+00 pdb=" CG PHE A 50 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 50 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 50 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 50 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 50 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 50 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 456 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" CD GLN A 456 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLN A 456 " 0.012 2.00e-02 2.50e+03 pdb=" NE2 GLN A 456 " 0.011 2.00e-02 2.50e+03 ... (remaining 1708 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 167 2.64 - 3.21: 9682 3.21 - 3.77: 16598 3.77 - 4.34: 20791 4.34 - 4.90: 33527 Nonbonded interactions: 80765 Sorted by model distance: nonbonded pdb=" O VAL C 109 " pdb=" ND2 ASN C 162 " model vdw 2.080 3.120 nonbonded pdb=" O VAL A 522 " pdb=" OG SER A 634 " model vdw 2.194 3.040 nonbonded pdb=" O GLY C 48 " pdb=" OG1 THR C 51 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASP A 145 " pdb=" OG1 THR A 150 " model vdw 2.206 3.040 nonbonded pdb=" OG1 THR B 27 " pdb=" OE1 GLN B 223 " model vdw 2.220 3.040 ... (remaining 80760 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' selection = chain 'C' } 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: 1.160 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.650 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9826 Z= 0.172 Angle : 0.653 8.762 13334 Z= 0.327 Chirality : 0.042 0.183 1549 Planarity : 0.004 0.033 1711 Dihedral : 13.386 81.470 3632 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.99 (0.24), residues: 1241 helix: 1.81 (0.21), residues: 616 sheet: -0.31 (0.41), residues: 156 loop : -0.51 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 405 HIS 0.004 0.001 HIS A 512 PHE 0.042 0.002 PHE A 50 TYR 0.007 0.001 TYR A 356 ARG 0.005 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.13424 ( 537) hydrogen bonds : angle 5.21290 ( 1554) covalent geometry : bond 0.00358 ( 9826) covalent geometry : angle 0.65322 (13334) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.111 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: symmetry clash REVERT: A 50 PHE cc_start: 0.7791 (m-80) cc_final: 0.6725 (t80) REVERT: A 51 MET cc_start: 0.3954 (tpt) cc_final: 0.3577 (tpt) REVERT: A 175 MET cc_start: 0.7973 (ttt) cc_final: 0.7361 (ttm) REVERT: A 297 MET cc_start: 0.8529 (mmt) cc_final: 0.8206 (mmp) REVERT: A 344 MET cc_start: 0.8576 (ppp) cc_final: 0.8282 (ppp) REVERT: A 704 MET cc_start: 0.8697 (mmp) cc_final: 0.8336 (mmm) REVERT: A 709 GLN cc_start: 0.8613 (pp30) cc_final: 0.8404 (pp30) REVERT: B 41 LEU cc_start: 0.8778 (tp) cc_final: 0.8557 (tt) REVERT: C 88 LYS cc_start: 0.9456 (tppp) cc_final: 0.9073 (tppp) REVERT: C 103 LEU cc_start: 0.9084 (mm) cc_final: 0.8880 (mt) REVERT: C 202 MET cc_start: 0.8503 (tpt) cc_final: 0.8195 (tpp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2000 time to fit residues: 43.8191 Evaluate side-chains 119 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 50.0000 chunk 49 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 HIS ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.064698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.044907 restraints weight = 56191.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.046415 restraints weight = 34857.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.047451 restraints weight = 25002.737| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9826 Z= 0.175 Angle : 0.622 8.652 13334 Z= 0.315 Chirality : 0.041 0.163 1549 Planarity : 0.004 0.034 1711 Dihedral : 4.162 33.270 1333 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.24), residues: 1241 helix: 1.71 (0.21), residues: 627 sheet: -0.41 (0.41), residues: 156 loop : -0.43 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 339 HIS 0.005 0.001 HIS A 558 PHE 0.037 0.002 PHE A 50 TYR 0.012 0.001 TYR A 356 ARG 0.004 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04878 ( 537) hydrogen bonds : angle 4.72889 ( 1554) covalent geometry : bond 0.00361 ( 9826) covalent geometry : angle 0.62177 (13334) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.160 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: symmetry clash REVERT: A 51 MET cc_start: 0.4706 (tpt) cc_final: 0.4415 (tpt) REVERT: A 175 MET cc_start: 0.7947 (ttt) cc_final: 0.7501 (ttm) REVERT: A 297 MET cc_start: 0.8555 (mmt) cc_final: 0.8226 (mmp) REVERT: A 344 MET cc_start: 0.8744 (ppp) cc_final: 0.8436 (tmm) REVERT: A 704 MET cc_start: 0.8752 (mmp) cc_final: 0.8401 (tpp) REVERT: A 709 GLN cc_start: 0.8759 (pp30) cc_final: 0.8499 (pp30) REVERT: B 124 ARG cc_start: 0.9122 (ptp-110) cc_final: 0.8892 (ptp-110) REVERT: C 88 LYS cc_start: 0.9425 (tppp) cc_final: 0.9058 (tppp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2047 time to fit residues: 44.0856 Evaluate side-chains 113 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 119 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 37 optimal weight: 0.0000 chunk 62 optimal weight: 7.9990 overall best weight: 2.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 HIS B 108 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** 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 = 0.3591 r_free = 0.3591 target = 0.064335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.044762 restraints weight = 56423.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.046373 restraints weight = 33442.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.047464 restraints weight = 23302.149| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9826 Z= 0.166 Angle : 0.619 7.984 13334 Z= 0.311 Chirality : 0.041 0.193 1549 Planarity : 0.004 0.035 1711 Dihedral : 4.193 32.536 1333 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.97 (0.24), residues: 1241 helix: 1.70 (0.21), residues: 629 sheet: -0.12 (0.40), residues: 170 loop : -0.52 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 339 HIS 0.006 0.001 HIS C 196 PHE 0.072 0.002 PHE A 50 TYR 0.012 0.001 TYR A 356 ARG 0.006 0.000 ARG C 164 Details of bonding type rmsd hydrogen bonds : bond 0.04657 ( 537) hydrogen bonds : angle 4.60773 ( 1554) covalent geometry : bond 0.00347 ( 9826) covalent geometry : angle 0.61895 (13334) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.8060 (m-80) cc_final: 0.6788 (t80) REVERT: A 51 MET cc_start: 0.5161 (tpt) cc_final: 0.4605 (tpt) REVERT: A 297 MET cc_start: 0.8647 (mmt) cc_final: 0.8289 (mmp) REVERT: A 424 MET cc_start: 0.8764 (mmt) cc_final: 0.8558 (mmt) REVERT: A 465 MET cc_start: 0.8735 (mmp) cc_final: 0.8517 (mmm) REVERT: A 709 GLN cc_start: 0.9104 (pp30) cc_final: 0.8530 (pp30) REVERT: A 710 GLU cc_start: 0.8775 (tp30) cc_final: 0.8450 (tp30) REVERT: B 124 ARG cc_start: 0.9158 (ptp-110) cc_final: 0.8940 (ptp-110) REVERT: C 202 MET cc_start: 0.8537 (tpt) cc_final: 0.8311 (tpp) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.2112 time to fit residues: 43.9327 Evaluate side-chains 119 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 1 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 114 optimal weight: 0.0980 chunk 85 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 54 optimal weight: 40.0000 chunk 56 optimal weight: 10.0000 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN A 652 ASN B 21 HIS ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** 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 = 0.3630 r_free = 0.3630 target = 0.064511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.045341 restraints weight = 57196.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.046784 restraints weight = 35979.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.047799 restraints weight = 25989.651| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9826 Z= 0.179 Angle : 0.612 8.270 13334 Z= 0.308 Chirality : 0.041 0.160 1549 Planarity : 0.004 0.044 1711 Dihedral : 4.158 30.798 1333 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.90 (0.24), residues: 1241 helix: 1.66 (0.21), residues: 629 sheet: -0.16 (0.40), residues: 170 loop : -0.59 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 339 HIS 0.005 0.001 HIS C 196 PHE 0.053 0.002 PHE A 50 TYR 0.010 0.001 TYR A 356 ARG 0.005 0.000 ARG C 164 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 537) hydrogen bonds : angle 4.58316 ( 1554) covalent geometry : bond 0.00368 ( 9826) covalent geometry : angle 0.61210 (13334) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.7947 (m-80) cc_final: 0.6666 (t80) REVERT: A 51 MET cc_start: 0.4806 (tpt) cc_final: 0.4414 (tpt) REVERT: A 175 MET cc_start: 0.8160 (ttt) cc_final: 0.7295 (ttt) REVERT: A 297 MET cc_start: 0.8434 (mmt) cc_final: 0.8137 (mmp) REVERT: A 465 MET cc_start: 0.8803 (mmp) cc_final: 0.8553 (mmp) REVERT: A 709 GLN cc_start: 0.9046 (pp30) cc_final: 0.8650 (tm-30) REVERT: B 124 ARG cc_start: 0.9098 (ptp-110) cc_final: 0.8836 (ptp-110) REVERT: B 125 ASN cc_start: 0.9085 (m110) cc_final: 0.8839 (m110) REVERT: B 128 LYS cc_start: 0.9269 (ptpp) cc_final: 0.9062 (pttm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2076 time to fit residues: 43.2351 Evaluate side-chains 114 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 53 optimal weight: 50.0000 chunk 92 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 146 GLN ** C 153 GLN ** 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 = 0.3667 r_free = 0.3667 target = 0.065840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.046650 restraints weight = 57357.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.048150 restraints weight = 35718.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.049162 restraints weight = 25731.388| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9826 Z= 0.125 Angle : 0.589 8.650 13334 Z= 0.293 Chirality : 0.040 0.166 1549 Planarity : 0.004 0.053 1711 Dihedral : 4.103 28.095 1333 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.97 (0.24), residues: 1241 helix: 1.74 (0.21), residues: 630 sheet: -0.09 (0.41), residues: 168 loop : -0.63 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 339 HIS 0.004 0.001 HIS C 196 PHE 0.044 0.002 PHE A 50 TYR 0.011 0.001 TYR A 356 ARG 0.003 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 537) hydrogen bonds : angle 4.51410 ( 1554) covalent geometry : bond 0.00259 ( 9826) covalent geometry : angle 0.58917 (13334) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.126 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: A 50 PHE cc_start: 0.7889 (m-80) cc_final: 0.6719 (t80) REVERT: A 51 MET cc_start: 0.4992 (tpt) cc_final: 0.4554 (tpt) REVERT: A 175 MET cc_start: 0.8103 (ttt) cc_final: 0.7424 (ttm) REVERT: A 297 MET cc_start: 0.8400 (mmt) cc_final: 0.8113 (mmp) REVERT: A 402 MET cc_start: 0.7801 (tpp) cc_final: 0.7091 (ppp) REVERT: A 709 GLN cc_start: 0.9045 (pp30) cc_final: 0.8318 (pp30) REVERT: A 710 GLU cc_start: 0.8493 (tp30) cc_final: 0.8204 (tp30) REVERT: B 124 ARG cc_start: 0.9082 (ptp-110) cc_final: 0.8855 (ptp-110) REVERT: C 88 LYS cc_start: 0.9362 (tppp) cc_final: 0.9004 (tppp) REVERT: C 202 MET cc_start: 0.8416 (tpt) cc_final: 0.8211 (tpp) REVERT: C 221 ASN cc_start: 0.8927 (m-40) cc_final: 0.8576 (p0) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1924 time to fit residues: 42.4378 Evaluate side-chains 121 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 30.0000 chunk 55 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN C 153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.062604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.043559 restraints weight = 60149.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.044987 restraints weight = 37464.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.045908 restraints weight = 27094.614| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9826 Z= 0.278 Angle : 0.745 9.083 13334 Z= 0.369 Chirality : 0.043 0.167 1549 Planarity : 0.005 0.042 1711 Dihedral : 4.366 27.271 1333 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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 (0.24), residues: 1241 helix: 1.33 (0.20), residues: 636 sheet: -0.36 (0.40), residues: 172 loop : -0.74 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 339 HIS 0.011 0.002 HIS C 196 PHE 0.046 0.002 PHE A 50 TYR 0.008 0.001 TYR A 106 ARG 0.010 0.001 ARG A 705 Details of bonding type rmsd hydrogen bonds : bond 0.04957 ( 537) hydrogen bonds : angle 4.84975 ( 1554) covalent geometry : bond 0.00569 ( 9826) covalent geometry : angle 0.74468 (13334) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.8042 (m-10) cc_final: 0.6830 (t80) REVERT: A 51 MET cc_start: 0.5034 (tpt) cc_final: 0.4474 (tpt) REVERT: A 175 MET cc_start: 0.8335 (ttt) cc_final: 0.7698 (ttm) REVERT: A 297 MET cc_start: 0.8466 (mmt) cc_final: 0.8224 (mmp) REVERT: A 412 VAL cc_start: 0.9452 (t) cc_final: 0.9211 (p) REVERT: A 461 SER cc_start: 0.9034 (p) cc_final: 0.8706 (p) REVERT: A 647 MET cc_start: 0.6783 (ppp) cc_final: 0.6568 (ppp) REVERT: A 682 GLU cc_start: 0.8759 (pp20) cc_final: 0.8499 (pp20) REVERT: A 710 GLU cc_start: 0.8513 (tp30) cc_final: 0.8106 (tp30) REVERT: B 124 ARG cc_start: 0.9084 (ptp-110) cc_final: 0.8881 (ptp-110) REVERT: C 100 ILE cc_start: 0.8547 (mm) cc_final: 0.8189 (mm) REVERT: C 202 MET cc_start: 0.8447 (tpt) cc_final: 0.8180 (tpp) REVERT: C 221 ASN cc_start: 0.9053 (m-40) cc_final: 0.8707 (p0) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2058 time to fit residues: 43.0744 Evaluate side-chains 119 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 9.9990 chunk 57 optimal weight: 40.0000 chunk 95 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 59 optimal weight: 40.0000 chunk 90 optimal weight: 9.9990 chunk 43 optimal weight: 0.3980 chunk 61 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 overall best weight: 4.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN C 89 HIS C 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.062840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.043837 restraints weight = 59991.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.045316 restraints weight = 36918.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.046298 restraints weight = 26486.019| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9826 Z= 0.235 Angle : 0.686 7.977 13334 Z= 0.345 Chirality : 0.043 0.211 1549 Planarity : 0.004 0.044 1711 Dihedral : 4.386 29.536 1333 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.51 (0.24), residues: 1241 helix: 1.33 (0.21), residues: 631 sheet: -0.45 (0.41), residues: 159 loop : -0.72 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 405 HIS 0.009 0.002 HIS C 196 PHE 0.072 0.002 PHE A 50 TYR 0.019 0.002 TYR A 356 ARG 0.005 0.000 ARG C 164 Details of bonding type rmsd hydrogen bonds : bond 0.04798 ( 537) hydrogen bonds : angle 4.70623 ( 1554) covalent geometry : bond 0.00484 ( 9826) covalent geometry : angle 0.68648 (13334) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.8142 (m-80) cc_final: 0.6652 (t80) REVERT: A 51 MET cc_start: 0.4892 (tpt) cc_final: 0.4440 (tpt) REVERT: A 175 MET cc_start: 0.8292 (ttt) cc_final: 0.7662 (ttm) REVERT: A 297 MET cc_start: 0.8426 (mmt) cc_final: 0.8199 (mmp) REVERT: A 461 SER cc_start: 0.9054 (p) cc_final: 0.8728 (p) REVERT: B 138 LYS cc_start: 0.8792 (pttp) cc_final: 0.8555 (ptmt) REVERT: C 202 MET cc_start: 0.8440 (tpt) cc_final: 0.8201 (tpp) REVERT: C 221 ASN cc_start: 0.9046 (m-40) cc_final: 0.8713 (p0) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1959 time to fit residues: 40.0135 Evaluate side-chains 119 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 116 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.065021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.045847 restraints weight = 58998.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.047404 restraints weight = 36045.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.048457 restraints weight = 25646.659| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9826 Z= 0.135 Angle : 0.639 9.919 13334 Z= 0.317 Chirality : 0.042 0.177 1549 Planarity : 0.004 0.043 1711 Dihedral : 4.298 28.502 1333 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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 (0.24), residues: 1241 helix: 1.43 (0.21), residues: 630 sheet: -0.31 (0.40), residues: 170 loop : -0.77 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 763 HIS 0.006 0.001 HIS C 196 PHE 0.060 0.002 PHE A 50 TYR 0.007 0.001 TYR A 356 ARG 0.004 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 537) hydrogen bonds : angle 4.58938 ( 1554) covalent geometry : bond 0.00281 ( 9826) covalent geometry : angle 0.63861 (13334) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.058 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: A 50 PHE cc_start: 0.8091 (m-80) cc_final: 0.6667 (t80) REVERT: A 51 MET cc_start: 0.5056 (tpt) cc_final: 0.4776 (tpt) REVERT: A 175 MET cc_start: 0.8245 (ttt) cc_final: 0.7600 (ttm) REVERT: A 297 MET cc_start: 0.8372 (mmt) cc_final: 0.8131 (mmp) REVERT: A 412 VAL cc_start: 0.9440 (t) cc_final: 0.9192 (p) REVERT: A 461 SER cc_start: 0.8999 (p) cc_final: 0.8664 (p) REVERT: A 647 MET cc_start: 0.7027 (ppp) cc_final: 0.6748 (ppp) REVERT: A 709 GLN cc_start: 0.9033 (pp30) cc_final: 0.8655 (tm-30) REVERT: B 110 GLU cc_start: 0.8785 (tt0) cc_final: 0.8198 (tt0) REVERT: C 88 LYS cc_start: 0.9322 (tppp) cc_final: 0.9001 (tppp) REVERT: C 221 ASN cc_start: 0.9011 (m-40) cc_final: 0.8725 (p0) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1981 time to fit residues: 44.6563 Evaluate side-chains 126 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 0.0670 chunk 70 optimal weight: 0.2980 chunk 7 optimal weight: 6.9990 overall best weight: 1.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN A 484 GLN ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.065423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.046315 restraints weight = 58579.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.047850 restraints weight = 36058.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.048914 restraints weight = 25791.269| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9826 Z= 0.130 Angle : 0.630 9.318 13334 Z= 0.313 Chirality : 0.042 0.178 1549 Planarity : 0.004 0.041 1711 Dihedral : 4.238 26.560 1333 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.24), residues: 1241 helix: 1.55 (0.20), residues: 631 sheet: -0.18 (0.40), residues: 168 loop : -0.74 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 405 HIS 0.005 0.001 HIS C 196 PHE 0.048 0.002 PHE A 50 TYR 0.023 0.001 TYR A 356 ARG 0.004 0.000 ARG A 705 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 537) hydrogen bonds : angle 4.47717 ( 1554) covalent geometry : bond 0.00271 ( 9826) covalent geometry : angle 0.63000 (13334) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.8008 (m-80) cc_final: 0.6431 (t80) REVERT: A 51 MET cc_start: 0.4893 (tpt) cc_final: 0.4531 (tpt) REVERT: A 175 MET cc_start: 0.8272 (ttt) cc_final: 0.7633 (ttm) REVERT: A 297 MET cc_start: 0.8375 (mmt) cc_final: 0.8125 (mmp) REVERT: A 461 SER cc_start: 0.8969 (p) cc_final: 0.8680 (p) REVERT: A 647 MET cc_start: 0.7036 (ppp) cc_final: 0.6748 (ppp) REVERT: A 709 GLN cc_start: 0.9038 (pp30) cc_final: 0.8623 (tm-30) REVERT: B 110 GLU cc_start: 0.8793 (tt0) cc_final: 0.8219 (tt0) REVERT: B 138 LYS cc_start: 0.8781 (pttp) cc_final: 0.8399 (tmtt) REVERT: C 39 ILE cc_start: 0.9058 (mm) cc_final: 0.8406 (tp) REVERT: C 88 LYS cc_start: 0.9327 (tppp) cc_final: 0.9005 (tppp) REVERT: C 202 MET cc_start: 0.8232 (tpt) cc_final: 0.7923 (tpp) REVERT: C 221 ASN cc_start: 0.8990 (m-40) cc_final: 0.8732 (p0) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2688 time to fit residues: 60.9154 Evaluate side-chains 129 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 5 optimal weight: 40.0000 chunk 39 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 60 optimal weight: 50.0000 chunk 114 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.065998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.046881 restraints weight = 58473.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.048441 restraints weight = 35941.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.049486 restraints weight = 25644.448| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9826 Z= 0.123 Angle : 0.623 9.469 13334 Z= 0.306 Chirality : 0.041 0.180 1549 Planarity : 0.004 0.041 1711 Dihedral : 4.216 25.587 1333 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.81 (0.24), residues: 1241 helix: 1.60 (0.20), residues: 630 sheet: -0.16 (0.40), residues: 168 loop : -0.67 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 405 HIS 0.004 0.001 HIS C 11 PHE 0.049 0.002 PHE A 50 TYR 0.018 0.001 TYR A 356 ARG 0.003 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04379 ( 537) hydrogen bonds : angle 4.43882 ( 1554) covalent geometry : bond 0.00254 ( 9826) covalent geometry : angle 0.62303 (13334) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.368 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: symmetry clash REVERT: A 50 PHE cc_start: 0.7962 (m-80) cc_final: 0.6381 (t80) REVERT: A 51 MET cc_start: 0.4807 (tpt) cc_final: 0.4430 (tpt) REVERT: A 175 MET cc_start: 0.8284 (ttt) cc_final: 0.7651 (ttt) REVERT: A 297 MET cc_start: 0.8339 (mmt) cc_final: 0.8080 (mmp) REVERT: A 412 VAL cc_start: 0.9413 (t) cc_final: 0.9147 (p) REVERT: A 709 GLN cc_start: 0.9035 (pp30) cc_final: 0.8549 (tm-30) REVERT: B 110 GLU cc_start: 0.8778 (tt0) cc_final: 0.8296 (tt0) REVERT: B 138 LYS cc_start: 0.8714 (pttp) cc_final: 0.8354 (tmtt) REVERT: C 39 ILE cc_start: 0.9052 (mm) cc_final: 0.8560 (tp) REVERT: C 88 LYS cc_start: 0.9303 (tppp) cc_final: 0.8990 (tppp) REVERT: C 202 MET cc_start: 0.8167 (tpt) cc_final: 0.7959 (tpp) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3088 time to fit residues: 72.9616 Evaluate side-chains 130 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 122 optimal weight: 0.4980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** 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 = 0.3687 r_free = 0.3687 target = 0.066581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.047465 restraints weight = 58042.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.049027 restraints weight = 36009.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.050077 restraints weight = 25761.180| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9826 Z= 0.119 Angle : 0.623 9.425 13334 Z= 0.303 Chirality : 0.041 0.178 1549 Planarity : 0.004 0.041 1711 Dihedral : 4.185 24.878 1333 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.84 (0.24), residues: 1241 helix: 1.57 (0.20), residues: 637 sheet: -0.12 (0.40), residues: 167 loop : -0.62 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 405 HIS 0.006 0.001 HIS C 11 PHE 0.047 0.002 PHE A 50 TYR 0.008 0.001 TYR A 356 ARG 0.002 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 537) hydrogen bonds : angle 4.39006 ( 1554) covalent geometry : bond 0.00244 ( 9826) covalent geometry : angle 0.62299 (13334) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3845.41 seconds wall clock time: 70 minutes 8.12 seconds (4208.12 seconds total)