Starting phenix.real_space_refine on Wed Mar 4 00:31:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zk8_14758/03_2026/7zk8_14758.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zk8_14758/03_2026/7zk8_14758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zk8_14758/03_2026/7zk8_14758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zk8_14758/03_2026/7zk8_14758.map" model { file = "/net/cci-nas-00/data/ceres_data/7zk8_14758/03_2026/7zk8_14758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zk8_14758/03_2026/7zk8_14758.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.013 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 P 6 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 5992 2.51 5 N 1569 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9331 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9162 Classifications: {'peptide': 1181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 1151} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 169 Unusual residues: {' MG': 2, 'ATP': 2, 'JIZ': 1, 'Y01': 2} Classifications: {'undetermined': 7, 'water': 4} Link IDs: {None: 10} Time building chain proxies: 2.38, per 1000 atoms: 0.26 Number of scatterers: 9331 At special positions: 0 Unit cell: (71.052, 86.523, 148.407, 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) S 36 16.00 P 6 15.00 Mg 2 11.99 O 1726 8.00 N 1569 7.00 C 5992 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 479.0 milliseconds 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 70.4% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 43 through 62 Processing helix chain 'A' and resid 62 through 71 removed outlier: 3.594A pdb=" N PHE A 71 " --> pdb=" O MET A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 86 removed outlier: 3.685A pdb=" N SER A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.514A pdb=" N MET A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 92 through 154 removed outlier: 3.570A pdb=" N LYS A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 145 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 180 removed outlier: 3.918A pdb=" N ASP A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 207 removed outlier: 4.060A pdb=" N GLY A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 256 Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 265 through 320 removed outlier: 3.555A pdb=" N LYS A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 Processing helix chain 'A' and resid 336 through 367 Proline residue: A 346 - end of helix removed outlier: 3.899A pdb=" N TYR A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLU A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 437 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 528 through 543 removed outlier: 4.069A pdb=" N ARG A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 572 removed outlier: 3.797A pdb=" N ALA A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 removed outlier: 4.104A pdb=" N VAL A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 616 through 624 Processing helix chain 'A' and resid 691 through 700 Processing helix chain 'A' and resid 703 through 737 removed outlier: 4.137A pdb=" N GLN A 721 " --> pdb=" O ASN A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix Processing helix chain 'A' and resid 744 through 795 removed outlier: 4.061A pdb=" N LEU A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 795 " --> pdb=" O SER A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 801 removed outlier: 3.664A pdb=" N PHE A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 822 removed outlier: 4.064A pdb=" N ALA A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 825 No H-bonds generated for 'chain 'A' and resid 823 through 825' Processing helix chain 'A' and resid 826 through 850 removed outlier: 3.889A pdb=" N ALA A 830 " --> pdb=" O GLY A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 899 removed outlier: 4.132A pdb=" N VAL A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Proline residue: A 862 - end of helix removed outlier: 4.022A pdb=" N MET A 874 " --> pdb=" O VAL A 870 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 880 " --> pdb=" O SER A 876 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 889 " --> pdb=" O GLU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 906 Processing helix chain 'A' and resid 908 through 962 removed outlier: 4.708A pdb=" N ILE A 922 " --> pdb=" O GLN A 918 " (cutoff:3.500A) Proline residue: A 923 - end of helix Processing helix chain 'A' and resid 966 through 989 removed outlier: 3.618A pdb=" N VAL A 970 " --> pdb=" O THR A 966 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N CYS A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 989 " --> pdb=" O GLY A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1009 removed outlier: 3.561A pdb=" N VAL A 999 " --> pdb=" O ALA A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1080 removed outlier: 3.714A pdb=" N VAL A1076 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1108 Processing helix chain 'A' and resid 1122 through 1129 Processing helix chain 'A' and resid 1137 through 1148 Processing helix chain 'A' and resid 1150 through 1157 Processing helix chain 'A' and resid 1159 through 1163 Processing helix chain 'A' and resid 1166 through 1170 Processing helix chain 'A' and resid 1173 through 1188 removed outlier: 4.154A pdb=" N ARG A1188 " --> pdb=" O ARG A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1217 removed outlier: 3.598A pdb=" N ALA A1217 " --> pdb=" O ALA A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1233 removed outlier: 3.730A pdb=" N THR A1232 " --> pdb=" O ARG A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1259 Processing helix chain 'A' and resid 1261 through 1268 Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 413 removed outlier: 6.538A pdb=" N LYS A 407 " --> pdb=" O HIS A 394 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N HIS A 394 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU A 409 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE A 393 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP A 444 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 466 through 469 removed outlier: 6.280A pdb=" N LEU A 548 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE A 581 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 550 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR A 418 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA A 595 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ALA A 420 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE A 597 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL A 422 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE A 594 " --> pdb=" O GLN A 605 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A 605 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY A 596 " --> pdb=" O VAL A 603 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1053 through 1056 removed outlier: 5.487A pdb=" N PHE A1033 " --> pdb=" O PHE A1091 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE A1091 " --> pdb=" O PHE A1033 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLY A1035 " --> pdb=" O SER A1089 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER A1089 " --> pdb=" O GLY A1035 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1109 through 1112 removed outlier: 6.199A pdb=" N LEU A1062 " --> pdb=" O VAL A1225 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N THR A1061 " --> pdb=" O LEU A1238 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL A1240 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA A1063 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE A1242 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL A1065 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A1239 " --> pdb=" O HIS A1250 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HIS A1250 " --> pdb=" O ILE A1239 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A1241 " --> pdb=" O LYS A1248 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A1248 " --> pdb=" O VAL A1241 " (cutoff:3.500A) 622 hydrogen bonds defined for protein. 1824 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: 1.80 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1521 1.31 - 1.44: 2454 1.44 - 1.56: 5450 1.56 - 1.69: 17 1.69 - 1.82: 64 Bond restraints: 9506 Sorted by residual: bond pdb=" C03 JIZ A2005 " pdb=" N02 JIZ A2005 " ideal model delta sigma weight residual 1.367 1.639 -0.272 2.00e-02 2.50e+03 1.85e+02 bond pdb=" C08 JIZ A2005 " pdb=" N04 JIZ A2005 " ideal model delta sigma weight residual 1.366 1.617 -0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C13 JIZ A2005 " pdb=" N06 JIZ A2005 " ideal model delta sigma weight residual 1.366 1.617 -0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C02 JIZ A2005 " pdb=" S01 JIZ A2005 " ideal model delta sigma weight residual 1.728 1.546 0.182 2.00e-02 2.50e+03 8.29e+01 bond pdb=" C03 JIZ A2005 " pdb=" C04 JIZ A2005 " ideal model delta sigma weight residual 1.360 1.520 -0.160 2.00e-02 2.50e+03 6.40e+01 ... (remaining 9501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 12708 3.51 - 7.03: 152 7.03 - 10.54: 15 10.54 - 14.05: 2 14.05 - 17.56: 3 Bond angle restraints: 12880 Sorted by residual: angle pdb=" N ASP A 76 " pdb=" CA ASP A 76 " pdb=" C ASP A 76 " ideal model delta sigma weight residual 111.36 101.04 10.32 1.09e+00 8.42e-01 8.96e+01 angle pdb=" N THR A 108 " pdb=" CA THR A 108 " pdb=" C THR A 108 " ideal model delta sigma weight residual 112.23 101.47 10.76 1.26e+00 6.30e-01 7.29e+01 angle pdb=" N ILE A 324 " pdb=" CA ILE A 324 " pdb=" C ILE A 324 " ideal model delta sigma weight residual 110.62 103.31 7.31 1.02e+00 9.61e-01 5.14e+01 angle pdb=" N ARG A 745 " pdb=" CA ARG A 745 " pdb=" C ARG A 745 " ideal model delta sigma weight residual 111.36 103.62 7.74 1.09e+00 8.42e-01 5.04e+01 angle pdb=" N PHE A 331 " pdb=" CA PHE A 331 " pdb=" C PHE A 331 " ideal model delta sigma weight residual 111.36 103.69 7.67 1.09e+00 8.42e-01 4.95e+01 ... (remaining 12875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.56: 5484 24.56 - 49.13: 266 49.13 - 73.69: 39 73.69 - 98.25: 11 98.25 - 122.81: 2 Dihedral angle restraints: 5802 sinusoidal: 2419 harmonic: 3383 Sorted by residual: dihedral pdb=" C GLN A 963 " pdb=" N GLN A 963 " pdb=" CA GLN A 963 " pdb=" CB GLN A 963 " ideal model delta harmonic sigma weight residual -122.60 -133.85 11.25 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" CBC Y01 A2007 " pdb=" CAR Y01 A2007 " pdb=" CAT Y01 A2007 " pdb=" CBH Y01 A2007 " ideal model delta sinusoidal sigma weight residual -57.13 65.68 -122.81 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" CA ALA A 582 " pdb=" C ALA A 582 " pdb=" N HIS A 583 " pdb=" CA HIS A 583 " ideal model delta harmonic sigma weight residual 180.00 160.60 19.40 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 5799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1292 0.073 - 0.147: 140 0.147 - 0.220: 24 0.220 - 0.294: 16 0.294 - 0.367: 6 Chirality restraints: 1478 Sorted by residual: chirality pdb=" CA GLN A 963 " pdb=" N GLN A 963 " pdb=" C GLN A 963 " pdb=" CB GLN A 963 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA MET A 99 " pdb=" N MET A 99 " pdb=" C MET A 99 " pdb=" CB MET A 99 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA TRP A 208 " pdb=" N TRP A 208 " pdb=" C TRP A 208 " pdb=" CB TRP A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 1475 not shown) Planarity restraints: 1618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 65 " -0.018 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C PRO A 65 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO A 65 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU A 66 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 743 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C THR A 743 " -0.060 2.00e-02 2.50e+03 pdb=" O THR A 743 " 0.022 2.00e-02 2.50e+03 pdb=" N GLN A 744 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 207 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C GLY A 207 " -0.055 2.00e-02 2.50e+03 pdb=" O GLY A 207 " 0.020 2.00e-02 2.50e+03 pdb=" N TRP A 208 " 0.019 2.00e-02 2.50e+03 ... (remaining 1615 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 59 2.54 - 3.13: 7487 3.13 - 3.72: 14797 3.72 - 4.31: 21160 4.31 - 4.90: 34561 Nonbonded interactions: 78064 Sorted by model distance: nonbonded pdb="MG MG A2002 " pdb=" O HOH A2102 " model vdw 1.946 2.170 nonbonded pdb="MG MG A2002 " pdb=" O HOH A2101 " model vdw 1.975 2.170 nonbonded pdb=" O2G ATP A2003 " pdb="MG MG A2004 " model vdw 2.021 2.170 nonbonded pdb=" OE1 GLN A 471 " pdb="MG MG A2002 " model vdw 2.065 2.170 nonbonded pdb=" O2B ATP A2001 " pdb="MG MG A2002 " model vdw 2.092 2.170 ... (remaining 78059 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.620 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:9.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 0.009 0.272 9507 Z= 0.497 Angle : 0.969 17.564 12880 Z= 0.617 Chirality : 0.059 0.367 1478 Planarity : 0.005 0.066 1618 Dihedral : 14.592 122.813 3634 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.10 % Allowed : 1.96 % Favored : 97.93 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.24), residues: 1177 helix: 0.95 (0.18), residues: 782 sheet: 0.35 (0.62), residues: 66 loop : -0.79 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 589 TYR 0.033 0.002 TYR A 114 PHE 0.017 0.002 PHE A 934 TRP 0.007 0.001 TRP A 158 HIS 0.007 0.001 HIS A1003 Details of bonding type rmsd covalent geometry : bond 0.00885 ( 9506) covalent geometry : angle 0.96860 (12880) hydrogen bonds : bond 0.16236 ( 622) hydrogen bonds : angle 6.22230 ( 1824) Misc. bond : bond 0.02119 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.352 Fit side-chains REVERT: A 315 SER cc_start: 0.8824 (t) cc_final: 0.8473 (m) REVERT: A 607 ASN cc_start: 0.7451 (t0) cc_final: 0.7206 (m110) REVERT: A 620 LYS cc_start: 0.8155 (mttt) cc_final: 0.7621 (ttpt) REVERT: A 955 PHE cc_start: 0.8642 (t80) cc_final: 0.8393 (t80) REVERT: A 960 VAL cc_start: 0.7758 (t) cc_final: 0.7489 (m) REVERT: A 1007 ILE cc_start: 0.8282 (tp) cc_final: 0.8019 (tp) REVERT: A 1244 ASN cc_start: 0.6847 (p0) cc_final: 0.6102 (t160) outliers start: 1 outliers final: 1 residues processed: 193 average time/residue: 0.5244 time to fit residues: 108.3922 Evaluate side-chains 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.0010 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.164890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122213 restraints weight = 10797.885| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.26 r_work: 0.3305 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9507 Z= 0.142 Angle : 0.576 8.938 12880 Z= 0.303 Chirality : 0.042 0.228 1478 Planarity : 0.004 0.046 1618 Dihedral : 9.507 88.668 1512 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.79 % Allowed : 12.60 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.24), residues: 1177 helix: 1.44 (0.18), residues: 789 sheet: 0.61 (0.64), residues: 66 loop : -0.87 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 97 TYR 0.013 0.001 TYR A 312 PHE 0.018 0.001 PHE A 508 TRP 0.022 0.001 TRP A 208 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9506) covalent geometry : angle 0.57552 (12880) hydrogen bonds : bond 0.05349 ( 622) hydrogen bonds : angle 4.57909 ( 1824) Misc. bond : bond 0.00117 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.345 Fit side-chains REVERT: A 48 LEU cc_start: 0.6907 (mp) cc_final: 0.6573 (tt) REVERT: A 64 LEU cc_start: 0.8134 (tm) cc_final: 0.7886 (tt) REVERT: A 267 LYS cc_start: 0.7966 (mttt) cc_final: 0.7471 (mppt) REVERT: A 315 SER cc_start: 0.8479 (t) cc_final: 0.8193 (m) REVERT: A 331 PHE cc_start: 0.7722 (m-80) cc_final: 0.7321 (m-80) REVERT: A 452 GLN cc_start: 0.7413 (tt0) cc_final: 0.7206 (tt0) REVERT: A 562 GLU cc_start: 0.7446 (tt0) cc_final: 0.7014 (tt0) REVERT: A 607 ASN cc_start: 0.6353 (t0) cc_final: 0.5885 (m110) REVERT: A 620 LYS cc_start: 0.8099 (mttt) cc_final: 0.7254 (ttpt) REVERT: A 944 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7166 (tmm) REVERT: A 955 PHE cc_start: 0.8544 (t80) cc_final: 0.8128 (t80) REVERT: A 960 VAL cc_start: 0.7505 (t) cc_final: 0.7262 (m) REVERT: A 965 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7358 (tmt) REVERT: A 1026 MET cc_start: 0.7442 (ppp) cc_final: 0.6410 (ttt) REVERT: A 1244 ASN cc_start: 0.6572 (p0) cc_final: 0.5800 (t160) outliers start: 27 outliers final: 8 residues processed: 149 average time/residue: 0.5013 time to fit residues: 80.2253 Evaluate side-chains 123 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 89 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** A1050 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 = 0.3884 r_free = 0.3884 target = 0.164042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121050 restraints weight = 10785.522| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.25 r_work: 0.3297 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9507 Z= 0.133 Angle : 0.554 11.365 12880 Z= 0.287 Chirality : 0.041 0.247 1478 Planarity : 0.003 0.037 1618 Dihedral : 8.634 75.732 1510 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.00 % Allowed : 14.77 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.24), residues: 1177 helix: 1.54 (0.18), residues: 792 sheet: 0.54 (0.65), residues: 61 loop : -0.74 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 901 TYR 0.014 0.001 TYR A 110 PHE 0.013 0.001 PHE A 508 TRP 0.028 0.001 TRP A 208 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9506) covalent geometry : angle 0.55447 (12880) hydrogen bonds : bond 0.05028 ( 622) hydrogen bonds : angle 4.38646 ( 1824) Misc. bond : bond 0.00099 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.335 Fit side-chains REVERT: A 48 LEU cc_start: 0.6868 (mp) cc_final: 0.6497 (tt) REVERT: A 64 LEU cc_start: 0.8110 (tm) cc_final: 0.7808 (tt) REVERT: A 267 LYS cc_start: 0.7978 (mttt) cc_final: 0.7518 (mppt) REVERT: A 315 SER cc_start: 0.8488 (t) cc_final: 0.8201 (m) REVERT: A 331 PHE cc_start: 0.7739 (m-80) cc_final: 0.7388 (m-80) REVERT: A 452 GLN cc_start: 0.7503 (tt0) cc_final: 0.7280 (tt0) REVERT: A 562 GLU cc_start: 0.7396 (tt0) cc_final: 0.6937 (tt0) REVERT: A 607 ASN cc_start: 0.6018 (t0) cc_final: 0.5619 (m110) REVERT: A 620 LYS cc_start: 0.8120 (mttt) cc_final: 0.7259 (ttpt) REVERT: A 944 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7134 (tmm) REVERT: A 955 PHE cc_start: 0.8518 (t80) cc_final: 0.8088 (t80) REVERT: A 965 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7300 (tmt) REVERT: A 1026 MET cc_start: 0.7437 (ppp) cc_final: 0.6468 (ttt) REVERT: A 1243 GLN cc_start: 0.7133 (pt0) cc_final: 0.6878 (mm-40) outliers start: 29 outliers final: 11 residues processed: 138 average time/residue: 0.4656 time to fit residues: 69.4320 Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 41 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN A 437 GLN ** A1050 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 = 0.3867 r_free = 0.3867 target = 0.162182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119104 restraints weight = 10961.918| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.24 r_work: 0.3291 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9507 Z= 0.144 Angle : 0.528 6.779 12880 Z= 0.280 Chirality : 0.041 0.249 1478 Planarity : 0.003 0.040 1618 Dihedral : 8.413 77.648 1510 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.10 % Allowed : 16.84 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.24), residues: 1177 helix: 1.53 (0.18), residues: 793 sheet: 0.67 (0.66), residues: 61 loop : -0.73 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 206 TYR 0.015 0.001 TYR A 306 PHE 0.016 0.001 PHE A 508 TRP 0.019 0.001 TRP A 208 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9506) covalent geometry : angle 0.52811 (12880) hydrogen bonds : bond 0.05008 ( 622) hydrogen bonds : angle 4.35407 ( 1824) Misc. bond : bond 0.00087 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.321 Fit side-chains REVERT: A 48 LEU cc_start: 0.6994 (mp) cc_final: 0.6592 (tt) REVERT: A 64 LEU cc_start: 0.8201 (tm) cc_final: 0.7901 (tt) REVERT: A 267 LYS cc_start: 0.8061 (mttt) cc_final: 0.7606 (mppt) REVERT: A 315 SER cc_start: 0.8555 (t) cc_final: 0.8257 (m) REVERT: A 331 PHE cc_start: 0.7750 (m-80) cc_final: 0.7422 (m-80) REVERT: A 368 LYS cc_start: 0.8678 (ptpt) cc_final: 0.8222 (ptmm) REVERT: A 452 GLN cc_start: 0.7623 (tt0) cc_final: 0.7422 (tt0) REVERT: A 562 GLU cc_start: 0.7454 (tt0) cc_final: 0.7011 (tt0) REVERT: A 607 ASN cc_start: 0.5879 (t0) cc_final: 0.5646 (m110) REVERT: A 620 LYS cc_start: 0.8176 (mttt) cc_final: 0.7317 (ttpt) REVERT: A 944 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7176 (tmm) REVERT: A 955 PHE cc_start: 0.8540 (t80) cc_final: 0.8121 (t80) REVERT: A 965 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7309 (tmt) REVERT: A 1026 MET cc_start: 0.7410 (ppp) cc_final: 0.6461 (ttt) REVERT: A 1246 LYS cc_start: 0.6859 (mtpt) cc_final: 0.6244 (mmtt) REVERT: A 1260 LYS cc_start: 0.6839 (mttm) cc_final: 0.6438 (mttp) outliers start: 30 outliers final: 13 residues processed: 142 average time/residue: 0.4796 time to fit residues: 73.5753 Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1050 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.163147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120348 restraints weight = 10975.980| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.27 r_work: 0.3273 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9507 Z= 0.126 Angle : 0.522 7.058 12880 Z= 0.276 Chirality : 0.041 0.285 1478 Planarity : 0.003 0.041 1618 Dihedral : 8.285 78.023 1510 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.38 % Allowed : 18.18 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.24), residues: 1177 helix: 1.61 (0.18), residues: 794 sheet: 0.83 (0.67), residues: 61 loop : -0.79 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 282 TYR 0.015 0.001 TYR A 306 PHE 0.013 0.001 PHE A 78 TRP 0.016 0.001 TRP A 208 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9506) covalent geometry : angle 0.52168 (12880) hydrogen bonds : bond 0.04775 ( 622) hydrogen bonds : angle 4.25617 ( 1824) Misc. bond : bond 0.00077 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.264 Fit side-chains REVERT: A 48 LEU cc_start: 0.6885 (mp) cc_final: 0.6449 (tt) REVERT: A 64 LEU cc_start: 0.8133 (tm) cc_final: 0.7838 (tt) REVERT: A 201 ILE cc_start: 0.8434 (mt) cc_final: 0.8201 (mp) REVERT: A 267 LYS cc_start: 0.8000 (mttt) cc_final: 0.7543 (mppt) REVERT: A 315 SER cc_start: 0.8492 (t) cc_final: 0.8203 (m) REVERT: A 331 PHE cc_start: 0.7720 (m-80) cc_final: 0.7417 (m-80) REVERT: A 368 LYS cc_start: 0.8628 (ptpt) cc_final: 0.8153 (ptmm) REVERT: A 562 GLU cc_start: 0.7357 (tt0) cc_final: 0.6941 (tt0) REVERT: A 605 GLN cc_start: 0.7647 (tt0) cc_final: 0.7201 (mt0) REVERT: A 620 LYS cc_start: 0.8104 (mttt) cc_final: 0.7257 (ttpt) REVERT: A 944 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7052 (tmm) REVERT: A 955 PHE cc_start: 0.8513 (t80) cc_final: 0.8071 (t80) REVERT: A 965 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.7213 (tmt) REVERT: A 1026 MET cc_start: 0.7391 (ppp) cc_final: 0.6487 (ttt) REVERT: A 1164 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7862 (ttp-110) REVERT: A 1246 LYS cc_start: 0.6762 (mtpt) cc_final: 0.6146 (mmtt) outliers start: 23 outliers final: 9 residues processed: 136 average time/residue: 0.4871 time to fit residues: 71.1391 Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1164 ARG Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 9 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 12 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.164090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.120928 restraints weight = 10898.994| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.29 r_work: 0.3317 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9507 Z= 0.123 Angle : 0.515 7.373 12880 Z= 0.272 Chirality : 0.041 0.305 1478 Planarity : 0.003 0.042 1618 Dihedral : 8.236 79.694 1510 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.48 % Allowed : 19.32 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.24), residues: 1177 helix: 1.69 (0.18), residues: 793 sheet: 0.81 (0.67), residues: 61 loop : -0.76 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 206 TYR 0.015 0.001 TYR A 306 PHE 0.014 0.001 PHE A 508 TRP 0.015 0.001 TRP A 208 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9506) covalent geometry : angle 0.51505 (12880) hydrogen bonds : bond 0.04644 ( 622) hydrogen bonds : angle 4.17995 ( 1824) Misc. bond : bond 0.00143 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.343 Fit side-chains REVERT: A 48 LEU cc_start: 0.6911 (mp) cc_final: 0.6482 (tt) REVERT: A 64 LEU cc_start: 0.8089 (tm) cc_final: 0.7806 (tt) REVERT: A 267 LYS cc_start: 0.7993 (mttt) cc_final: 0.7545 (mppt) REVERT: A 315 SER cc_start: 0.8523 (t) cc_final: 0.8232 (m) REVERT: A 331 PHE cc_start: 0.7687 (m-80) cc_final: 0.7376 (m-80) REVERT: A 368 LYS cc_start: 0.8609 (ptpt) cc_final: 0.8138 (ptmm) REVERT: A 562 GLU cc_start: 0.7355 (tt0) cc_final: 0.6941 (tt0) REVERT: A 605 GLN cc_start: 0.7650 (tt0) cc_final: 0.7297 (mt0) REVERT: A 620 LYS cc_start: 0.8100 (mttt) cc_final: 0.7246 (ttpt) REVERT: A 944 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7035 (tmm) REVERT: A 955 PHE cc_start: 0.8537 (t80) cc_final: 0.8067 (t80) REVERT: A 965 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7150 (tmt) REVERT: A 1026 MET cc_start: 0.7380 (ppp) cc_final: 0.6502 (ttt) REVERT: A 1246 LYS cc_start: 0.6723 (mtpt) cc_final: 0.6149 (mmtt) outliers start: 24 outliers final: 15 residues processed: 132 average time/residue: 0.5025 time to fit residues: 71.4392 Evaluate side-chains 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.156112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.113195 restraints weight = 11091.451| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.19 r_work: 0.3226 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9507 Z= 0.238 Angle : 0.617 7.565 12880 Z= 0.328 Chirality : 0.045 0.323 1478 Planarity : 0.004 0.041 1618 Dihedral : 8.702 89.733 1510 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.31 % Allowed : 19.63 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.24), residues: 1177 helix: 1.39 (0.18), residues: 791 sheet: 0.81 (0.64), residues: 67 loop : -0.82 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 355 TYR 0.015 0.002 TYR A 306 PHE 0.023 0.002 PHE A 362 TRP 0.010 0.001 TRP A 158 HIS 0.006 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 9506) covalent geometry : angle 0.61738 (12880) hydrogen bonds : bond 0.05869 ( 622) hydrogen bonds : angle 4.52798 ( 1824) Misc. bond : bond 0.00155 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.346 Fit side-chains REVERT: A 64 LEU cc_start: 0.8256 (tm) cc_final: 0.7961 (tt) REVERT: A 173 ASP cc_start: 0.8017 (t0) cc_final: 0.7631 (m-30) REVERT: A 267 LYS cc_start: 0.8204 (mttt) cc_final: 0.7711 (mppt) REVERT: A 331 PHE cc_start: 0.7754 (m-80) cc_final: 0.7459 (m-80) REVERT: A 562 GLU cc_start: 0.7649 (tt0) cc_final: 0.7237 (tt0) REVERT: A 620 LYS cc_start: 0.8164 (mttt) cc_final: 0.7311 (ttpp) REVERT: A 944 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7237 (tmm) REVERT: A 955 PHE cc_start: 0.8613 (t80) cc_final: 0.8130 (t80) REVERT: A 960 VAL cc_start: 0.7646 (OUTLIER) cc_final: 0.7427 (m) REVERT: A 1026 MET cc_start: 0.7425 (ppp) cc_final: 0.6511 (ttt) REVERT: A 1164 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7790 (ttp-110) REVERT: A 1219 GLU cc_start: 0.7112 (mp0) cc_final: 0.6681 (mp0) REVERT: A 1246 LYS cc_start: 0.6806 (mtpt) cc_final: 0.6257 (mmtt) outliers start: 32 outliers final: 18 residues processed: 138 average time/residue: 0.5074 time to fit residues: 75.2357 Evaluate side-chains 136 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1164 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 53 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 ASN ** 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 = 0.3877 r_free = 0.3877 target = 0.161894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.119173 restraints weight = 11009.874| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.27 r_work: 0.3309 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9507 Z= 0.137 Angle : 0.543 8.721 12880 Z= 0.288 Chirality : 0.042 0.346 1478 Planarity : 0.003 0.042 1618 Dihedral : 8.435 79.598 1510 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.58 % Allowed : 21.49 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.24), residues: 1177 helix: 1.53 (0.18), residues: 795 sheet: 0.75 (0.65), residues: 64 loop : -0.76 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 282 TYR 0.025 0.001 TYR A 958 PHE 0.015 0.001 PHE A 724 TRP 0.014 0.001 TRP A 208 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9506) covalent geometry : angle 0.54350 (12880) hydrogen bonds : bond 0.04987 ( 622) hydrogen bonds : angle 4.31707 ( 1824) Misc. bond : bond 0.00125 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.322 Fit side-chains REVERT: A 64 LEU cc_start: 0.8190 (tm) cc_final: 0.7906 (tt) REVERT: A 173 ASP cc_start: 0.7932 (t0) cc_final: 0.7634 (m-30) REVERT: A 267 LYS cc_start: 0.8076 (mttt) cc_final: 0.7606 (mppt) REVERT: A 282 ARG cc_start: 0.7412 (mtm110) cc_final: 0.7176 (ttm-80) REVERT: A 315 SER cc_start: 0.8412 (t) cc_final: 0.8138 (m) REVERT: A 331 PHE cc_start: 0.7765 (m-80) cc_final: 0.7479 (m-80) REVERT: A 562 GLU cc_start: 0.7505 (tt0) cc_final: 0.7086 (tt0) REVERT: A 605 GLN cc_start: 0.7671 (tt0) cc_final: 0.7456 (mt0) REVERT: A 620 LYS cc_start: 0.8147 (mttt) cc_final: 0.7296 (ttpt) REVERT: A 944 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7133 (tmm) REVERT: A 955 PHE cc_start: 0.8605 (t80) cc_final: 0.8165 (t80) REVERT: A 960 VAL cc_start: 0.7615 (OUTLIER) cc_final: 0.7386 (m) REVERT: A 1026 MET cc_start: 0.7399 (ppp) cc_final: 0.6515 (ttt) REVERT: A 1164 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7875 (ttp-110) REVERT: A 1219 GLU cc_start: 0.7112 (mp0) cc_final: 0.6641 (mp0) REVERT: A 1246 LYS cc_start: 0.6881 (mtpt) cc_final: 0.6334 (mmtt) outliers start: 25 outliers final: 14 residues processed: 134 average time/residue: 0.4685 time to fit residues: 67.7951 Evaluate side-chains 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1164 ARG Chi-restraints excluded: chain A residue 1233 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** A1050 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 = 0.3861 r_free = 0.3861 target = 0.160335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.117366 restraints weight = 11112.543| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.27 r_work: 0.3194 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9507 Z= 0.158 Angle : 0.564 8.833 12880 Z= 0.299 Chirality : 0.043 0.352 1478 Planarity : 0.003 0.042 1618 Dihedral : 8.438 78.982 1510 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.58 % Allowed : 22.00 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.24), residues: 1177 helix: 1.50 (0.18), residues: 795 sheet: 0.77 (0.66), residues: 64 loop : -0.74 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 282 TYR 0.024 0.001 TYR A 958 PHE 0.019 0.001 PHE A 196 TRP 0.013 0.001 TRP A 208 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9506) covalent geometry : angle 0.56443 (12880) hydrogen bonds : bond 0.05154 ( 622) hydrogen bonds : angle 4.34536 ( 1824) Misc. bond : bond 0.00115 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.245 Fit side-chains REVERT: A 64 LEU cc_start: 0.8137 (tm) cc_final: 0.7855 (tt) REVERT: A 74 MET cc_start: 0.3605 (tpt) cc_final: 0.1237 (tmt) REVERT: A 173 ASP cc_start: 0.7913 (t0) cc_final: 0.7601 (m-30) REVERT: A 267 LYS cc_start: 0.8097 (mttt) cc_final: 0.7614 (mppt) REVERT: A 315 SER cc_start: 0.8400 (t) cc_final: 0.8118 (m) REVERT: A 331 PHE cc_start: 0.7693 (m-80) cc_final: 0.7405 (m-80) REVERT: A 339 PHE cc_start: 0.8401 (m-10) cc_final: 0.8155 (m-10) REVERT: A 562 GLU cc_start: 0.7466 (tt0) cc_final: 0.7104 (tt0) REVERT: A 620 LYS cc_start: 0.8117 (mttt) cc_final: 0.7270 (ttpt) REVERT: A 944 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7142 (tmm) REVERT: A 955 PHE cc_start: 0.8540 (t80) cc_final: 0.8081 (t80) REVERT: A 1026 MET cc_start: 0.7404 (ppp) cc_final: 0.6512 (ttt) REVERT: A 1164 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7860 (ttt-90) REVERT: A 1219 GLU cc_start: 0.7089 (mp0) cc_final: 0.6613 (mp0) REVERT: A 1246 LYS cc_start: 0.6772 (mtpt) cc_final: 0.6232 (mmtt) outliers start: 25 outliers final: 17 residues processed: 126 average time/residue: 0.4915 time to fit residues: 66.6028 Evaluate side-chains 135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1164 ARG Chi-restraints excluded: chain A residue 1233 ILE Chi-restraints excluded: chain A residue 1238 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 114 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 111 optimal weight: 0.0050 chunk 61 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A 605 GLN ** A1050 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 = 0.3902 r_free = 0.3902 target = 0.164205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122120 restraints weight = 11036.743| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.20 r_work: 0.3311 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9507 Z= 0.124 Angle : 0.536 9.680 12880 Z= 0.284 Chirality : 0.042 0.369 1478 Planarity : 0.003 0.042 1618 Dihedral : 8.292 81.350 1510 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.07 % Allowed : 22.21 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.24), residues: 1177 helix: 1.63 (0.18), residues: 795 sheet: 0.74 (0.67), residues: 63 loop : -0.66 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 282 TYR 0.024 0.001 TYR A 958 PHE 0.017 0.001 PHE A 196 TRP 0.014 0.001 TRP A 208 HIS 0.002 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9506) covalent geometry : angle 0.53551 (12880) hydrogen bonds : bond 0.04637 ( 622) hydrogen bonds : angle 4.20059 ( 1824) Misc. bond : bond 0.00099 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.315 Fit side-chains REVERT: A 48 LEU cc_start: 0.6996 (mp) cc_final: 0.6578 (tt) REVERT: A 64 LEU cc_start: 0.8105 (tm) cc_final: 0.7837 (tt) REVERT: A 74 MET cc_start: 0.3593 (tpt) cc_final: 0.1214 (tmt) REVERT: A 267 LYS cc_start: 0.8044 (mttt) cc_final: 0.7592 (mppt) REVERT: A 282 ARG cc_start: 0.7393 (mtm110) cc_final: 0.7173 (ttm-80) REVERT: A 315 SER cc_start: 0.8444 (t) cc_final: 0.8153 (m) REVERT: A 331 PHE cc_start: 0.7711 (m-80) cc_final: 0.7399 (m-80) REVERT: A 339 PHE cc_start: 0.8352 (m-10) cc_final: 0.8090 (m-10) REVERT: A 444 ASP cc_start: 0.7734 (m-30) cc_final: 0.6938 (t0) REVERT: A 562 GLU cc_start: 0.7442 (tt0) cc_final: 0.7096 (tt0) REVERT: A 620 LYS cc_start: 0.8132 (mttt) cc_final: 0.7266 (ttpt) REVERT: A 944 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7078 (tmm) REVERT: A 955 PHE cc_start: 0.8538 (t80) cc_final: 0.8083 (t80) REVERT: A 1026 MET cc_start: 0.7467 (ppp) cc_final: 0.6570 (ttt) REVERT: A 1219 GLU cc_start: 0.7121 (mp0) cc_final: 0.6639 (mp0) REVERT: A 1246 LYS cc_start: 0.6863 (mtpt) cc_final: 0.6356 (mmtt) outliers start: 20 outliers final: 17 residues processed: 134 average time/residue: 0.4687 time to fit residues: 68.0253 Evaluate side-chains 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1238 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 13 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.163665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.120877 restraints weight = 10948.937| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.27 r_work: 0.3326 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9507 Z= 0.130 Angle : 0.543 9.231 12880 Z= 0.287 Chirality : 0.042 0.370 1478 Planarity : 0.003 0.043 1618 Dihedral : 8.219 81.965 1510 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.07 % Allowed : 22.52 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.24), residues: 1177 helix: 1.66 (0.18), residues: 792 sheet: 0.73 (0.68), residues: 63 loop : -0.71 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 282 TYR 0.023 0.001 TYR A 958 PHE 0.018 0.001 PHE A 196 TRP 0.013 0.001 TRP A 208 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9506) covalent geometry : angle 0.54296 (12880) hydrogen bonds : bond 0.04653 ( 622) hydrogen bonds : angle 4.19095 ( 1824) Misc. bond : bond 0.00088 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3414.15 seconds wall clock time: 58 minutes 48.73 seconds (3528.73 seconds total)