Starting phenix.real_space_refine on Sun Jul 27 17:42:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zk8_14758/07_2025/7zk8_14758.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zk8_14758/07_2025/7zk8_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_14758/07_2025/7zk8_14758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zk8_14758/07_2025/7zk8_14758.map" model { file = "/net/cci-nas-00/data/ceres_data/7zk8_14758/07_2025/7zk8_14758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zk8_14758/07_2025/7zk8_14758.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.02, per 1000 atoms: 0.75 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: 2.62 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.36 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: 3.70 Time building geometry restraints manager: 3.08 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: 3.990 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: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.720 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.520 ------------------------------------------------------------------------------- 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 : 9.21 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 (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: 0.60 (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 TRP 0.007 0.001 TRP A 158 HIS 0.007 0.001 HIS A1003 PHE 0.017 0.002 PHE A 934 TYR 0.033 0.002 TYR A 114 ARG 0.007 0.001 ARG A 589 Details of bonding type rmsd hydrogen bonds : bond 0.16236 ( 622) hydrogen bonds : angle 6.22230 ( 1824) covalent geometry : bond 0.00885 ( 9506) covalent geometry : angle 0.96860 (12880) 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 : 1.017 Fit side-chains REVERT: A 315 SER cc_start: 0.8825 (t) cc_final: 0.8473 (m) REVERT: A 607 ASN cc_start: 0.7450 (t0) cc_final: 0.7206 (m110) REVERT: A 620 LYS cc_start: 0.8156 (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: 0.8018 (tp) REVERT: A 1244 ASN cc_start: 0.6847 (p0) cc_final: 0.6101 (t160) outliers start: 1 outliers final: 1 residues processed: 193 average time/residue: 1.1443 time to fit residues: 237.6995 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 : 1.024 ------------------------------------------------------------------------------- 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 99 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 0.0870 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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** A1191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.165395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122931 restraints weight = 10684.350| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.24 r_work: 0.3335 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1844 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= 0.138 Angle : 0.574 9.031 12880 Z= 0.301 Chirality : 0.042 0.230 1478 Planarity : 0.004 0.046 1618 Dihedral : 9.480 87.628 1512 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.79 % Allowed : 12.71 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.24), residues: 1177 helix: 1.47 (0.18), residues: 789 sheet: 0.60 (0.63), residues: 66 loop : -0.86 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 208 HIS 0.004 0.001 HIS A1003 PHE 0.017 0.001 PHE A 508 TYR 0.013 0.001 TYR A 312 ARG 0.003 0.000 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.05289 ( 622) hydrogen bonds : angle 4.56953 ( 1824) covalent geometry : bond 0.00277 ( 9506) covalent geometry : angle 0.57412 (12880) Misc. bond : bond 0.00121 ( 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 : 0.944 Fit side-chains REVERT: A 48 LEU cc_start: 0.6932 (mp) cc_final: 0.6620 (tt) REVERT: A 64 LEU cc_start: 0.8151 (tm) cc_final: 0.7911 (tt) REVERT: A 315 SER cc_start: 0.8481 (t) cc_final: 0.8196 (m) REVERT: A 331 PHE cc_start: 0.7726 (m-80) cc_final: 0.7328 (m-80) REVERT: A 452 GLN cc_start: 0.7489 (tt0) cc_final: 0.7212 (tt0) REVERT: A 562 GLU cc_start: 0.7458 (tt0) cc_final: 0.7029 (tt0) REVERT: A 607 ASN cc_start: 0.6366 (t0) cc_final: 0.5895 (m110) REVERT: A 620 LYS cc_start: 0.8118 (mttt) cc_final: 0.7274 (ttpt) REVERT: A 944 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7152 (tmm) REVERT: A 955 PHE cc_start: 0.8549 (t80) cc_final: 0.8136 (t80) REVERT: A 960 VAL cc_start: 0.7510 (t) cc_final: 0.7267 (m) REVERT: A 965 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7371 (tmt) REVERT: A 1026 MET cc_start: 0.7454 (ppp) cc_final: 0.6420 (ttt) REVERT: A 1244 ASN cc_start: 0.6591 (p0) cc_final: 0.5816 (t160) outliers start: 27 outliers final: 8 residues processed: 149 average time/residue: 1.2777 time to fit residues: 205.7215 Evaluate side-chains 121 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 77 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.162500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119553 restraints weight = 10946.675| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.25 r_work: 0.3291 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2181 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= 0.152 Angle : 0.562 10.407 12880 Z= 0.294 Chirality : 0.042 0.248 1478 Planarity : 0.003 0.037 1618 Dihedral : 8.688 78.791 1510 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.20 % Allowed : 14.36 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.24), residues: 1177 helix: 1.49 (0.18), residues: 792 sheet: 0.54 (0.65), residues: 61 loop : -0.75 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 208 HIS 0.004 0.001 HIS A 60 PHE 0.015 0.001 PHE A 508 TYR 0.013 0.001 TYR A 110 ARG 0.005 0.000 ARG A 901 Details of bonding type rmsd hydrogen bonds : bond 0.05209 ( 622) hydrogen bonds : angle 4.44026 ( 1824) covalent geometry : bond 0.00328 ( 9506) covalent geometry : angle 0.56172 (12880) Misc. bond : bond 0.00105 ( 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 157 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.940 Fit side-chains REVERT: A 48 LEU cc_start: 0.6990 (mp) cc_final: 0.6608 (tt) REVERT: A 64 LEU cc_start: 0.8145 (tm) cc_final: 0.7852 (tt) REVERT: A 267 LYS cc_start: 0.8052 (mttt) cc_final: 0.7594 (mppt) REVERT: A 315 SER cc_start: 0.8520 (t) cc_final: 0.8232 (m) REVERT: A 331 PHE cc_start: 0.7774 (m-80) cc_final: 0.7422 (m-80) REVERT: A 452 GLN cc_start: 0.7606 (tt0) cc_final: 0.7355 (tt0) REVERT: A 562 GLU cc_start: 0.7474 (tt0) cc_final: 0.7011 (tt0) REVERT: A 607 ASN cc_start: 0.6092 (t0) cc_final: 0.5696 (m110) REVERT: A 620 LYS cc_start: 0.8165 (mttt) cc_final: 0.7301 (ttpt) REVERT: A 944 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7196 (tmm) REVERT: A 955 PHE cc_start: 0.8559 (t80) cc_final: 0.8138 (t80) REVERT: A 965 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7355 (tmt) REVERT: A 1026 MET cc_start: 0.7465 (ppp) cc_final: 0.6478 (ttt) REVERT: A 1244 ASN cc_start: 0.6675 (p0) cc_final: 0.5822 (t160) REVERT: A 1246 LYS cc_start: 0.6874 (mtpt) cc_final: 0.6214 (mmtt) outliers start: 31 outliers final: 13 residues processed: 140 average time/residue: 1.0732 time to fit residues: 162.7139 Evaluate side-chains 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 295 MET 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 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 46 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.162643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119554 restraints weight = 10909.981| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.24 r_work: 0.3303 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9507 Z= 0.135 Angle : 0.523 6.756 12880 Z= 0.277 Chirality : 0.041 0.261 1478 Planarity : 0.003 0.040 1618 Dihedral : 8.416 75.832 1510 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.41 % Allowed : 16.22 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1177 helix: 1.53 (0.18), residues: 794 sheet: 0.59 (0.65), residues: 61 loop : -0.80 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 208 HIS 0.003 0.001 HIS A 60 PHE 0.014 0.001 PHE A 508 TYR 0.014 0.001 TYR A 306 ARG 0.004 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.04929 ( 622) hydrogen bonds : angle 4.34137 ( 1824) covalent geometry : bond 0.00290 ( 9506) covalent geometry : angle 0.52293 (12880) Misc. bond : bond 0.00083 ( 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 153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 1.308 Fit side-chains REVERT: A 48 LEU cc_start: 0.6926 (mp) cc_final: 0.6536 (tt) REVERT: A 64 LEU cc_start: 0.8171 (tm) cc_final: 0.7864 (tt) REVERT: A 267 LYS cc_start: 0.8058 (mttt) cc_final: 0.7602 (mppt) REVERT: A 315 SER cc_start: 0.8540 (t) cc_final: 0.8247 (m) REVERT: A 331 PHE cc_start: 0.7739 (m-80) cc_final: 0.7411 (m-80) REVERT: A 452 GLN cc_start: 0.7649 (tt0) cc_final: 0.7407 (tt0) REVERT: A 562 GLU cc_start: 0.7450 (tt0) cc_final: 0.7002 (tt0) REVERT: A 607 ASN cc_start: 0.5920 (t0) cc_final: 0.5689 (m110) REVERT: A 620 LYS cc_start: 0.8167 (mttt) cc_final: 0.7318 (ttpt) REVERT: A 944 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7181 (tmm) REVERT: A 955 PHE cc_start: 0.8542 (t80) cc_final: 0.8116 (t80) REVERT: A 965 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7350 (tmt) REVERT: A 1026 MET cc_start: 0.7415 (ppp) cc_final: 0.6464 (ttt) REVERT: A 1244 ASN cc_start: 0.6747 (p0) cc_final: 0.5778 (t160) REVERT: A 1246 LYS cc_start: 0.6853 (mtpt) cc_final: 0.6247 (mmtt) REVERT: A 1260 LYS cc_start: 0.6812 (mttm) cc_final: 0.6417 (mttp) outliers start: 33 outliers final: 12 residues processed: 139 average time/residue: 1.2806 time to fit residues: 193.1667 Evaluate side-chains 128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 725 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 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 55 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 44 optimal weight: 0.0670 chunk 117 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.1924 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.161036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.118032 restraints weight = 10907.376| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.24 r_work: 0.3262 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9507 Z= 0.147 Angle : 0.532 6.794 12880 Z= 0.284 Chirality : 0.041 0.275 1478 Planarity : 0.003 0.040 1618 Dihedral : 8.352 78.246 1510 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.79 % Allowed : 17.87 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.24), residues: 1177 helix: 1.55 (0.18), residues: 792 sheet: 0.77 (0.65), residues: 62 loop : -0.84 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 208 HIS 0.004 0.001 HIS A 60 PHE 0.015 0.001 PHE A 508 TYR 0.015 0.001 TYR A 306 ARG 0.004 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.05009 ( 622) hydrogen bonds : angle 4.32588 ( 1824) covalent geometry : bond 0.00328 ( 9506) covalent geometry : angle 0.53230 (12880) Misc. bond : bond 0.00141 ( 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 150 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 1.017 Fit side-chains REVERT: A 48 LEU cc_start: 0.6941 (mp) cc_final: 0.6506 (tt) REVERT: A 64 LEU cc_start: 0.8169 (tm) cc_final: 0.7866 (tt) REVERT: A 173 ASP cc_start: 0.7923 (t0) cc_final: 0.7616 (m-30) REVERT: A 267 LYS cc_start: 0.8041 (mttt) cc_final: 0.7575 (mppt) REVERT: A 315 SER cc_start: 0.8505 (t) cc_final: 0.8212 (m) REVERT: A 331 PHE cc_start: 0.7741 (m-80) cc_final: 0.7434 (m-80) REVERT: A 452 GLN cc_start: 0.7634 (tt0) cc_final: 0.7403 (tt0) REVERT: A 562 GLU cc_start: 0.7407 (tt0) cc_final: 0.6976 (tt0) REVERT: A 620 LYS cc_start: 0.8122 (mttt) cc_final: 0.7273 (ttpt) REVERT: A 944 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7165 (tmm) REVERT: A 955 PHE cc_start: 0.8539 (t80) cc_final: 0.8104 (t80) REVERT: A 965 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.7218 (tmt) REVERT: A 1026 MET cc_start: 0.7391 (ppp) cc_final: 0.6490 (ttt) REVERT: A 1164 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7860 (ttp-110) REVERT: A 1244 ASN cc_start: 0.6689 (p0) cc_final: 0.5802 (t160) REVERT: A 1246 LYS cc_start: 0.6746 (mtpt) cc_final: 0.6162 (mmtt) outliers start: 27 outliers final: 12 residues processed: 138 average time/residue: 1.1757 time to fit residues: 176.4068 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 : 1.007 ------------------------------------------------------------------------------- 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 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 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 6 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.159860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.116743 restraints weight = 10855.444| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.26 r_work: 0.3205 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9507 Z= 0.179 Angle : 0.564 7.399 12880 Z= 0.299 Chirality : 0.043 0.296 1478 Planarity : 0.003 0.041 1618 Dihedral : 8.501 81.188 1510 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.31 % Allowed : 19.11 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.24), residues: 1177 helix: 1.48 (0.18), residues: 795 sheet: 0.80 (0.66), residues: 62 loop : -0.83 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 208 HIS 0.005 0.001 HIS A 60 PHE 0.019 0.001 PHE A 508 TYR 0.015 0.001 TYR A 306 ARG 0.004 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.05333 ( 622) hydrogen bonds : angle 4.39840 ( 1824) covalent geometry : bond 0.00414 ( 9506) covalent geometry : angle 0.56432 (12880) Misc. bond : bond 0.00148 ( 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 154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.399 Fit side-chains REVERT: A 64 LEU cc_start: 0.8170 (tm) cc_final: 0.7864 (tt) REVERT: A 173 ASP cc_start: 0.7880 (t0) cc_final: 0.7557 (m-30) REVERT: A 267 LYS cc_start: 0.8018 (mttt) cc_final: 0.7524 (mppt) REVERT: A 331 PHE cc_start: 0.7667 (m-80) cc_final: 0.7366 (m-80) REVERT: A 452 GLN cc_start: 0.7608 (tt0) cc_final: 0.7359 (tt0) REVERT: A 562 GLU cc_start: 0.7386 (tt0) cc_final: 0.7024 (tt0) REVERT: A 620 LYS cc_start: 0.8089 (mttt) cc_final: 0.7249 (ttpt) REVERT: A 944 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7111 (tmm) REVERT: A 955 PHE cc_start: 0.8525 (t80) cc_final: 0.8072 (t80) REVERT: A 960 VAL cc_start: 0.7509 (OUTLIER) cc_final: 0.7302 (m) REVERT: A 1026 MET cc_start: 0.7335 (ppp) cc_final: 0.6455 (ttt) REVERT: A 1164 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7845 (ttp-110) REVERT: A 1244 ASN cc_start: 0.6702 (p0) cc_final: 0.5893 (t160) REVERT: A 1246 LYS cc_start: 0.6632 (mtpt) cc_final: 0.6072 (mmtt) outliers start: 32 outliers final: 15 residues processed: 138 average time/residue: 1.8772 time to fit residues: 282.4572 Evaluate side-chains 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 585 LEU Chi-restraints excluded: chain A residue 725 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 54 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 87 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.163191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.120293 restraints weight = 10956.021| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.28 r_work: 0.3219 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2842 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= 0.130 Angle : 0.526 7.613 12880 Z= 0.279 Chirality : 0.042 0.324 1478 Planarity : 0.003 0.041 1618 Dihedral : 8.365 80.803 1510 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.69 % Allowed : 20.45 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.24), residues: 1177 helix: 1.58 (0.18), residues: 795 sheet: 0.80 (0.69), residues: 61 loop : -0.81 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 208 HIS 0.003 0.001 HIS A 60 PHE 0.015 0.001 PHE A 724 TYR 0.019 0.001 TYR A 949 ARG 0.005 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.04842 ( 622) hydrogen bonds : angle 4.28681 ( 1824) covalent geometry : bond 0.00276 ( 9506) covalent geometry : angle 0.52621 (12880) Misc. bond : bond 0.00126 ( 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 149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.046 Fit side-chains REVERT: A 48 LEU cc_start: 0.6970 (mp) cc_final: 0.6528 (tt) REVERT: A 64 LEU cc_start: 0.8116 (tm) cc_final: 0.7830 (tt) REVERT: A 267 LYS cc_start: 0.8034 (mttt) cc_final: 0.7562 (mppt) REVERT: A 282 ARG cc_start: 0.7352 (mtm110) cc_final: 0.7124 (ttm-80) REVERT: A 315 SER cc_start: 0.8386 (t) cc_final: 0.8122 (m) REVERT: A 331 PHE cc_start: 0.7691 (m-80) cc_final: 0.7388 (m-80) REVERT: A 452 GLN cc_start: 0.7670 (tt0) cc_final: 0.7408 (tt0) REVERT: A 562 GLU cc_start: 0.7414 (tt0) cc_final: 0.6989 (tt0) REVERT: A 605 GLN cc_start: 0.7674 (tt0) cc_final: 0.7408 (mt0) REVERT: A 620 LYS cc_start: 0.8115 (mttt) cc_final: 0.7266 (ttpt) REVERT: A 944 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7091 (tmm) REVERT: A 955 PHE cc_start: 0.8565 (t80) cc_final: 0.8098 (t80) REVERT: A 1026 MET cc_start: 0.7383 (ppp) cc_final: 0.6510 (ttt) REVERT: A 1050 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7691 (mp10) REVERT: A 1058 LYS cc_start: 0.7649 (tptm) cc_final: 0.7427 (tptm) REVERT: A 1164 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7926 (ttp-110) REVERT: A 1244 ASN cc_start: 0.6786 (p0) cc_final: 0.5782 (t160) REVERT: A 1246 LYS cc_start: 0.6703 (mtpt) cc_final: 0.6160 (mmtt) outliers start: 26 outliers final: 16 residues processed: 137 average time/residue: 1.0173 time to fit residues: 151.9124 Evaluate side-chains 139 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 542 VAL Chi-restraints excluded: chain A residue 580 VAL 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 1050 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 14 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 chunk 55 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.163761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.121399 restraints weight = 11052.336| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.22 r_work: 0.3231 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9507 Z= 0.126 Angle : 0.525 7.765 12880 Z= 0.279 Chirality : 0.042 0.337 1478 Planarity : 0.003 0.042 1618 Dihedral : 8.309 81.332 1510 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.17 % Allowed : 21.80 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1177 helix: 1.61 (0.18), residues: 795 sheet: 0.72 (0.68), residues: 61 loop : -0.78 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 208 HIS 0.005 0.001 HIS A 608 PHE 0.016 0.001 PHE A 724 TYR 0.015 0.001 TYR A 306 ARG 0.004 0.000 ARG A 589 Details of bonding type rmsd hydrogen bonds : bond 0.04729 ( 622) hydrogen bonds : angle 4.25038 ( 1824) covalent geometry : bond 0.00264 ( 9506) covalent geometry : angle 0.52467 (12880) Misc. bond : bond 0.00114 ( 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 141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.934 Fit side-chains REVERT: A 64 LEU cc_start: 0.8131 (tm) cc_final: 0.7846 (tt) REVERT: A 267 LYS cc_start: 0.8062 (mttt) cc_final: 0.7607 (mppt) REVERT: A 282 ARG cc_start: 0.7377 (mtm110) cc_final: 0.7162 (ttm-80) REVERT: A 315 SER cc_start: 0.8424 (t) cc_final: 0.8149 (m) REVERT: A 331 PHE cc_start: 0.7737 (m-80) cc_final: 0.7447 (m-80) REVERT: A 452 GLN cc_start: 0.7700 (tt0) cc_final: 0.7485 (tt0) REVERT: A 562 GLU cc_start: 0.7445 (tt0) cc_final: 0.7024 (tt0) REVERT: A 605 GLN cc_start: 0.7662 (tt0) cc_final: 0.7444 (mt0) REVERT: A 620 LYS cc_start: 0.8141 (mttt) cc_final: 0.7283 (ttpt) REVERT: A 944 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7098 (tmm) REVERT: A 955 PHE cc_start: 0.8575 (t80) cc_final: 0.8084 (t80) REVERT: A 1026 MET cc_start: 0.7388 (ppp) cc_final: 0.6510 (ttt) REVERT: A 1058 LYS cc_start: 0.7641 (tptm) cc_final: 0.7378 (tptm) REVERT: A 1244 ASN cc_start: 0.6846 (p0) cc_final: 0.6002 (t160) REVERT: A 1246 LYS cc_start: 0.6722 (mtpt) cc_final: 0.6200 (mmtt) outliers start: 21 outliers final: 15 residues processed: 131 average time/residue: 0.9569 time to fit residues: 136.6720 Evaluate side-chains 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 542 VAL Chi-restraints excluded: chain A residue 580 VAL 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 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 1097 ILE Chi-restraints excluded: chain A residue 1135 VAL 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 9 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.161190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117947 restraints weight = 10996.871| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.27 r_work: 0.3287 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9507 Z= 0.158 Angle : 0.548 8.332 12880 Z= 0.292 Chirality : 0.043 0.350 1478 Planarity : 0.003 0.042 1618 Dihedral : 8.389 80.551 1510 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.58 % Allowed : 21.38 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.24), residues: 1177 helix: 1.51 (0.18), residues: 794 sheet: 0.58 (0.65), residues: 64 loop : -0.78 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 208 HIS 0.005 0.001 HIS A 60 PHE 0.018 0.001 PHE A 196 TYR 0.016 0.001 TYR A 506 ARG 0.003 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.05079 ( 622) hydrogen bonds : angle 4.33004 ( 1824) covalent geometry : bond 0.00361 ( 9506) covalent geometry : angle 0.54833 (12880) Misc. bond : bond 0.00119 ( 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 147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.954 Fit side-chains REVERT: A 64 LEU cc_start: 0.8205 (tm) cc_final: 0.7914 (tt) REVERT: A 74 MET cc_start: 0.3527 (tpt) cc_final: 0.1113 (tmt) REVERT: A 173 ASP cc_start: 0.7966 (t0) cc_final: 0.7641 (m-30) REVERT: A 267 LYS cc_start: 0.8178 (mttt) cc_final: 0.7726 (mppt) REVERT: A 315 SER cc_start: 0.8458 (t) cc_final: 0.8181 (m) REVERT: A 331 PHE cc_start: 0.7767 (m-80) cc_final: 0.7462 (m-80) REVERT: A 452 GLN cc_start: 0.7815 (tt0) cc_final: 0.7588 (tt0) REVERT: A 562 GLU cc_start: 0.7562 (tt0) cc_final: 0.7207 (tt0) REVERT: A 620 LYS cc_start: 0.8171 (mttt) cc_final: 0.7323 (ttpt) REVERT: A 944 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7171 (tmm) REVERT: A 955 PHE cc_start: 0.8622 (t80) cc_final: 0.8148 (t80) REVERT: A 1026 MET cc_start: 0.7404 (ppp) cc_final: 0.6533 (ttt) REVERT: A 1244 ASN cc_start: 0.6927 (p0) cc_final: 0.6138 (t160) REVERT: A 1246 LYS cc_start: 0.6832 (mtpt) cc_final: 0.6330 (mmtt) outliers start: 25 outliers final: 15 residues processed: 134 average time/residue: 1.0680 time to fit residues: 155.1292 Evaluate side-chains 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 725 SER Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 791 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 1011 THR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1135 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 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 = 0.161888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118888 restraints weight = 11198.712| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.28 r_work: 0.3306 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9507 Z= 0.144 Angle : 0.546 9.374 12880 Z= 0.291 Chirality : 0.043 0.358 1478 Planarity : 0.003 0.042 1618 Dihedral : 8.362 81.152 1510 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.96 % Allowed : 21.90 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1177 helix: 1.56 (0.18), residues: 795 sheet: 0.64 (0.65), residues: 64 loop : -0.78 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 208 HIS 0.004 0.001 HIS A 60 PHE 0.017 0.001 PHE A 508 TYR 0.016 0.001 TYR A 306 ARG 0.006 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.04944 ( 622) hydrogen bonds : angle 4.28993 ( 1824) covalent geometry : bond 0.00322 ( 9506) covalent geometry : angle 0.54588 (12880) Misc. bond : bond 0.00106 ( 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 136 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 1.037 Fit side-chains REVERT: A 64 LEU cc_start: 0.8138 (tm) cc_final: 0.7847 (tt) REVERT: A 74 MET cc_start: 0.3565 (tpt) cc_final: 0.1072 (tmt) REVERT: A 173 ASP cc_start: 0.7913 (t0) cc_final: 0.7593 (m-30) REVERT: A 267 LYS cc_start: 0.8060 (mttt) cc_final: 0.7594 (mppt) REVERT: A 282 ARG cc_start: 0.7395 (mtm110) cc_final: 0.7158 (ttm-80) REVERT: A 315 SER cc_start: 0.8416 (t) cc_final: 0.8129 (m) REVERT: A 331 PHE cc_start: 0.7696 (m-80) cc_final: 0.7399 (m-80) REVERT: A 452 GLN cc_start: 0.7756 (tt0) cc_final: 0.7548 (tt0) REVERT: A 562 GLU cc_start: 0.7478 (tt0) cc_final: 0.7123 (tt0) REVERT: A 620 LYS cc_start: 0.8145 (mttt) cc_final: 0.7282 (ttpt) REVERT: A 944 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7089 (tmm) REVERT: A 955 PHE cc_start: 0.8577 (t80) cc_final: 0.8135 (t80) REVERT: A 1026 MET cc_start: 0.7416 (ppp) cc_final: 0.6538 (ttt) REVERT: A 1244 ASN cc_start: 0.6815 (p0) cc_final: 0.6042 (t160) REVERT: A 1246 LYS cc_start: 0.6696 (mtpt) cc_final: 0.6190 (mmtt) outliers start: 19 outliers final: 17 residues processed: 127 average time/residue: 1.0495 time to fit residues: 145.0144 Evaluate side-chains 135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 791 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 1011 THR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1135 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 102 optimal weight: 0.0470 chunk 38 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 66 optimal weight: 0.0370 chunk 92 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.166034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.123148 restraints weight = 11067.330| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.30 r_work: 0.3364 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 9507 Z= 0.115 Angle : 0.516 10.085 12880 Z= 0.275 Chirality : 0.041 0.367 1478 Planarity : 0.003 0.043 1618 Dihedral : 8.163 83.652 1510 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.34 % Allowed : 22.42 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.24), residues: 1177 helix: 1.76 (0.18), residues: 792 sheet: 0.66 (0.67), residues: 63 loop : -0.83 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 208 HIS 0.002 0.000 HIS A 60 PHE 0.019 0.001 PHE A 196 TYR 0.014 0.001 TYR A 306 ARG 0.006 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.04346 ( 622) hydrogen bonds : angle 4.10273 ( 1824) covalent geometry : bond 0.00234 ( 9506) covalent geometry : angle 0.51606 (12880) Misc. bond : bond 0.00082 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7883.48 seconds wall clock time: 139 minutes 32.92 seconds (8372.92 seconds total)