Starting phenix.real_space_refine on Wed Feb 14 15:29:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wdk_32438/02_2024/7wdk_32438_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wdk_32438/02_2024/7wdk_32438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wdk_32438/02_2024/7wdk_32438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wdk_32438/02_2024/7wdk_32438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wdk_32438/02_2024/7wdk_32438_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wdk_32438/02_2024/7wdk_32438_neut.pdb" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 5992 2.51 5 N 1678 2.21 5 O 1758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 639": "OE1" <-> "OE2" Residue "A GLU 760": "OE1" <-> "OE2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A GLU 1021": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 304": "OE1" <-> "OE2" Residue "B GLU 358": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9461 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6635 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 48, 'TRANS': 818} Chain breaks: 1 Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 15, 'ARG:plan': 8, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2826 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 19, 'TRANS': 328} Time building chain proxies: 5.43, per 1000 atoms: 0.57 Number of scatterers: 9461 At special positions: 0 Unit cell: (112.224, 93.52, 84.836, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1758 8.00 N 1678 7.00 C 5992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 29 " - pdb=" SG CYS B 222 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 1.9 seconds 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2248 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 12 sheets defined 34.9% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 56 through 71 removed outlier: 3.705A pdb=" N TYR A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 105 Processing helix chain 'A' and resid 128 through 137 removed outlier: 3.775A pdb=" N ASN A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.847A pdb=" N ALA A 163 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.594A pdb=" N LEU A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 429 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 475 through 496 removed outlier: 3.518A pdb=" N ASP A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 521 Processing helix chain 'A' and resid 575 through 590 Processing helix chain 'A' and resid 607 through 619 Processing helix chain 'A' and resid 647 through 655 Processing helix chain 'A' and resid 660 through 668 removed outlier: 3.691A pdb=" N ARG A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A 667 " --> pdb=" O PHE A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 676 Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 694 through 712 removed outlier: 3.872A pdb=" N LYS A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 746 Processing helix chain 'A' and resid 765 through 780 Processing helix chain 'A' and resid 785 through 799 Processing helix chain 'A' and resid 804 through 812 removed outlier: 4.078A pdb=" N ARG A 809 " --> pdb=" O PRO A 805 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 874 through 879 Processing helix chain 'A' and resid 910 through 924 Processing helix chain 'A' and resid 937 through 941 Processing helix chain 'A' and resid 942 through 946 removed outlier: 4.134A pdb=" N SER A 945 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 971 removed outlier: 4.003A pdb=" N TRP A 953 " --> pdb=" O ALA A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 992 removed outlier: 3.557A pdb=" N LYS A 991 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 removed outlier: 5.373A pdb=" N TRP B 52 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 126 removed outlier: 3.694A pdb=" N SER B 97 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 148 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 355 through 368 removed outlier: 3.871A pdb=" N VAL B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Proline residue: B 361 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54 removed outlier: 6.320A pdb=" N ILE A 75 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N MET A 113 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE A 77 " --> pdb=" O MET A 113 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 110 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 167 removed outlier: 3.935A pdb=" N LEU A 886 " --> pdb=" O HIS A 167 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL A 890 " --> pdb=" O ALA A 866 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 866 " --> pdb=" O VAL A 890 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 624 " --> pdb=" O ILE A 860 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE A 623 " --> pdb=" O TYR A 752 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N VAL A 754 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 625 " --> pdb=" O VAL A 754 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL A 751 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N LEU A 835 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 753 " --> pdb=" O LEU A 835 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N LEU A 837 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 846 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 605 through 606 removed outlier: 4.118A pdb=" N SER A 573 " --> pdb=" O GLU A 885 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A 885 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL A 890 " --> pdb=" O ALA A 866 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 866 " --> pdb=" O VAL A 890 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 624 " --> pdb=" O ILE A 860 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE A 623 " --> pdb=" O TYR A 752 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N VAL A 754 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 625 " --> pdb=" O VAL A 754 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL A 751 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N LEU A 835 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 753 " --> pdb=" O LEU A 835 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N LEU A 837 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 465 through 466 Processing sheet with id=AA5, first strand: chain 'A' and resid 896 through 898 Processing sheet with id=AA6, first strand: chain 'A' and resid 1005 through 1007 removed outlier: 3.550A pdb=" N GLN A1018 " --> pdb=" O ALA A1006 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AA8, first strand: chain 'B' and resid 41 through 43 removed outlier: 3.701A pdb=" N ARG B 243 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 83 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR B 186 " --> pdb=" O TYR B 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 41 through 43 removed outlier: 3.701A pdb=" N ARG B 243 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE B 244 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 250 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 341 " --> pdb=" O TRP B 321 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N TRP B 321 " --> pdb=" O THR B 341 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 320 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 290 " --> pdb=" O GLY B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 155 through 157 removed outlier: 4.340A pdb=" N ILE B 166 " --> pdb=" O HIS B 157 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 167 " --> pdb=" O PHE B 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 207 through 208 Processing sheet with id=AB3, first strand: chain 'B' and resid 294 through 296 389 hydrogen bonds defined for protein. 1056 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: 3.16 Time building geometry restraints manager: 3.84 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: 1590 1.31 - 1.44: 2632 1.44 - 1.56: 5410 1.56 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 9690 Sorted by residual: bond pdb=" C SER A1033 " pdb=" O SER A1033 " ideal model delta sigma weight residual 1.234 1.183 0.052 1.19e-02 7.06e+03 1.88e+01 bond pdb=" N SER A1033 " pdb=" CA SER A1033 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.58e+00 bond pdb=" N THR A 986 " pdb=" CA THR A 986 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.04e-02 9.25e+03 8.51e+00 bond pdb=" N MET B 33 " pdb=" CA MET B 33 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.48e+00 bond pdb=" N LEU A 985 " pdb=" CA LEU A 985 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.49e+00 ... (remaining 9685 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.38: 329 106.38 - 113.32: 5087 113.32 - 120.26: 3499 120.26 - 127.20: 4115 127.20 - 134.14: 134 Bond angle restraints: 13164 Sorted by residual: angle pdb=" C SER A1033 " pdb=" N ASN A1034 " pdb=" CA ASN A1034 " ideal model delta sigma weight residual 120.28 126.65 -6.37 1.34e+00 5.57e-01 2.26e+01 angle pdb=" CA SER A1033 " pdb=" C SER A1033 " pdb=" O SER A1033 " ideal model delta sigma weight residual 121.19 116.11 5.08 1.10e+00 8.26e-01 2.13e+01 angle pdb=" N PRO A 989 " pdb=" CA PRO A 989 " pdb=" C PRO A 989 " ideal model delta sigma weight residual 110.70 115.68 -4.98 1.22e+00 6.72e-01 1.67e+01 angle pdb=" C TYR A 125 " pdb=" N ASP A 126 " pdb=" CA ASP A 126 " ideal model delta sigma weight residual 122.41 130.01 -7.60 2.09e+00 2.29e-01 1.32e+01 angle pdb=" C PRO A 989 " pdb=" N PRO A 990 " pdb=" CA PRO A 990 " ideal model delta sigma weight residual 119.28 123.06 -3.78 1.10e+00 8.26e-01 1.18e+01 ... (remaining 13159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 5161 17.81 - 35.63: 518 35.63 - 53.44: 83 53.44 - 71.26: 18 71.26 - 89.07: 7 Dihedral angle restraints: 5787 sinusoidal: 2290 harmonic: 3497 Sorted by residual: dihedral pdb=" CA LEU A 720 " pdb=" C LEU A 720 " pdb=" N GLY A 721 " pdb=" CA GLY A 721 " ideal model delta harmonic sigma weight residual -180.00 -160.66 -19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA MET A 218 " pdb=" C MET A 218 " pdb=" N ALA A 219 " pdb=" CA ALA A 219 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA GLU A 626 " pdb=" C GLU A 626 " pdb=" N ASN A 627 " pdb=" CA ASN A 627 " ideal model delta harmonic sigma weight residual -180.00 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 5784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1016 0.044 - 0.089: 294 0.089 - 0.133: 92 0.133 - 0.177: 11 0.177 - 0.222: 3 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CA LYS A 991 " pdb=" N LYS A 991 " pdb=" C LYS A 991 " pdb=" CB LYS A 991 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA GLN A 984 " pdb=" N GLN A 984 " pdb=" C GLN A 984 " pdb=" CB GLN A 984 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA CYS B 222 " pdb=" N CYS B 222 " pdb=" C CYS B 222 " pdb=" CB CYS B 222 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 1413 not shown) Planarity restraints: 1736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 953 " -0.035 2.00e-02 2.50e+03 2.68e-02 1.80e+01 pdb=" CG TRP A 953 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP A 953 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 953 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 953 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 953 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 953 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 953 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 953 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 953 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 924 " 0.009 2.00e-02 2.50e+03 1.75e-02 5.39e+00 pdb=" CG PHE A 924 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 924 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 924 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 924 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 924 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 924 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 261 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.76e+00 pdb=" N PRO B 262 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 262 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 262 " -0.030 5.00e-02 4.00e+02 ... (remaining 1733 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 875 2.74 - 3.28: 9385 3.28 - 3.82: 15747 3.82 - 4.36: 18602 4.36 - 4.90: 31671 Nonbonded interactions: 76280 Sorted by model distance: nonbonded pdb=" OH TYR B 185 " pdb=" O TYR B 225 " model vdw 2.201 2.440 nonbonded pdb=" NE2 GLN A 984 " pdb=" OE2 GLU A1021 " model vdw 2.202 2.520 nonbonded pdb=" OG1 THR B 63 " pdb=" OD2 ASP B 347 " model vdw 2.226 2.440 nonbonded pdb=" O THR A 717 " pdb=" ND2 ASN A1069 " model vdw 2.234 2.520 nonbonded pdb=" NH1 ARG A 654 " pdb=" O ASP A1065 " model vdw 2.260 2.520 ... (remaining 76275 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: 1.230 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: 5.650 Check model and map are aligned: 0.160 Set scattering table: 0.080 Process input model: 28.810 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9690 Z= 0.273 Angle : 0.737 7.598 13164 Z= 0.411 Chirality : 0.047 0.222 1416 Planarity : 0.005 0.055 1736 Dihedral : 14.655 89.069 3536 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.51 % Allowed : 0.41 % Favored : 99.08 % 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: -1.03 (0.23), residues: 1209 helix: 1.22 (0.26), residues: 365 sheet: -1.19 (0.37), residues: 187 loop : -1.70 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP A 953 HIS 0.008 0.002 HIS A 469 PHE 0.038 0.002 PHE A 924 TYR 0.014 0.002 TYR A 84 ARG 0.009 0.001 ARG A1008 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 1.102 Fit side-chains REVERT: A 227 MET cc_start: 0.4136 (tpp) cc_final: 0.3858 (ptm) REVERT: A 982 GLN cc_start: 0.6134 (tp40) cc_final: 0.5643 (pt0) outliers start: 5 outliers final: 4 residues processed: 95 average time/residue: 0.2797 time to fit residues: 35.7025 Evaluate side-chains 83 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 145 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 83 ASN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9690 Z= 0.256 Angle : 0.646 7.788 13164 Z= 0.327 Chirality : 0.045 0.146 1416 Planarity : 0.005 0.048 1736 Dihedral : 5.411 58.195 1336 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.34 % Allowed : 6.99 % Favored : 91.68 % 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: -1.06 (0.24), residues: 1209 helix: 1.11 (0.26), residues: 371 sheet: -1.29 (0.36), residues: 190 loop : -1.65 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 953 HIS 0.008 0.002 HIS A 469 PHE 0.028 0.002 PHE A 924 TYR 0.013 0.002 TYR A 84 ARG 0.005 0.000 ARG A1008 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: A 153 GLN cc_start: 0.5609 (pp30) cc_final: 0.5294 (pm20) REVERT: A 982 GLN cc_start: 0.6424 (tp40) cc_final: 0.5808 (pt0) REVERT: A 993 PHE cc_start: 0.5649 (OUTLIER) cc_final: 0.4956 (m-10) outliers start: 13 outliers final: 12 residues processed: 96 average time/residue: 0.2783 time to fit residues: 36.5292 Evaluate side-chains 97 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1045 ASN Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 296 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 90 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 108 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9690 Z= 0.140 Angle : 0.533 6.995 13164 Z= 0.268 Chirality : 0.041 0.137 1416 Planarity : 0.004 0.045 1736 Dihedral : 4.661 54.812 1332 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.44 % Allowed : 10.38 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.24), residues: 1209 helix: 1.50 (0.27), residues: 371 sheet: -1.34 (0.35), residues: 203 loop : -1.56 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 953 HIS 0.006 0.001 HIS A 469 PHE 0.020 0.001 PHE A 924 TYR 0.011 0.001 TYR B 83 ARG 0.003 0.000 ARG A1008 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 427 MET cc_start: 0.4126 (tpp) cc_final: 0.3693 (tpp) REVERT: A 982 GLN cc_start: 0.6328 (tp40) cc_final: 0.5730 (pt0) REVERT: A 993 PHE cc_start: 0.5557 (OUTLIER) cc_final: 0.4865 (m-80) REVERT: A 1023 MET cc_start: 0.8280 (mmm) cc_final: 0.7473 (mmt) outliers start: 14 outliers final: 9 residues processed: 101 average time/residue: 0.2589 time to fit residues: 35.5658 Evaluate side-chains 93 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 889 MET Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 247 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 0.1980 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9690 Z= 0.173 Angle : 0.549 7.862 13164 Z= 0.276 Chirality : 0.042 0.139 1416 Planarity : 0.004 0.046 1736 Dihedral : 4.434 55.693 1329 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.64 % Allowed : 13.98 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.24), residues: 1209 helix: 1.56 (0.27), residues: 371 sheet: -1.19 (0.37), residues: 187 loop : -1.53 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 953 HIS 0.006 0.001 HIS A 469 PHE 0.032 0.001 PHE A 924 TYR 0.009 0.001 TYR A 853 ARG 0.005 0.000 ARG A1008 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 1.080 Fit side-chains REVERT: A 427 MET cc_start: 0.4105 (tpp) cc_final: 0.3693 (tpp) REVERT: A 993 PHE cc_start: 0.5603 (OUTLIER) cc_final: 0.4884 (m-10) outliers start: 16 outliers final: 12 residues processed: 96 average time/residue: 0.2615 time to fit residues: 34.2312 Evaluate side-chains 94 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 889 MET Chi-restraints excluded: chain A residue 976 GLN Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1045 ASN Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 296 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 47 optimal weight: 0.0570 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9690 Z= 0.216 Angle : 0.587 8.742 13164 Z= 0.297 Chirality : 0.043 0.142 1416 Planarity : 0.004 0.047 1736 Dihedral : 4.633 56.615 1329 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.16 % Allowed : 15.31 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.24), residues: 1209 helix: 1.41 (0.27), residues: 371 sheet: -1.21 (0.38), residues: 185 loop : -1.56 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 953 HIS 0.006 0.002 HIS A 469 PHE 0.041 0.002 PHE A 924 TYR 0.010 0.001 TYR A 853 ARG 0.006 0.000 ARG A1008 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 1.034 Fit side-chains REVERT: A 153 GLN cc_start: 0.5699 (pp30) cc_final: 0.5291 (pm20) REVERT: A 427 MET cc_start: 0.4221 (tpp) cc_final: 0.3747 (tpp) REVERT: A 463 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.7064 (tmm) REVERT: A 993 PHE cc_start: 0.5654 (OUTLIER) cc_final: 0.4949 (m-10) outliers start: 21 outliers final: 15 residues processed: 102 average time/residue: 0.2663 time to fit residues: 36.8857 Evaluate side-chains 96 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 889 MET Chi-restraints excluded: chain A residue 976 GLN Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1045 ASN Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 296 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.0870 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 116 optimal weight: 0.0870 chunk 96 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 overall best weight: 0.9138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9690 Z= 0.160 Angle : 0.549 8.939 13164 Z= 0.276 Chirality : 0.042 0.137 1416 Planarity : 0.004 0.047 1736 Dihedral : 4.452 54.434 1329 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.36 % Allowed : 15.93 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.24), residues: 1209 helix: 1.60 (0.27), residues: 371 sheet: -1.18 (0.37), residues: 194 loop : -1.49 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 953 HIS 0.004 0.001 HIS A 469 PHE 0.037 0.001 PHE A 924 TYR 0.009 0.001 TYR A 853 ARG 0.007 0.000 ARG A1008 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 1.027 Fit side-chains REVERT: A 153 GLN cc_start: 0.5680 (pp30) cc_final: 0.5259 (pm20) REVERT: A 427 MET cc_start: 0.4183 (tpp) cc_final: 0.3764 (tpp) REVERT: A 463 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7040 (tmm) REVERT: A 993 PHE cc_start: 0.5600 (OUTLIER) cc_final: 0.4870 (m-10) outliers start: 23 outliers final: 17 residues processed: 103 average time/residue: 0.2555 time to fit residues: 36.1298 Evaluate side-chains 104 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 889 MET Chi-restraints excluded: chain A residue 924 PHE Chi-restraints excluded: chain A residue 976 GLN Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1045 ASN Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 360 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9690 Z= 0.291 Angle : 0.648 9.631 13164 Z= 0.327 Chirality : 0.045 0.162 1416 Planarity : 0.005 0.049 1736 Dihedral : 4.905 58.140 1329 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.36 % Allowed : 17.78 % Favored : 79.86 % 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: -0.87 (0.24), residues: 1209 helix: 1.25 (0.27), residues: 371 sheet: -0.96 (0.39), residues: 174 loop : -1.60 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 953 HIS 0.007 0.002 HIS A 913 PHE 0.044 0.002 PHE A 924 TYR 0.011 0.002 TYR A 752 ARG 0.008 0.001 ARG A1008 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 1.110 Fit side-chains REVERT: A 153 GLN cc_start: 0.5707 (pp30) cc_final: 0.5235 (pm20) REVERT: A 427 MET cc_start: 0.4304 (tpp) cc_final: 0.3824 (tpp) REVERT: A 993 PHE cc_start: 0.5819 (OUTLIER) cc_final: 0.5200 (m-10) REVERT: A 1069 ASN cc_start: 0.5166 (m110) cc_final: 0.4926 (t0) outliers start: 23 outliers final: 20 residues processed: 100 average time/residue: 0.2909 time to fit residues: 39.5540 Evaluate side-chains 102 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 889 MET Chi-restraints excluded: chain A residue 976 GLN Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1045 ASN Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 296 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 34 optimal weight: 0.4980 chunk 22 optimal weight: 20.0000 chunk 73 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9690 Z= 0.154 Angle : 0.560 10.195 13164 Z= 0.278 Chirality : 0.042 0.136 1416 Planarity : 0.004 0.049 1736 Dihedral : 4.483 53.647 1329 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.57 % Allowed : 17.57 % Favored : 79.86 % 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: -0.70 (0.24), residues: 1209 helix: 1.55 (0.27), residues: 371 sheet: -1.10 (0.38), residues: 188 loop : -1.53 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 953 HIS 0.005 0.001 HIS A 223 PHE 0.036 0.001 PHE A 924 TYR 0.009 0.001 TYR A 853 ARG 0.008 0.000 ARG A1008 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 81 time to evaluate : 1.028 Fit side-chains REVERT: A 153 GLN cc_start: 0.5772 (pp30) cc_final: 0.5269 (pm20) REVERT: A 427 MET cc_start: 0.4200 (tpp) cc_final: 0.3738 (tpp) REVERT: A 463 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7017 (tmm) REVERT: A 993 PHE cc_start: 0.5633 (OUTLIER) cc_final: 0.4954 (m-10) outliers start: 25 outliers final: 20 residues processed: 98 average time/residue: 0.2584 time to fit residues: 34.3889 Evaluate side-chains 102 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 889 MET Chi-restraints excluded: chain A residue 924 PHE Chi-restraints excluded: chain A residue 976 GLN Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1045 ASN Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 360 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.0570 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9690 Z= 0.234 Angle : 0.616 11.015 13164 Z= 0.307 Chirality : 0.044 0.146 1416 Planarity : 0.005 0.050 1736 Dihedral : 4.732 56.632 1329 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.67 % Allowed : 17.78 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.24), residues: 1209 helix: 1.37 (0.27), residues: 371 sheet: -1.05 (0.39), residues: 177 loop : -1.57 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 953 HIS 0.006 0.002 HIS B 165 PHE 0.043 0.002 PHE A 924 TYR 0.011 0.001 TYR A 853 ARG 0.008 0.000 ARG A1008 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 1.049 Fit side-chains REVERT: A 153 GLN cc_start: 0.5674 (pp30) cc_final: 0.5181 (pm20) REVERT: A 427 MET cc_start: 0.4261 (tpp) cc_final: 0.3774 (tpp) REVERT: A 463 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7012 (tmm) REVERT: A 993 PHE cc_start: 0.5739 (OUTLIER) cc_final: 0.5093 (m-10) REVERT: A 1069 ASN cc_start: 0.5128 (m110) cc_final: 0.4912 (t0) outliers start: 26 outliers final: 20 residues processed: 100 average time/residue: 0.2792 time to fit residues: 37.2684 Evaluate side-chains 103 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 889 MET Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 924 PHE Chi-restraints excluded: chain A residue 976 GLN Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1045 ASN Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 110 optimal weight: 0.0030 chunk 95 optimal weight: 7.9990 chunk 9 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9690 Z= 0.147 Angle : 0.554 10.056 13164 Z= 0.275 Chirality : 0.042 0.150 1416 Planarity : 0.004 0.050 1736 Dihedral : 4.378 52.360 1329 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.16 % Allowed : 18.09 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.24), residues: 1209 helix: 1.63 (0.27), residues: 371 sheet: -1.18 (0.37), residues: 193 loop : -1.51 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 953 HIS 0.006 0.001 HIS A 223 PHE 0.036 0.001 PHE A 924 TYR 0.010 0.001 TYR B 83 ARG 0.010 0.000 ARG A1008 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 1.025 Fit side-chains REVERT: A 153 GLN cc_start: 0.5753 (pp30) cc_final: 0.5278 (pm20) REVERT: A 427 MET cc_start: 0.4104 (tpp) cc_final: 0.3658 (tpp) REVERT: A 463 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.6985 (tmm) REVERT: A 993 PHE cc_start: 0.5591 (OUTLIER) cc_final: 0.4901 (m-10) outliers start: 21 outliers final: 18 residues processed: 98 average time/residue: 0.2686 time to fit residues: 35.6518 Evaluate side-chains 102 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 889 MET Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 924 PHE Chi-restraints excluded: chain A residue 976 GLN Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1045 ASN Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 256 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 HIS ** 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 = 0.4781 r_free = 0.4781 target = 0.270922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.248076 restraints weight = 9719.717| |-----------------------------------------------------------------------------| r_work (start): 0.4593 rms_B_bonded: 1.09 r_work: 0.4423 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9690 Z= 0.234 Angle : 0.610 9.299 13164 Z= 0.306 Chirality : 0.044 0.144 1416 Planarity : 0.005 0.050 1736 Dihedral : 4.691 56.183 1329 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.26 % Allowed : 18.09 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.24), residues: 1209 helix: 1.43 (0.27), residues: 371 sheet: -1.18 (0.39), residues: 182 loop : -1.50 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 953 HIS 0.007 0.002 HIS B 165 PHE 0.042 0.002 PHE A 924 TYR 0.011 0.001 TYR A 752 ARG 0.009 0.000 ARG A1008 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2110.11 seconds wall clock time: 39 minutes 40.48 seconds (2380.48 seconds total)