Starting phenix.real_space_refine on Mon May 4 22:18:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lco_62988/05_2026/9lco_62988.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lco_62988/05_2026/9lco_62988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lco_62988/05_2026/9lco_62988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lco_62988/05_2026/9lco_62988.map" model { file = "/net/cci-nas-00/data/ceres_data/9lco_62988/05_2026/9lco_62988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lco_62988/05_2026/9lco_62988.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 1 5.49 5 S 35 5.16 5 C 7420 2.51 5 N 2106 2.21 5 O 2165 1.98 5 H 11502 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 124 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23229 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 22230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1418, 22230 Classifications: {'peptide': 1418} Link IDs: {'CIS': 2, 'PTRANS': 88, 'TRANS': 1327} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 999 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 3, 'TRANS': 57} Time building chain proxies: 3.65, per 1000 atoms: 0.16 Number of scatterers: 23229 At special positions: 0 Unit cell: (90.64, 107.12, 183.752, 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 35 16.00 P 1 15.00 O 2165 8.00 N 2106 7.00 C 7420 6.00 H 11502 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 684.5 milliseconds 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2730 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 12 sheets defined 43.5% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 2707 through 2721 Processing helix chain 'A' and resid 2737 through 2751 Processing helix chain 'A' and resid 2756 through 2763 Processing helix chain 'A' and resid 2765 through 2773 removed outlier: 3.890A pdb=" N ALA A2771 " --> pdb=" O GLN A2767 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A2772 " --> pdb=" O SER A2768 " (cutoff:3.500A) Processing helix chain 'A' and resid 2793 through 2802 Processing helix chain 'A' and resid 2823 through 2838 Processing helix chain 'A' and resid 2839 through 2843 Processing helix chain 'A' and resid 2872 through 2874 No H-bonds generated for 'chain 'A' and resid 2872 through 2874' Processing helix chain 'A' and resid 2875 through 2886 removed outlier: 4.683A pdb=" N LEU A2879 " --> pdb=" O GLU A2875 " (cutoff:3.500A) Processing helix chain 'A' and resid 2916 through 2918 No H-bonds generated for 'chain 'A' and resid 2916 through 2918' Processing helix chain 'A' and resid 2919 through 2939 removed outlier: 3.540A pdb=" N ARG A2924 " --> pdb=" O GLY A2920 " (cutoff:3.500A) Processing helix chain 'A' and resid 2951 through 2963 Processing helix chain 'A' and resid 2965 through 2970 Processing helix chain 'A' and resid 2971 through 2980 removed outlier: 3.687A pdb=" N ARG A2978 " --> pdb=" O TRP A2974 " (cutoff:3.500A) Processing helix chain 'A' and resid 2996 through 2998 No H-bonds generated for 'chain 'A' and resid 2996 through 2998' Processing helix chain 'A' and resid 3008 through 3018 Processing helix chain 'A' and resid 3026 through 3044 Processing helix chain 'A' and resid 3086 through 3100 Processing helix chain 'A' and resid 3101 through 3104 removed outlier: 3.670A pdb=" N LYS A3104 " --> pdb=" O VAL A3101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3101 through 3104' Processing helix chain 'A' and resid 3105 through 3114 removed outlier: 4.255A pdb=" N GLY A3109 " --> pdb=" O GLY A3105 " (cutoff:3.500A) Processing helix chain 'A' and resid 3116 through 3125 Processing helix chain 'A' and resid 3192 through 3215 Processing helix chain 'A' and resid 3223 through 3227 Processing helix chain 'A' and resid 3233 through 3238 Processing helix chain 'A' and resid 3254 through 3267 removed outlier: 3.664A pdb=" N GLY A3259 " --> pdb=" O PRO A3255 " (cutoff:3.500A) Processing helix chain 'A' and resid 3286 through 3299 Processing helix chain 'A' and resid 3302 through 3304 No H-bonds generated for 'chain 'A' and resid 3302 through 3304' Processing helix chain 'A' and resid 3339 through 3356 removed outlier: 4.687A pdb=" N GLU A3343 " --> pdb=" O ASP A3339 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A3354 " --> pdb=" O LYS A3350 " (cutoff:3.500A) Processing helix chain 'A' and resid 3389 through 3410 removed outlier: 3.714A pdb=" N GLY A3394 " --> pdb=" O ALA A3390 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A3395 " --> pdb=" O TRP A3391 " (cutoff:3.500A) Processing helix chain 'A' and resid 3420 through 3429 removed outlier: 3.995A pdb=" N TYR A3424 " --> pdb=" O ARG A3420 " (cutoff:3.500A) Processing helix chain 'A' and resid 3432 through 3445 removed outlier: 4.302A pdb=" N SER A3436 " --> pdb=" O ASP A3432 " (cutoff:3.500A) Processing helix chain 'A' and resid 3462 through 3466 Processing helix chain 'A' and resid 3480 through 3490 Processing helix chain 'A' and resid 3497 through 3514 Processing helix chain 'A' and resid 3532 through 3538 removed outlier: 3.592A pdb=" N GLN A3536 " --> pdb=" O PRO A3533 " (cutoff:3.500A) Processing helix chain 'A' and resid 3560 through 3577 removed outlier: 3.605A pdb=" N GLU A3577 " --> pdb=" O LEU A3573 " (cutoff:3.500A) Processing helix chain 'A' and resid 3582 through 3590 removed outlier: 3.925A pdb=" N GLU A3588 " --> pdb=" O VAL A3584 " (cutoff:3.500A) Processing helix chain 'A' and resid 3611 through 3621 Processing helix chain 'A' and resid 3658 through 3679 Processing helix chain 'A' and resid 3683 through 3687 Processing helix chain 'A' and resid 3691 through 3699 Processing helix chain 'A' and resid 3699 through 3704 Processing helix chain 'A' and resid 3713 through 3726 removed outlier: 4.404A pdb=" N ARG A3717 " --> pdb=" O GLN A3713 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN A3722 " --> pdb=" O LEU A3718 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL A3723 " --> pdb=" O PHE A3719 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA A3724 " --> pdb=" O GLU A3720 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A3725 " --> pdb=" O ALA A3721 " (cutoff:3.500A) Processing helix chain 'A' and resid 3741 through 3758 removed outlier: 3.656A pdb=" N ARG A3746 " --> pdb=" O ALA A3742 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG A3747 " --> pdb=" O GLU A3743 " (cutoff:3.500A) Processing helix chain 'A' and resid 3773 through 3786 removed outlier: 4.348A pdb=" N LEU A3777 " --> pdb=" O GLY A3773 " (cutoff:3.500A) Processing helix chain 'A' and resid 3798 through 3809 removed outlier: 3.571A pdb=" N LEU A3802 " --> pdb=" O PRO A3798 " (cutoff:3.500A) Processing helix chain 'A' and resid 3820 through 3831 Processing helix chain 'A' and resid 3842 through 3847 Processing helix chain 'A' and resid 3884 through 3898 removed outlier: 4.690A pdb=" N LYS A3894 " --> pdb=" O ASN A3890 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL A3895 " --> pdb=" O GLN A3891 " (cutoff:3.500A) Proline residue: A3896 - end of helix Processing helix chain 'A' and resid 3916 through 3927 removed outlier: 4.698A pdb=" N LEU A3922 " --> pdb=" O VAL A3918 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A3924 " --> pdb=" O GLN A3920 " (cutoff:3.500A) Proline residue: A3925 - end of helix Processing helix chain 'A' and resid 3935 through 3940 Processing helix chain 'A' and resid 3943 through 3948 Processing helix chain 'A' and resid 3949 through 3953 removed outlier: 3.607A pdb=" N GLN A3952 " --> pdb=" O VAL A3949 " (cutoff:3.500A) Processing helix chain 'A' and resid 3963 through 3968 removed outlier: 3.854A pdb=" N MET A3967 " --> pdb=" O LEU A3963 " (cutoff:3.500A) Processing helix chain 'A' and resid 3989 through 4000 Processing helix chain 'A' and resid 4011 through 4015 Processing helix chain 'A' and resid 4024 through 4030 removed outlier: 4.034A pdb=" N SER A4030 " --> pdb=" O SER A4027 " (cutoff:3.500A) Processing helix chain 'A' and resid 4080 through 4087 removed outlier: 3.560A pdb=" N GLN A4086 " --> pdb=" O LEU A4082 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 62 through 67 Processing sheet with id=AA1, first strand: chain 'A' and resid 2865 through 2869 removed outlier: 6.416A pdb=" N TRP A2866 " --> pdb=" O LEU A2899 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ASP A2901 " --> pdb=" O TRP A2866 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL A2868 " --> pdb=" O ASP A2901 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N GLN A2907 " --> pdb=" O PRO A2818 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2844 through 2847 Processing sheet with id=AA3, first strand: chain 'A' and resid 3000 through 3006 removed outlier: 6.720A pdb=" N THR A3132 " --> pdb=" O VAL A3171 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY A3173 " --> pdb=" O THR A3132 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASN A3134 " --> pdb=" O GLY A3173 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N VAL A3175 " --> pdb=" O ASN A3134 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N LEU A3136 " --> pdb=" O VAL A3175 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE A3131 " --> pdb=" O LEU A3049 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU A3053 " --> pdb=" O PHE A3133 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR A3135 " --> pdb=" O GLU A3053 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3247 through 3252 removed outlier: 6.863A pdb=" N ILE A3320 " --> pdb=" O GLU A3248 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL A3250 " --> pdb=" O GLN A3318 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLN A3318 " --> pdb=" O VAL A3250 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 3328 through 3331 removed outlier: 6.218A pdb=" N ARG A3376 " --> pdb=" O LEU A3372 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN A3276 " --> pdb=" O GLY A3628 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY A3628 " --> pdb=" O GLN A3276 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ARG A3278 " --> pdb=" O ASP A3626 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 3472 through 3478 removed outlier: 6.258A pdb=" N LEU A3602 " --> pdb=" O VAL A3638 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N CYS A3640 " --> pdb=" O LEU A3602 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A3604 " --> pdb=" O CYS A3640 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N SER A3601 " --> pdb=" O LEU A3520 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE A3605 " --> pdb=" O THR A3524 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ALA A3526 " --> pdb=" O PHE A3605 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 3738 through 3740 removed outlier: 7.055A pdb=" N TRP A3739 " --> pdb=" O ALA A3731 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA A3731 " --> pdb=" O VAL A3931 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ILE A3933 " --> pdb=" O ALA A3731 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER A3733 " --> pdb=" O ILE A3933 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A3958 " --> pdb=" O ALA A3907 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU A3957 " --> pdb=" O LEU A3982 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A4006 " --> pdb=" O MET A3981 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 3766 through 3769 Processing sheet with id=AA9, first strand: chain 'A' and resid 3864 through 3870 removed outlier: 4.301A pdb=" N GLY A3879 " --> pdb=" O VAL A4078 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY A4076 " --> pdb=" O MET A3881 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 4042 through 4047 removed outlier: 4.672A pdb=" N ASP A4105 " --> pdb=" O LEU A4066 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N VAL A4068 " --> pdb=" O THR A4103 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR A4103 " --> pdb=" O VAL A4068 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N GLY A4070 " --> pdb=" O TYR A4101 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYR A4101 " --> pdb=" O GLY A4070 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 4042 through 4047 removed outlier: 4.672A pdb=" N ASP A4105 " --> pdb=" O LEU A4066 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N VAL A4068 " --> pdb=" O THR A4103 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR A4103 " --> pdb=" O VAL A4068 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N GLY A4070 " --> pdb=" O TYR A4101 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYR A4101 " --> pdb=" O GLY A4070 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 22 through 26 removed outlier: 4.887A pdb=" N LYS B 40 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL B 16 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA B 38 " --> pdb=" O VAL B 16 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1479 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: 6.16 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 11487 1.13 - 1.31: 2262 1.31 - 1.49: 4682 1.49 - 1.67: 5027 1.67 - 1.85: 54 Bond restraints: 23512 Sorted by residual: bond pdb=" NR 4HH A2738 " pdb=" HR 4HH A2738 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.81e+01 bond pdb=" NN 4HH A2738 " pdb=" HN 4HH A2738 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.81e+01 bond pdb=" CH2 TRP B 35 " pdb=" HH2 TRP B 35 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N SER A3307 " pdb=" H SER A3307 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CE1 TYR A3869 " pdb=" HE1 TYR A3869 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 23507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 38833 3.44 - 6.88: 3339 6.88 - 10.33: 255 10.33 - 13.77: 14 13.77 - 17.21: 4 Bond angle restraints: 42445 Sorted by residual: angle pdb=" O LEU A3331 " pdb=" C LEU A3331 " pdb=" N ASP A3332 " ideal model delta sigma weight residual 123.24 115.54 7.70 1.23e+00 6.61e-01 3.92e+01 angle pdb=" CA LEU A3331 " pdb=" C LEU A3331 " pdb=" N ASP A3332 " ideal model delta sigma weight residual 115.58 124.82 -9.24 1.48e+00 4.57e-01 3.89e+01 angle pdb=" CA ASP A3172 " pdb=" CB ASP A3172 " pdb=" CG ASP A3172 " ideal model delta sigma weight residual 112.60 118.70 -6.10 1.00e+00 1.00e+00 3.73e+01 angle pdb=" CB 4HH A2738 " pdb=" OG 4HH A2738 " pdb=" P 4HH A2738 " ideal model delta sigma weight residual 117.42 134.63 -17.21 3.00e+00 1.11e-01 3.29e+01 angle pdb=" C SER A4037 " pdb=" N PRO A4038 " pdb=" CA PRO A4038 " ideal model delta sigma weight residual 119.84 126.61 -6.77 1.25e+00 6.40e-01 2.93e+01 ... (remaining 42440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.81: 10618 29.81 - 59.62: 421 59.62 - 89.43: 41 89.43 - 119.24: 1 119.24 - 149.05: 2 Dihedral angle restraints: 11083 sinusoidal: 6104 harmonic: 4979 Sorted by residual: dihedral pdb=" CA ASN A2811 " pdb=" C ASN A2811 " pdb=" N GLN A2812 " pdb=" CA GLN A2812 " ideal model delta harmonic sigma weight residual 180.00 151.09 28.91 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA GLY A3515 " pdb=" C GLY A3515 " pdb=" N GLU A3516 " pdb=" CA GLU A3516 " ideal model delta harmonic sigma weight residual -180.00 -151.76 -28.24 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA ARG A2774 " pdb=" C ARG A2774 " pdb=" N HIS A2775 " pdb=" CA HIS A2775 " ideal model delta harmonic sigma weight residual 180.00 151.93 28.07 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 11080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1046 0.078 - 0.157: 569 0.157 - 0.235: 119 0.235 - 0.314: 18 0.314 - 0.392: 6 Chirality restraints: 1758 Sorted by residual: chirality pdb=" CA ASP A4016 " pdb=" N ASP A4016 " pdb=" C ASP A4016 " pdb=" CB ASP A4016 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA VAL A2707 " pdb=" N VAL A2707 " pdb=" C VAL A2707 " pdb=" CB VAL A2707 " both_signs ideal model delta sigma weight residual False 2.44 2.08 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA ASP A3474 " pdb=" N ASP A3474 " pdb=" C ASP A3474 " pdb=" CB ASP A3474 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 1755 not shown) Planarity restraints: 3566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CL3 4HH A2738 " 0.061 2.00e-02 2.50e+03 2.09e-01 6.53e+02 pdb=" CM 4HH A2738 " -0.274 2.00e-02 2.50e+03 pdb=" CO 4HH A2738 " -0.302 2.00e-02 2.50e+03 pdb=" NN 4HH A2738 " 0.163 2.00e-02 2.50e+03 pdb=" ON 4HH A2738 " 0.136 2.00e-02 2.50e+03 pdb=" HN 4HH A2738 " 0.215 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A3486 " -0.725 9.50e-02 1.11e+02 2.59e-01 2.52e+02 pdb=" NE ARG A3486 " -0.094 2.00e-02 2.50e+03 pdb=" CZ ARG A3486 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A3486 " -0.064 2.00e-02 2.50e+03 pdb=" NH2 ARG A3486 " 0.065 2.00e-02 2.50e+03 pdb="HH11 ARG A3486 " 0.198 2.00e-02 2.50e+03 pdb="HH12 ARG A3486 " -0.089 2.00e-02 2.50e+03 pdb="HH21 ARG A3486 " 0.096 2.00e-02 2.50e+03 pdb="HH22 ARG A3486 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A3439 " 0.154 2.00e-02 2.50e+03 6.71e-02 1.80e+02 pdb=" CG TRP A3439 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A3439 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A3439 " -0.042 2.00e-02 2.50e+03 pdb=" NE1 TRP A3439 " -0.064 2.00e-02 2.50e+03 pdb=" CE2 TRP A3439 " -0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP A3439 " -0.068 2.00e-02 2.50e+03 pdb=" CZ2 TRP A3439 " 0.021 2.00e-02 2.50e+03 pdb=" CZ3 TRP A3439 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A3439 " 0.041 2.00e-02 2.50e+03 pdb=" HD1 TRP A3439 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TRP A3439 " -0.100 2.00e-02 2.50e+03 pdb=" HE3 TRP A3439 " -0.108 2.00e-02 2.50e+03 pdb=" HZ2 TRP A3439 " 0.053 2.00e-02 2.50e+03 pdb=" HZ3 TRP A3439 " 0.004 2.00e-02 2.50e+03 pdb=" HH2 TRP A3439 " 0.087 2.00e-02 2.50e+03 ... (remaining 3563 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1786 2.20 - 2.80: 42571 2.80 - 3.40: 65895 3.40 - 4.00: 88258 4.00 - 4.60: 128246 Nonbonded interactions: 326756 Sorted by model distance: nonbonded pdb=" HG SER A2872 " pdb=" OD1 ASP A2874 " model vdw 1.599 2.450 nonbonded pdb=" OD2 ASP A3794 " pdb=" HG SER A3911 " model vdw 1.605 2.450 nonbonded pdb=" OE2 GLU A3096 " pdb=" HG SER A3225 " model vdw 1.606 2.450 nonbonded pdb=" OD1 ASP A4024 " pdb=" HG SER A4027 " model vdw 1.609 2.450 nonbonded pdb=" HH TYR A4009 " pdb=" OD2 ASP A4105 " model vdw 1.617 2.450 ... (remaining 326751 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 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: 0.120 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.290 Find NCS groups from input model: 0.070 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 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 : 0.012 0.101 12010 Z= 0.758 Angle : 1.789 17.210 16341 Z= 1.206 Chirality : 0.093 0.392 1758 Planarity : 0.017 0.215 2180 Dihedral : 14.476 149.045 4476 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 0.17 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.37 % Favored : 94.36 % Rotamer: Outliers : 0.99 % Allowed : 4.28 % Favored : 94.74 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.20), residues: 1472 helix: -1.37 (0.18), residues: 561 sheet: -0.04 (0.32), residues: 239 loop : -0.88 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A3190 TYR 0.125 0.021 TYR A3421 PHE 0.098 0.013 PHE A3357 TRP 0.118 0.023 TRP A3506 HIS 0.012 0.004 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.01225 (12010) covalent geometry : angle 1.78865 (16341) hydrogen bonds : bond 0.17362 ( 511) hydrogen bonds : angle 7.07877 ( 1479) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3033 THR cc_start: 0.8767 (m) cc_final: 0.8544 (m) REVERT: A 3630 THR cc_start: 0.8122 (m) cc_final: 0.7634 (p) REVERT: A 4066 LEU cc_start: 0.9319 (tp) cc_final: 0.9046 (tt) REVERT: A 4067 CYS cc_start: 0.7050 (m) cc_final: 0.5103 (m) REVERT: B 58 MET cc_start: 0.3266 (mtm) cc_final: 0.2638 (mtp) outliers start: 12 outliers final: 5 residues processed: 148 average time/residue: 0.3089 time to fit residues: 62.1023 Evaluate side-chains 84 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3572 ASN Chi-restraints excluded: chain A residue 3723 VAL Chi-restraints excluded: chain A residue 3842 TRP Chi-restraints excluded: chain A residue 4014 CYS Chi-restraints excluded: chain B residue 55 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.089348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.051661 restraints weight = 138495.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.054387 restraints weight = 53113.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.056139 restraints weight = 32312.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.056974 restraints weight = 24534.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.057513 restraints weight = 21445.218| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12010 Z= 0.155 Angle : 0.664 9.747 16341 Z= 0.356 Chirality : 0.040 0.169 1758 Planarity : 0.005 0.053 2180 Dihedral : 9.100 129.776 1682 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.33 % Rotamer: Outliers : 0.41 % Allowed : 6.83 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.21), residues: 1472 helix: -0.06 (0.21), residues: 576 sheet: -0.14 (0.30), residues: 257 loop : -0.39 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A3528 TYR 0.017 0.002 TYR A3176 PHE 0.032 0.002 PHE A3143 TRP 0.012 0.001 TRP A3333 HIS 0.006 0.001 HIS A2763 Details of bonding type rmsd covalent geometry : bond 0.00330 (12010) covalent geometry : angle 0.66432 (16341) hydrogen bonds : bond 0.04827 ( 511) hydrogen bonds : angle 5.44879 ( 1479) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2765 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.9060 (t) REVERT: A 3630 THR cc_start: 0.8482 (m) cc_final: 0.8104 (p) REVERT: A 3684 LEU cc_start: 0.9046 (tp) cc_final: 0.8715 (tt) REVERT: B 22 TYR cc_start: 0.8700 (m-80) cc_final: 0.8471 (m-80) outliers start: 5 outliers final: 4 residues processed: 90 average time/residue: 0.2512 time to fit residues: 32.8400 Evaluate side-chains 73 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2765 THR Chi-restraints excluded: chain A residue 3008 ASP Chi-restraints excluded: chain A residue 3210 LEU Chi-restraints excluded: chain A residue 3592 LEU Chi-restraints excluded: chain A residue 4040 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 109 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3383 ASN A3891 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.089251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.052217 restraints weight = 140335.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.054999 restraints weight = 52577.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.056585 restraints weight = 31786.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.057420 restraints weight = 24067.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.057987 restraints weight = 21056.766| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12010 Z= 0.146 Angle : 0.582 8.865 16341 Z= 0.307 Chirality : 0.039 0.153 1758 Planarity : 0.005 0.054 2180 Dihedral : 8.302 121.920 1674 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.74 % Favored : 96.20 % Rotamer: Outliers : 1.07 % Allowed : 7.48 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.22), residues: 1472 helix: 0.46 (0.21), residues: 577 sheet: -0.19 (0.31), residues: 262 loop : -0.18 (0.27), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3629 TYR 0.035 0.002 TYR A3273 PHE 0.021 0.002 PHE A3357 TRP 0.010 0.001 TRP A3333 HIS 0.010 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00313 (12010) covalent geometry : angle 0.58181 (16341) hydrogen bonds : bond 0.03872 ( 511) hydrogen bonds : angle 4.92979 ( 1479) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2765 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8977 (t) REVERT: A 3921 PHE cc_start: 0.7133 (m-10) cc_final: 0.6858 (m-10) outliers start: 13 outliers final: 11 residues processed: 74 average time/residue: 0.2179 time to fit residues: 24.3568 Evaluate side-chains 72 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2765 THR Chi-restraints excluded: chain A residue 3008 ASP Chi-restraints excluded: chain A residue 3033 THR Chi-restraints excluded: chain A residue 3210 LEU Chi-restraints excluded: chain A residue 3509 THR Chi-restraints excluded: chain A residue 3592 LEU Chi-restraints excluded: chain A residue 3996 TRP Chi-restraints excluded: chain A residue 4007 ASN Chi-restraints excluded: chain A residue 4014 CYS Chi-restraints excluded: chain A residue 4040 ASP Chi-restraints excluded: chain A residue 4067 CYS Chi-restraints excluded: chain B residue 55 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 10 optimal weight: 0.6980 chunk 136 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3633 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.085518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.047960 restraints weight = 140417.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.050556 restraints weight = 54627.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.052169 restraints weight = 33906.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.052860 restraints weight = 26070.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.053295 restraints weight = 22439.163| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 12010 Z= 0.344 Angle : 0.696 8.425 16341 Z= 0.368 Chirality : 0.040 0.147 1758 Planarity : 0.005 0.046 2180 Dihedral : 8.815 121.980 1674 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.69 % Favored : 95.24 % Rotamer: Outliers : 1.40 % Allowed : 8.06 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.22), residues: 1472 helix: 0.00 (0.21), residues: 583 sheet: -0.60 (0.30), residues: 259 loop : -0.42 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2978 TYR 0.017 0.002 TYR A3421 PHE 0.025 0.002 PHE A3357 TRP 0.014 0.002 TRP A2974 HIS 0.009 0.002 HIS A2763 Details of bonding type rmsd covalent geometry : bond 0.00749 (12010) covalent geometry : angle 0.69578 (16341) hydrogen bonds : bond 0.04350 ( 511) hydrogen bonds : angle 5.42849 ( 1479) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3065 ASP cc_start: 0.8693 (t0) cc_final: 0.8284 (p0) REVERT: A 3217 ASP cc_start: 0.8620 (t0) cc_final: 0.8233 (p0) REVERT: A 3535 MET cc_start: 0.9047 (mmm) cc_final: 0.8757 (mmm) REVERT: A 3921 PHE cc_start: 0.7026 (m-10) cc_final: 0.6768 (m-10) REVERT: B 20 GLU cc_start: 0.9164 (mp0) cc_final: 0.8842 (mp0) outliers start: 17 outliers final: 12 residues processed: 77 average time/residue: 0.2229 time to fit residues: 26.3048 Evaluate side-chains 68 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2765 THR Chi-restraints excluded: chain A residue 3008 ASP Chi-restraints excluded: chain A residue 3033 THR Chi-restraints excluded: chain A residue 3172 ASP Chi-restraints excluded: chain A residue 3210 LEU Chi-restraints excluded: chain A residue 3509 THR Chi-restraints excluded: chain A residue 3996 TRP Chi-restraints excluded: chain A residue 4007 ASN Chi-restraints excluded: chain A residue 4014 CYS Chi-restraints excluded: chain A residue 4040 ASP Chi-restraints excluded: chain A residue 4067 CYS Chi-restraints excluded: chain B residue 59 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 0 optimal weight: 5.9990 chunk 131 optimal weight: 30.0000 chunk 60 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 108 optimal weight: 40.0000 chunk 118 optimal weight: 20.0000 chunk 35 optimal weight: 0.0870 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.087772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.050825 restraints weight = 139346.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.053209 restraints weight = 54268.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.054846 restraints weight = 33495.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.055620 restraints weight = 25676.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.056141 restraints weight = 22517.523| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12010 Z= 0.150 Angle : 0.546 8.043 16341 Z= 0.283 Chirality : 0.038 0.146 1758 Planarity : 0.004 0.039 2180 Dihedral : 8.376 127.534 1674 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 1.07 % Allowed : 9.21 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.23), residues: 1472 helix: 0.60 (0.22), residues: 575 sheet: -0.51 (0.31), residues: 263 loop : -0.21 (0.27), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2978 TYR 0.011 0.001 TYR A3176 PHE 0.016 0.001 PHE A3357 TRP 0.012 0.001 TRP A3506 HIS 0.007 0.001 HIS A2763 Details of bonding type rmsd covalent geometry : bond 0.00327 (12010) covalent geometry : angle 0.54576 (16341) hydrogen bonds : bond 0.03494 ( 511) hydrogen bonds : angle 4.87633 ( 1479) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3065 ASP cc_start: 0.8654 (t0) cc_final: 0.8334 (p0) REVERT: A 3217 ASP cc_start: 0.8409 (t0) cc_final: 0.8078 (p0) REVERT: A 3921 PHE cc_start: 0.7077 (m-10) cc_final: 0.6801 (m-10) outliers start: 13 outliers final: 7 residues processed: 68 average time/residue: 0.2372 time to fit residues: 24.6296 Evaluate side-chains 62 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3210 LEU Chi-restraints excluded: chain A residue 3509 THR Chi-restraints excluded: chain A residue 3996 TRP Chi-restraints excluded: chain A residue 4007 ASN Chi-restraints excluded: chain A residue 4014 CYS Chi-restraints excluded: chain A residue 4067 CYS Chi-restraints excluded: chain B residue 59 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 43 optimal weight: 0.1980 chunk 28 optimal weight: 0.0270 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.088878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.052222 restraints weight = 138906.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.054850 restraints weight = 52523.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.056441 restraints weight = 32069.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.057118 restraints weight = 24487.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.057729 restraints weight = 21761.923| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12010 Z= 0.091 Angle : 0.498 7.748 16341 Z= 0.254 Chirality : 0.038 0.183 1758 Planarity : 0.004 0.043 2180 Dihedral : 7.877 126.327 1674 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.33 % Rotamer: Outliers : 0.74 % Allowed : 9.62 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1472 helix: 1.12 (0.22), residues: 580 sheet: -0.32 (0.31), residues: 265 loop : -0.00 (0.28), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 64 TYR 0.011 0.001 TYR A3869 PHE 0.014 0.001 PHE A3357 TRP 0.012 0.001 TRP A3506 HIS 0.005 0.001 HIS A2763 Details of bonding type rmsd covalent geometry : bond 0.00203 (12010) covalent geometry : angle 0.49839 (16341) hydrogen bonds : bond 0.02986 ( 511) hydrogen bonds : angle 4.46588 ( 1479) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3217 ASP cc_start: 0.8334 (t0) cc_final: 0.8017 (p0) outliers start: 9 outliers final: 8 residues processed: 72 average time/residue: 0.2390 time to fit residues: 25.6802 Evaluate side-chains 65 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2733 GLU Chi-restraints excluded: chain A residue 2765 THR Chi-restraints excluded: chain A residue 3210 LEU Chi-restraints excluded: chain A residue 3509 THR Chi-restraints excluded: chain A residue 3592 LEU Chi-restraints excluded: chain A residue 3996 TRP Chi-restraints excluded: chain A residue 4007 ASN Chi-restraints excluded: chain A residue 4014 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 14 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 103 optimal weight: 30.0000 chunk 139 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.088112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.051298 restraints weight = 140404.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.053819 restraints weight = 53532.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.055350 restraints weight = 32959.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.056221 restraints weight = 25628.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.056641 restraints weight = 22140.573| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12010 Z= 0.142 Angle : 0.515 7.493 16341 Z= 0.262 Chirality : 0.037 0.139 1758 Planarity : 0.004 0.040 2180 Dihedral : 7.731 121.782 1674 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.94 % Favored : 95.99 % Rotamer: Outliers : 0.66 % Allowed : 10.44 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.23), residues: 1472 helix: 1.10 (0.22), residues: 588 sheet: -0.46 (0.31), residues: 274 loop : -0.00 (0.28), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2978 TYR 0.009 0.001 TYR A3176 PHE 0.015 0.001 PHE A3921 TRP 0.008 0.001 TRP A3506 HIS 0.005 0.001 HIS A2763 Details of bonding type rmsd covalent geometry : bond 0.00313 (12010) covalent geometry : angle 0.51508 (16341) hydrogen bonds : bond 0.03060 ( 511) hydrogen bonds : angle 4.52021 ( 1479) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3065 ASP cc_start: 0.8649 (t0) cc_final: 0.8357 (p0) REVERT: A 3217 ASP cc_start: 0.8408 (t0) cc_final: 0.8064 (p0) REVERT: A 3921 PHE cc_start: 0.7309 (m-10) cc_final: 0.7061 (m-10) outliers start: 8 outliers final: 7 residues processed: 64 average time/residue: 0.2005 time to fit residues: 19.9115 Evaluate side-chains 63 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3210 LEU Chi-restraints excluded: chain A residue 3509 THR Chi-restraints excluded: chain A residue 3592 LEU Chi-restraints excluded: chain A residue 3996 TRP Chi-restraints excluded: chain A residue 4007 ASN Chi-restraints excluded: chain A residue 4014 CYS Chi-restraints excluded: chain A residue 4067 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 12 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 107 optimal weight: 40.0000 chunk 19 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4086 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.086139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.048923 restraints weight = 141014.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.051423 restraints weight = 55138.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.052851 restraints weight = 34318.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.053745 restraints weight = 26410.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.054182 restraints weight = 22886.792| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12010 Z= 0.285 Angle : 0.616 7.435 16341 Z= 0.320 Chirality : 0.039 0.137 1758 Planarity : 0.005 0.040 2180 Dihedral : 8.164 120.965 1674 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.43 % Favored : 94.50 % Rotamer: Outliers : 0.90 % Allowed : 10.44 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.23), residues: 1472 helix: 0.60 (0.22), residues: 585 sheet: -0.77 (0.30), residues: 277 loop : -0.26 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A2978 TYR 0.013 0.002 TYR A3251 PHE 0.021 0.002 PHE A3400 TRP 0.011 0.001 TRP A2974 HIS 0.007 0.001 HIS A2838 Details of bonding type rmsd covalent geometry : bond 0.00619 (12010) covalent geometry : angle 0.61582 (16341) hydrogen bonds : bond 0.03716 ( 511) hydrogen bonds : angle 5.00547 ( 1479) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3065 ASP cc_start: 0.8588 (t0) cc_final: 0.8227 (p0) REVERT: A 3535 MET cc_start: 0.9010 (mmm) cc_final: 0.8626 (mmm) outliers start: 11 outliers final: 8 residues processed: 63 average time/residue: 0.2288 time to fit residues: 21.8539 Evaluate side-chains 60 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3008 ASP Chi-restraints excluded: chain A residue 3210 LEU Chi-restraints excluded: chain A residue 3509 THR Chi-restraints excluded: chain A residue 3592 LEU Chi-restraints excluded: chain A residue 3996 TRP Chi-restraints excluded: chain A residue 4007 ASN Chi-restraints excluded: chain A residue 4014 CYS Chi-restraints excluded: chain B residue 59 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 85 optimal weight: 0.9990 chunk 112 optimal weight: 20.0000 chunk 101 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 114 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3745 ASN B 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.087444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.050379 restraints weight = 141509.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.052955 restraints weight = 53966.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.054435 restraints weight = 32903.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.055202 restraints weight = 25682.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.055710 restraints weight = 22744.648| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12010 Z= 0.146 Angle : 0.521 7.407 16341 Z= 0.266 Chirality : 0.037 0.144 1758 Planarity : 0.004 0.041 2180 Dihedral : 7.883 123.579 1674 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 0.58 % Allowed : 11.02 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.23), residues: 1472 helix: 0.96 (0.22), residues: 582 sheet: -0.72 (0.30), residues: 277 loop : -0.14 (0.27), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 64 TYR 0.011 0.001 TYR A3869 PHE 0.020 0.001 PHE A3921 TRP 0.011 0.001 TRP A3506 HIS 0.007 0.001 HIS A2763 Details of bonding type rmsd covalent geometry : bond 0.00319 (12010) covalent geometry : angle 0.52114 (16341) hydrogen bonds : bond 0.03206 ( 511) hydrogen bonds : angle 4.64851 ( 1479) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3065 ASP cc_start: 0.8686 (t0) cc_final: 0.8336 (p0) REVERT: A 3881 MET cc_start: 0.4151 (mtm) cc_final: 0.3391 (mpp) outliers start: 7 outliers final: 7 residues processed: 61 average time/residue: 0.2227 time to fit residues: 21.0713 Evaluate side-chains 60 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3210 LEU Chi-restraints excluded: chain A residue 3509 THR Chi-restraints excluded: chain A residue 3592 LEU Chi-restraints excluded: chain A residue 3996 TRP Chi-restraints excluded: chain A residue 4007 ASN Chi-restraints excluded: chain A residue 4014 CYS Chi-restraints excluded: chain B residue 59 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 92 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 57 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 124 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.087643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.050517 restraints weight = 141414.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.053175 restraints weight = 54223.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.054707 restraints weight = 33288.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.055575 restraints weight = 25447.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.056005 restraints weight = 22166.182| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12010 Z= 0.135 Angle : 0.504 7.313 16341 Z= 0.256 Chirality : 0.037 0.139 1758 Planarity : 0.004 0.045 2180 Dihedral : 7.623 122.204 1674 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.42 % Favored : 95.52 % Rotamer: Outliers : 0.49 % Allowed : 10.94 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.23), residues: 1472 helix: 1.16 (0.22), residues: 588 sheet: -0.69 (0.30), residues: 280 loop : -0.07 (0.28), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3511 TYR 0.011 0.001 TYR A3869 PHE 0.022 0.001 PHE A3921 TRP 0.010 0.001 TRP A3506 HIS 0.006 0.001 HIS A2763 Details of bonding type rmsd covalent geometry : bond 0.00297 (12010) covalent geometry : angle 0.50424 (16341) hydrogen bonds : bond 0.02991 ( 511) hydrogen bonds : angle 4.51011 ( 1479) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3065 ASP cc_start: 0.8694 (t0) cc_final: 0.8371 (p0) REVERT: A 3881 MET cc_start: 0.4171 (mtm) cc_final: 0.3326 (mpp) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.1760 time to fit residues: 18.2280 Evaluate side-chains 58 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3210 LEU Chi-restraints excluded: chain A residue 3509 THR Chi-restraints excluded: chain A residue 3592 LEU Chi-restraints excluded: chain A residue 3996 TRP Chi-restraints excluded: chain A residue 4007 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 136 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 125 optimal weight: 30.0000 chunk 19 optimal weight: 5.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS 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 = 0.087523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.050684 restraints weight = 139921.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.053162 restraints weight = 54523.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.054641 restraints weight = 34023.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.055375 restraints weight = 26471.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.055944 restraints weight = 23485.461| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12010 Z= 0.141 Angle : 0.504 7.221 16341 Z= 0.256 Chirality : 0.037 0.136 1758 Planarity : 0.004 0.044 2180 Dihedral : 7.475 120.276 1674 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.35 % Favored : 95.58 % Rotamer: Outliers : 0.41 % Allowed : 11.18 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.23), residues: 1472 helix: 1.21 (0.22), residues: 590 sheet: -0.68 (0.31), residues: 279 loop : -0.03 (0.28), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2978 TYR 0.011 0.001 TYR A3869 PHE 0.018 0.001 PHE A3921 TRP 0.009 0.001 TRP A3506 HIS 0.006 0.001 HIS A2763 Details of bonding type rmsd covalent geometry : bond 0.00311 (12010) covalent geometry : angle 0.50414 (16341) hydrogen bonds : bond 0.02980 ( 511) hydrogen bonds : angle 4.48717 ( 1479) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4904.47 seconds wall clock time: 83 minutes 49.96 seconds (5029.96 seconds total)