Starting phenix.real_space_refine on Sat Jul 20 06:27:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k11_22620/07_2024/7k11_22620.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k11_22620/07_2024/7k11_22620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k11_22620/07_2024/7k11_22620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k11_22620/07_2024/7k11_22620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k11_22620/07_2024/7k11_22620.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k11_22620/07_2024/7k11_22620.cif" } resolution = 3.21 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= 0.002 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 57 5.16 5 C 6378 2.51 5 N 1716 2.21 5 O 1860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 2819": "OE1" <-> "OE2" Residue "A PHE 2823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2940": "NH1" <-> "NH2" Residue "A GLU 2967": "OE1" <-> "OE2" Residue "A GLU 2974": "OE1" <-> "OE2" Residue "A ASP 3020": "OD1" <-> "OD2" Residue "A GLU 3056": "OE1" <-> "OE2" Residue "A GLU 3072": "OE1" <-> "OE2" Residue "A TYR 3082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3125": "NH1" <-> "NH2" Residue "A GLU 3140": "OE1" <-> "OE2" Residue "A ASP 3180": "OD1" <-> "OD2" Residue "A GLU 3195": "OE1" <-> "OE2" Residue "A ASP 3226": "OD1" <-> "OD2" Residue "A ARG 3232": "NH1" <-> "NH2" Residue "A ASP 3244": "OD1" <-> "OD2" Residue "A ARG 3247": "NH1" <-> "NH2" Residue "A TYR 3280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3287": "NH1" <-> "NH2" Residue "A ARG 3289": "NH1" <-> "NH2" Residue "A ARG 3335": "NH1" <-> "NH2" Residue "A GLU 3344": "OE1" <-> "OE2" Residue "A GLU 3353": "OE1" <-> "OE2" Residue "A ARG 3358": "NH1" <-> "NH2" Residue "A GLU 3429": "OE1" <-> "OE2" Residue "A ARG 3467": "NH1" <-> "NH2" Residue "A ARG 3474": "NH1" <-> "NH2" Residue "A TYR 3475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3478": "OE1" <-> "OE2" Residue "A PHE 3554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3563": "OD1" <-> "OD2" Residue "A ASP 3576": "OD1" <-> "OD2" Residue "A ASP 3591": "OD1" <-> "OD2" Residue "A ARG 3593": "NH1" <-> "NH2" Residue "A ARG 3629": "NH1" <-> "NH2" Residue "A ASP 3641": "OD1" <-> "OD2" Residue "A ARG 3653": "NH1" <-> "NH2" Residue "A ASP 3658": "OD1" <-> "OD2" Residue "A ASP 3689": "OD1" <-> "OD2" Residue "A GLU 3693": "OE1" <-> "OE2" Residue "A ARG 3696": "NH1" <-> "NH2" Residue "A ARG 3708": "NH1" <-> "NH2" Residue "A ASP 3723": "OD1" <-> "OD2" Residue "A GLU 3724": "OE1" <-> "OE2" Residue "A ARG 3733": "NH1" <-> "NH2" Residue "A ASP 3744": "OD1" <-> "OD2" Residue "A ARG 3746": "NH1" <-> "NH2" Residue "A ARG 3763": "NH1" <-> "NH2" Residue "A ARG 3833": "NH1" <-> "NH2" Residue "A GLU 3838": "OE1" <-> "OE2" Residue "A ARG 3864": "NH1" <-> "NH2" Residue "A ARG 3889": "NH1" <-> "NH2" Residue "A PHE 3904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3922": "OD1" <-> "OD2" Residue "A ARG 3923": "NH1" <-> "NH2" Residue "A GLU 3933": "OE1" <-> "OE2" Residue "A ASP 3941": "OD1" <-> "OD2" Residue "A PHE 3961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3962": "NH1" <-> "NH2" Residue "A ASP 4012": "OD1" <-> "OD2" Residue "A ARG 4041": "NH1" <-> "NH2" Residue "A GLU 4095": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10011 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1254, 10011 Classifications: {'peptide': 1254} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1201} Chain breaks: 5 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Time building chain proxies: 6.38, per 1000 atoms: 0.64 Number of scatterers: 10011 At special positions: 0 Unit cell: (113.68, 100.92, 122.96, 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 57 16.00 O 1860 8.00 N 1716 7.00 C 6378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 3.79 Conformation dependent library (CDL) restraints added in 1.9 seconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2398 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 2 sheets defined 64.5% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 2801 through 2820 removed outlier: 3.728A pdb=" N ALA A2805 " --> pdb=" O ASP A2801 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A2814 " --> pdb=" O SER A2810 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2847 removed outlier: 3.797A pdb=" N ASN A2830 " --> pdb=" O LEU A2826 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN A2831 " --> pdb=" O SER A2827 " (cutoff:3.500A) Processing helix chain 'A' and resid 2851 through 2863 removed outlier: 4.192A pdb=" N CYS A2857 " --> pdb=" O PRO A2853 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N CYS A2863 " --> pdb=" O GLN A2859 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2884 removed outlier: 3.794A pdb=" N SER A2877 " --> pdb=" O PRO A2873 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A2878 " --> pdb=" O ALA A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2898 removed outlier: 3.962A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG A2891 " --> pdb=" O PRO A2887 " (cutoff:3.500A) Processing helix chain 'A' and resid 2918 through 2932 removed outlier: 3.609A pdb=" N ARG A2922 " --> pdb=" O PRO A2918 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TRP A2923 " --> pdb=" O ASP A2919 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) Processing helix chain 'A' and resid 2935 through 2940 removed outlier: 3.684A pdb=" N ARG A2940 " --> pdb=" O TYR A2936 " (cutoff:3.500A) Processing helix chain 'A' and resid 2941 through 2946 removed outlier: 3.960A pdb=" N SER A2945 " --> pdb=" O GLY A2941 " (cutoff:3.500A) Processing helix chain 'A' and resid 2952 through 2962 removed outlier: 4.192A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2966 through 2977 removed outlier: 4.081A pdb=" N TYR A2972 " --> pdb=" O ALA A2968 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP A2973 " --> pdb=" O ALA A2969 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA A2975 " --> pdb=" O GLN A2971 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN A2977 " --> pdb=" O ASP A2973 " (cutoff:3.500A) Processing helix chain 'A' and resid 2991 through 3005 removed outlier: 3.974A pdb=" N GLU A2995 " --> pdb=" O LYS A2991 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A3005 " --> pdb=" O CYS A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3011 through 3017 Processing helix chain 'A' and resid 3034 through 3039 removed outlier: 3.661A pdb=" N THR A3039 " --> pdb=" O PHE A3035 " (cutoff:3.500A) Processing helix chain 'A' and resid 3039 through 3053 removed outlier: 4.610A pdb=" N TYR A3043 " --> pdb=" O THR A3039 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A3044 " --> pdb=" O TYR A3040 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A3051 " --> pdb=" O SER A3047 " (cutoff:3.500A) Processing helix chain 'A' and resid 3060 through 3069 removed outlier: 3.562A pdb=" N PHE A3064 " --> pdb=" O SER A3060 " (cutoff:3.500A) Processing helix chain 'A' and resid 3075 through 3081 Processing helix chain 'A' and resid 3083 through 3093 Processing helix chain 'A' and resid 3096 through 3115 Processing helix chain 'A' and resid 3123 through 3130 Processing helix chain 'A' and resid 3131 through 3147 removed outlier: 3.905A pdb=" N LYS A3147 " --> pdb=" O SER A3143 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3165 Processing helix chain 'A' and resid 3175 through 3197 removed outlier: 3.594A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) Processing helix chain 'A' and resid 3227 through 3249 removed outlier: 3.818A pdb=" N ILE A3231 " --> pdb=" O ILE A3227 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A3232 " --> pdb=" O SER A3228 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS A3234 " --> pdb=" O LEU A3230 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A3248 " --> pdb=" O ASP A3244 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN A3249 " --> pdb=" O SER A3245 " (cutoff:3.500A) Processing helix chain 'A' and resid 3251 through 3262 removed outlier: 3.800A pdb=" N LYS A3257 " --> pdb=" O SER A3253 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A3258 " --> pdb=" O LEU A3254 " (cutoff:3.500A) Processing helix chain 'A' and resid 3269 through 3288 Processing helix chain 'A' and resid 3292 through 3297 removed outlier: 4.076A pdb=" N VAL A3297 " --> pdb=" O CYS A3293 " (cutoff:3.500A) Processing helix chain 'A' and resid 3304 through 3308 Processing helix chain 'A' and resid 3320 through 3344 removed outlier: 3.905A pdb=" N ASN A3327 " --> pdb=" O PHE A3323 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A3342 " --> pdb=" O ALA A3338 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A3343 " --> pdb=" O ASN A3339 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A3344 " --> pdb=" O ALA A3340 " (cutoff:3.500A) Processing helix chain 'A' and resid 3346 through 3351 Processing helix chain 'A' and resid 3354 through 3361 Processing helix chain 'A' and resid 3373 through 3391 removed outlier: 3.633A pdb=" N GLN A3379 " --> pdb=" O ALA A3375 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS A3384 " --> pdb=" O ARG A3380 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A3388 " --> pdb=" O HIS A3384 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL A3389 " --> pdb=" O LEU A3385 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN A3390 " --> pdb=" O SER A3386 " (cutoff:3.500A) Processing helix chain 'A' and resid 3409 through 3428 removed outlier: 3.970A pdb=" N LEU A3416 " --> pdb=" O ALA A3412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3455 removed outlier: 3.892A pdb=" N LEU A3445 " --> pdb=" O ALA A3441 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A3448 " --> pdb=" O ALA A3444 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A3449 " --> pdb=" O LEU A3445 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA A3453 " --> pdb=" O LYS A3449 " (cutoff:3.500A) Processing helix chain 'A' and resid 3464 through 3475 removed outlier: 3.855A pdb=" N LEU A3468 " --> pdb=" O LYS A3464 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) Processing helix chain 'A' and resid 3480 through 3488 Processing helix chain 'A' and resid 3498 through 3503 Processing helix chain 'A' and resid 3515 through 3525 Processing helix chain 'A' and resid 3529 through 3537 removed outlier: 3.909A pdb=" N ILE A3535 " --> pdb=" O TYR A3531 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A3536 " --> pdb=" O PRO A3532 " (cutoff:3.500A) Processing helix chain 'A' and resid 3545 through 3548 Processing helix chain 'A' and resid 3549 through 3562 removed outlier: 3.949A pdb=" N GLU A3553 " --> pdb=" O HIS A3549 " (cutoff:3.500A) Processing helix chain 'A' and resid 3567 through 3577 Processing helix chain 'A' and resid 3581 through 3594 removed outlier: 3.877A pdb=" N LYS A3586 " --> pdb=" O GLU A3582 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A3587 " --> pdb=" O LEU A3583 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A3594 " --> pdb=" O ASN A3590 " (cutoff:3.500A) Processing helix chain 'A' and resid 3604 through 3617 removed outlier: 4.325A pdb=" N GLU A3611 " --> pdb=" O GLU A3607 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET A3613 " --> pdb=" O MET A3609 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A3616 " --> pdb=" O ARG A3612 " (cutoff:3.500A) Processing helix chain 'A' and resid 3620 through 3627 removed outlier: 3.898A pdb=" N GLY A3624 " --> pdb=" O PRO A3620 " (cutoff:3.500A) Processing helix chain 'A' and resid 3632 through 3637 Processing helix chain 'A' and resid 3644 through 3650 Processing helix chain 'A' and resid 3651 through 3654 removed outlier: 3.636A pdb=" N MET A3654 " --> pdb=" O LEU A3651 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3651 through 3654' Processing helix chain 'A' and resid 3660 through 3670 removed outlier: 3.730A pdb=" N LEU A3666 " --> pdb=" O ILE A3662 " (cutoff:3.500A) Processing helix chain 'A' and resid 3684 through 3689 removed outlier: 3.895A pdb=" N SER A3688 " --> pdb=" O SER A3684 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP A3689 " --> pdb=" O PRO A3685 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3684 through 3689' Processing helix chain 'A' and resid 3758 through 3775 removed outlier: 3.621A pdb=" N GLN A3762 " --> pdb=" O LEU A3758 " (cutoff:3.500A) Processing helix chain 'A' and resid 3778 through 3783 Processing helix chain 'A' and resid 3812 through 3820 removed outlier: 4.008A pdb=" N MET A3820 " --> pdb=" O LEU A3816 " (cutoff:3.500A) Processing helix chain 'A' and resid 3823 through 3830 Processing helix chain 'A' and resid 3834 through 3847 removed outlier: 3.715A pdb=" N TYR A3839 " --> pdb=" O PRO A3835 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3859 removed outlier: 3.650A pdb=" N LEU A3857 " --> pdb=" O GLY A3853 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A3859 " --> pdb=" O TYR A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3876 removed outlier: 3.952A pdb=" N THR A3867 " --> pdb=" O ASN A3863 " (cutoff:3.500A) Processing helix chain 'A' and resid 3883 through 3890 removed outlier: 3.831A pdb=" N MET A3890 " --> pdb=" O ALA A3886 " (cutoff:3.500A) Processing helix chain 'A' and resid 3893 through 3918 removed outlier: 3.895A pdb=" N LEU A3898 " --> pdb=" O PRO A3894 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS A3903 " --> pdb=" O ALA A3899 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE A3904 " --> pdb=" O LEU A3900 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TRP A3916 " --> pdb=" O CYS A3912 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE A3917 " --> pdb=" O ILE A3913 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU A3918 " --> pdb=" O SER A3914 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3970 Processing helix chain 'A' and resid 3978 through 3992 Processing helix chain 'A' and resid 3996 through 4007 Processing helix chain 'A' and resid 4013 through 4022 Processing helix chain 'A' and resid 4033 through 4037 Processing helix chain 'A' and resid 4039 through 4052 removed outlier: 3.970A pdb=" N LYS A4043 " --> pdb=" O TYR A4039 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE A4044 " --> pdb=" O PRO A4040 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4068 removed outlier: 3.508A pdb=" N ILE A4059 " --> pdb=" O ASN A4055 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A4060 " --> pdb=" O PRO A4056 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS A4061 " --> pdb=" O ALA A4057 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4081 Processing helix chain 'A' and resid 4088 through 4092 removed outlier: 3.527A pdb=" N ALA A4091 " --> pdb=" O ASN A4088 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4112 Processing helix chain 'A' and resid 4113 through 4118 Processing sheet with id=AA1, first strand: chain 'A' and resid 3727 through 3728 removed outlier: 3.559A pdb=" N THR A3727 " --> pdb=" O ARG A3737 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A3753 " --> pdb=" O GLY A3801 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3809 through 3811 465 hydrogen bonds defined for protein. 1374 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: 3.23 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3245 1.34 - 1.46: 2180 1.46 - 1.58: 4699 1.58 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 10218 Sorted by residual: bond pdb=" CB ASN A3311 " pdb=" CG ASN A3311 " ideal model delta sigma weight residual 1.516 1.573 -0.057 2.50e-02 1.60e+03 5.23e+00 bond pdb=" C LEU A3041 " pdb=" N PRO A3042 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.36e-02 5.41e+03 4.53e+00 bond pdb=" C PRO A2852 " pdb=" N PRO A2853 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.10e+00 bond pdb=" C PRO A3676 " pdb=" N PRO A3677 " ideal model delta sigma weight residual 1.334 1.379 -0.046 2.34e-02 1.83e+03 3.79e+00 bond pdb=" CB PRO A2853 " pdb=" CG PRO A2853 " ideal model delta sigma weight residual 1.492 1.405 0.087 5.00e-02 4.00e+02 3.05e+00 ... (remaining 10213 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.74: 294 106.74 - 114.00: 5731 114.00 - 121.26: 5249 121.26 - 128.52: 2434 128.52 - 135.78: 93 Bond angle restraints: 13801 Sorted by residual: angle pdb=" C ASN A3310 " pdb=" N ASN A3311 " pdb=" CA ASN A3311 " ideal model delta sigma weight residual 125.66 134.84 -9.18 1.85e+00 2.92e-01 2.46e+01 angle pdb=" C HIS A3122 " pdb=" N GLN A3123 " pdb=" CA GLN A3123 " ideal model delta sigma weight residual 121.54 131.01 -9.47 1.91e+00 2.74e-01 2.46e+01 angle pdb=" C ASP A4012 " pdb=" N TRP A4013 " pdb=" CA TRP A4013 " ideal model delta sigma weight residual 121.54 130.92 -9.38 1.91e+00 2.74e-01 2.41e+01 angle pdb=" C ASP A3058 " pdb=" N GLN A3059 " pdb=" CA GLN A3059 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C ASP A3369 " pdb=" N SER A3370 " pdb=" CA SER A3370 " ideal model delta sigma weight residual 121.54 129.95 -8.41 1.91e+00 2.74e-01 1.94e+01 ... (remaining 13796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 5340 16.05 - 32.10: 699 32.10 - 48.15: 163 48.15 - 64.20: 26 64.20 - 80.25: 10 Dihedral angle restraints: 6238 sinusoidal: 2555 harmonic: 3683 Sorted by residual: dihedral pdb=" CA GLY A3707 " pdb=" C GLY A3707 " pdb=" N ARG A3708 " pdb=" CA ARG A3708 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA SER A3314 " pdb=" C SER A3314 " pdb=" N TYR A3315 " pdb=" CA TYR A3315 " ideal model delta harmonic sigma weight residual 180.00 155.49 24.51 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA GLU A3344 " pdb=" C GLU A3344 " pdb=" N PRO A3345 " pdb=" CA PRO A3345 " ideal model delta harmonic sigma weight residual -180.00 -156.12 -23.88 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 6235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1094 0.053 - 0.105: 351 0.105 - 0.158: 62 0.158 - 0.210: 19 0.210 - 0.263: 2 Chirality restraints: 1528 Sorted by residual: chirality pdb=" CB ILE A3739 " pdb=" CA ILE A3739 " pdb=" CG1 ILE A3739 " pdb=" CG2 ILE A3739 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE A4031 " pdb=" CA ILE A4031 " pdb=" CG1 ILE A4031 " pdb=" CG2 ILE A4031 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB VAL A3514 " pdb=" CA VAL A3514 " pdb=" CG1 VAL A3514 " pdb=" CG2 VAL A3514 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.93e-01 ... (remaining 1525 not shown) Planarity restraints: 1767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A3531 " -0.054 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO A3532 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A3532 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A3532 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A3123 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C GLN A3123 " -0.055 2.00e-02 2.50e+03 pdb=" O GLN A3123 " 0.020 2.00e-02 2.50e+03 pdb=" N SER A3124 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A3676 " -0.050 5.00e-02 4.00e+02 7.60e-02 9.24e+00 pdb=" N PRO A3677 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A3677 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A3677 " -0.044 5.00e-02 4.00e+02 ... (remaining 1764 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2567 2.80 - 3.32: 8733 3.32 - 3.85: 15323 3.85 - 4.37: 17838 4.37 - 4.90: 31736 Nonbonded interactions: 76197 Sorted by model distance: nonbonded pdb=" O TYR A3043 " pdb=" OG SER A3047 " model vdw 2.271 2.440 nonbonded pdb=" O PHE A3887 " pdb=" OG SER A3891 " model vdw 2.302 2.440 nonbonded pdb=" O SER A3489 " pdb=" OG SER A3489 " model vdw 2.311 2.440 nonbonded pdb=" O ASP A3180 " pdb=" OG1 THR A3184 " model vdw 2.317 2.440 nonbonded pdb=" O MET A4108 " pdb=" OG1 THR A4112 " model vdw 2.333 2.440 ... (remaining 76192 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 30.600 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 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 : 0.005 0.087 10218 Z= 0.348 Angle : 0.924 10.777 13801 Z= 0.501 Chirality : 0.053 0.263 1528 Planarity : 0.008 0.081 1767 Dihedral : 15.327 80.254 3840 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.58 % Favored : 90.34 % Rotamer: Outliers : 0.46 % Allowed : 9.52 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -5.00 (0.17), residues: 1242 helix: -2.91 (0.13), residues: 793 sheet: -3.07 (0.73), residues: 32 loop : -3.84 (0.23), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A4013 HIS 0.005 0.001 HIS A3743 PHE 0.020 0.002 PHE A3110 TYR 0.020 0.002 TYR A3705 ARG 0.004 0.000 ARG A3425 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 161 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3178 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7903 (mp) REVERT: A 3426 LYS cc_start: 0.6963 (tttt) cc_final: 0.6572 (ttpp) REVERT: A 3650 LYS cc_start: 0.6568 (tmmt) cc_final: 0.6270 (ttpt) REVERT: A 3974 MET cc_start: 0.7860 (mpp) cc_final: 0.7601 (mmm) REVERT: A 4044 ILE cc_start: 0.7943 (mm) cc_final: 0.7719 (tp) outliers start: 5 outliers final: 2 residues processed: 166 average time/residue: 0.2511 time to fit residues: 56.9269 Evaluate side-chains 122 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3178 ILE Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3955 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.0000 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2859 GLN A2885 GLN A3104 GLN A3150 ASN A3327 ASN A3423 GLN A3459 ASN ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3590 ASN A3602 ASN A3679 ASN A4088 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10218 Z= 0.215 Angle : 0.596 7.966 13801 Z= 0.316 Chirality : 0.041 0.156 1528 Planarity : 0.006 0.059 1767 Dihedral : 5.581 42.837 1354 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.58 % Favored : 90.34 % Rotamer: Outliers : 1.92 % Allowed : 15.00 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -3.25 (0.21), residues: 1242 helix: -1.40 (0.17), residues: 807 sheet: -2.41 (0.89), residues: 26 loop : -3.54 (0.25), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A3493 HIS 0.003 0.001 HIS A3743 PHE 0.020 0.001 PHE A3110 TYR 0.018 0.001 TYR A3280 ARG 0.005 0.000 ARG A3159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 3176 MET cc_start: 0.8924 (mmm) cc_final: 0.8649 (mmm) REVERT: A 3341 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6664 (pt) REVERT: A 3426 LYS cc_start: 0.6925 (tttt) cc_final: 0.6574 (ttpp) REVERT: A 3628 PHE cc_start: 0.3225 (OUTLIER) cc_final: 0.2999 (t80) REVERT: A 3974 MET cc_start: 0.7937 (mpp) cc_final: 0.7656 (mmm) outliers start: 21 outliers final: 11 residues processed: 152 average time/residue: 0.2399 time to fit residues: 50.3533 Evaluate side-chains 140 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2980 ASP Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3045 ILE Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3341 LEU Chi-restraints excluded: chain A residue 3360 LEU Chi-restraints excluded: chain A residue 3410 ILE Chi-restraints excluded: chain A residue 3490 VAL Chi-restraints excluded: chain A residue 3628 PHE Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3953 LEU Chi-restraints excluded: chain A residue 3955 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.0870 chunk 35 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 122 optimal weight: 0.0870 chunk 101 optimal weight: 0.0030 chunk 112 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 overall best weight: 0.2746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3510 GLN A3643 HIS A3679 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10218 Z= 0.146 Angle : 0.533 7.757 13801 Z= 0.281 Chirality : 0.039 0.158 1528 Planarity : 0.004 0.046 1767 Dihedral : 4.944 37.859 1352 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 2.10 % Allowed : 17.47 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.23 (0.23), residues: 1242 helix: -0.55 (0.19), residues: 800 sheet: -1.93 (0.93), residues: 26 loop : -3.25 (0.26), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A3842 HIS 0.002 0.001 HIS A3908 PHE 0.023 0.001 PHE A3110 TYR 0.013 0.001 TYR A3280 ARG 0.006 0.000 ARG A3159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2835 LYS cc_start: 0.7234 (ttmt) cc_final: 0.6882 (mtpt) REVERT: A 3176 MET cc_start: 0.8947 (mmm) cc_final: 0.8664 (mmm) REVERT: A 3178 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7723 (mp) REVERT: A 3533 PHE cc_start: 0.7452 (t80) cc_final: 0.7236 (t80) REVERT: A 3628 PHE cc_start: 0.2972 (OUTLIER) cc_final: 0.2768 (t80) REVERT: A 3974 MET cc_start: 0.7782 (mpp) cc_final: 0.7531 (mmm) outliers start: 23 outliers final: 12 residues processed: 158 average time/residue: 0.2536 time to fit residues: 54.8342 Evaluate side-chains 145 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3178 ILE Chi-restraints excluded: chain A residue 3256 MET Chi-restraints excluded: chain A residue 3303 THR Chi-restraints excluded: chain A residue 3490 VAL Chi-restraints excluded: chain A residue 3599 THR Chi-restraints excluded: chain A residue 3628 PHE Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3719 ILE Chi-restraints excluded: chain A residue 3888 VAL Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3955 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.9980 chunk 85 optimal weight: 0.0570 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3679 ASN ** A3924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10218 Z= 0.232 Angle : 0.588 7.627 13801 Z= 0.308 Chirality : 0.041 0.162 1528 Planarity : 0.005 0.047 1767 Dihedral : 5.161 43.924 1352 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.23 % Favored : 89.69 % Rotamer: Outliers : 3.11 % Allowed : 19.21 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.09 (0.23), residues: 1242 helix: -0.43 (0.19), residues: 800 sheet: -2.00 (0.91), residues: 26 loop : -3.21 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A3842 HIS 0.004 0.001 HIS A3743 PHE 0.021 0.001 PHE A3110 TYR 0.018 0.001 TYR A3280 ARG 0.006 0.000 ARG A3159 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: A 2835 LYS cc_start: 0.7333 (ttmt) cc_final: 0.6973 (mtpt) REVERT: A 3178 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7938 (mp) REVERT: A 3590 ASN cc_start: 0.6935 (m-40) cc_final: 0.6694 (m110) REVERT: A 3974 MET cc_start: 0.7866 (mpp) cc_final: 0.7594 (mmm) outliers start: 34 outliers final: 23 residues processed: 159 average time/residue: 0.2147 time to fit residues: 48.9276 Evaluate side-chains 152 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2881 LEU Chi-restraints excluded: chain A residue 2980 ASP Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3079 GLU Chi-restraints excluded: chain A residue 3178 ILE Chi-restraints excluded: chain A residue 3268 THR Chi-restraints excluded: chain A residue 3303 THR Chi-restraints excluded: chain A residue 3360 LEU Chi-restraints excluded: chain A residue 3410 ILE Chi-restraints excluded: chain A residue 3445 LEU Chi-restraints excluded: chain A residue 3490 VAL Chi-restraints excluded: chain A residue 3599 THR Chi-restraints excluded: chain A residue 3687 MET Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3719 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3888 VAL Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 83 optimal weight: 0.0970 chunk 0 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 108 optimal weight: 0.0060 chunk 30 optimal weight: 0.0980 chunk 40 optimal weight: 0.9990 overall best weight: 0.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10218 Z= 0.135 Angle : 0.519 9.319 13801 Z= 0.270 Chirality : 0.038 0.143 1528 Planarity : 0.004 0.045 1767 Dihedral : 4.676 40.455 1352 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.47 % Allowed : 19.85 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.53 (0.24), residues: 1242 helix: 0.03 (0.19), residues: 801 sheet: -1.75 (0.93), residues: 26 loop : -3.05 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A3493 HIS 0.002 0.000 HIS A3501 PHE 0.024 0.001 PHE A3533 TYR 0.011 0.001 TYR A3315 ARG 0.007 0.000 ARG A3159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 1.203 Fit side-chains revert: symmetry clash REVERT: A 2835 LYS cc_start: 0.7260 (ttmt) cc_final: 0.6884 (mtpt) REVERT: A 3178 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7584 (mp) REVERT: A 3858 MET cc_start: 0.8725 (tmm) cc_final: 0.8517 (tmm) REVERT: A 3974 MET cc_start: 0.7756 (mpp) cc_final: 0.7505 (mmm) outliers start: 27 outliers final: 16 residues processed: 163 average time/residue: 0.2305 time to fit residues: 53.3725 Evaluate side-chains 147 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2980 ASP Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3178 ILE Chi-restraints excluded: chain A residue 3303 THR Chi-restraints excluded: chain A residue 3410 ILE Chi-restraints excluded: chain A residue 3490 VAL Chi-restraints excluded: chain A residue 3562 LEU Chi-restraints excluded: chain A residue 3599 THR Chi-restraints excluded: chain A residue 3687 MET Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3719 ILE Chi-restraints excluded: chain A residue 3888 VAL Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4028 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 70 optimal weight: 0.0470 chunk 29 optimal weight: 0.0870 chunk 120 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3590 ASN A3679 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10218 Z= 0.164 Angle : 0.561 8.145 13801 Z= 0.287 Chirality : 0.040 0.147 1528 Planarity : 0.004 0.045 1767 Dihedral : 4.714 43.156 1352 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.38 % Allowed : 21.23 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.38 (0.24), residues: 1242 helix: 0.12 (0.19), residues: 798 sheet: -1.47 (0.92), residues: 26 loop : -2.93 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A4027 HIS 0.002 0.001 HIS A3743 PHE 0.021 0.001 PHE A3571 TYR 0.011 0.001 TYR A3102 ARG 0.006 0.000 ARG A3557 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 2835 LYS cc_start: 0.7268 (ttmt) cc_final: 0.6911 (mtpt) REVERT: A 3121 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7779 (mp) REVERT: A 3178 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7871 (mp) REVERT: A 3665 MET cc_start: 0.7501 (ppp) cc_final: 0.6765 (ptt) REVERT: A 3772 ASN cc_start: 0.7798 (p0) cc_final: 0.7511 (p0) REVERT: A 3858 MET cc_start: 0.8750 (tmm) cc_final: 0.8526 (tmm) REVERT: A 3974 MET cc_start: 0.7794 (mpp) cc_final: 0.7525 (mmm) outliers start: 26 outliers final: 20 residues processed: 153 average time/residue: 0.2037 time to fit residues: 44.7089 Evaluate side-chains 151 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2980 ASP Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3178 ILE Chi-restraints excluded: chain A residue 3268 THR Chi-restraints excluded: chain A residue 3303 THR Chi-restraints excluded: chain A residue 3410 ILE Chi-restraints excluded: chain A residue 3490 VAL Chi-restraints excluded: chain A residue 3599 THR Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3687 MET Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3747 GLU Chi-restraints excluded: chain A residue 3888 VAL Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 0.0970 chunk 88 optimal weight: 0.0970 chunk 101 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3590 ASN A3679 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10218 Z= 0.217 Angle : 0.592 7.364 13801 Z= 0.305 Chirality : 0.041 0.155 1528 Planarity : 0.005 0.045 1767 Dihedral : 4.961 47.066 1352 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 2.65 % Allowed : 21.59 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.24), residues: 1242 helix: 0.02 (0.19), residues: 799 sheet: -1.54 (0.93), residues: 26 loop : -2.97 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A4027 HIS 0.003 0.001 HIS A3743 PHE 0.026 0.002 PHE A3110 TYR 0.014 0.001 TYR A3705 ARG 0.006 0.000 ARG A3557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: A 2835 LYS cc_start: 0.7307 (ttmt) cc_final: 0.6933 (mtpt) REVERT: A 3121 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8132 (mp) REVERT: A 3178 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7997 (mp) REVERT: A 3665 MET cc_start: 0.7418 (ppp) cc_final: 0.6660 (ptt) REVERT: A 3974 MET cc_start: 0.7903 (mpp) cc_final: 0.7610 (mmm) outliers start: 29 outliers final: 24 residues processed: 156 average time/residue: 0.2326 time to fit residues: 52.4747 Evaluate side-chains 152 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2881 LEU Chi-restraints excluded: chain A residue 2980 ASP Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3079 GLU Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3178 ILE Chi-restraints excluded: chain A residue 3268 THR Chi-restraints excluded: chain A residue 3303 THR Chi-restraints excluded: chain A residue 3410 ILE Chi-restraints excluded: chain A residue 3490 VAL Chi-restraints excluded: chain A residue 3599 THR Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3687 MET Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3719 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3747 GLU Chi-restraints excluded: chain A residue 3888 VAL Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 76 optimal weight: 0.3980 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 115 optimal weight: 0.1980 chunk 105 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3679 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10218 Z= 0.190 Angle : 0.577 7.944 13801 Z= 0.297 Chirality : 0.040 0.147 1528 Planarity : 0.004 0.045 1767 Dihedral : 4.878 47.302 1352 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 2.84 % Allowed : 21.23 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.38 (0.24), residues: 1242 helix: 0.10 (0.19), residues: 800 sheet: -1.45 (0.95), residues: 26 loop : -2.90 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A4027 HIS 0.002 0.001 HIS A3743 PHE 0.026 0.001 PHE A3110 TYR 0.012 0.001 TYR A3102 ARG 0.007 0.000 ARG A3159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 2835 LYS cc_start: 0.7291 (ttmt) cc_final: 0.6916 (mtpt) REVERT: A 3178 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7965 (mp) REVERT: A 3665 MET cc_start: 0.7425 (ppp) cc_final: 0.6697 (ptt) REVERT: A 3974 MET cc_start: 0.7845 (mpp) cc_final: 0.7585 (mmm) outliers start: 31 outliers final: 23 residues processed: 155 average time/residue: 0.2048 time to fit residues: 46.0436 Evaluate side-chains 152 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2980 ASP Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3079 GLU Chi-restraints excluded: chain A residue 3178 ILE Chi-restraints excluded: chain A residue 3268 THR Chi-restraints excluded: chain A residue 3303 THR Chi-restraints excluded: chain A residue 3410 ILE Chi-restraints excluded: chain A residue 3490 VAL Chi-restraints excluded: chain A residue 3599 THR Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3687 MET Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3719 ILE Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3747 GLU Chi-restraints excluded: chain A residue 3888 VAL Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.8980 chunk 115 optimal weight: 0.0020 chunk 67 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 118 optimal weight: 0.0970 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3679 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10218 Z= 0.183 Angle : 0.576 9.488 13801 Z= 0.295 Chirality : 0.040 0.146 1528 Planarity : 0.004 0.045 1767 Dihedral : 4.829 47.767 1352 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 2.93 % Allowed : 21.41 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.27 (0.24), residues: 1242 helix: 0.19 (0.19), residues: 793 sheet: -1.36 (0.96), residues: 26 loop : -2.83 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A4027 HIS 0.002 0.001 HIS A3743 PHE 0.025 0.001 PHE A3110 TYR 0.012 0.001 TYR A3102 ARG 0.007 0.000 ARG A3159 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 2835 LYS cc_start: 0.7268 (ttmt) cc_final: 0.6890 (mtpt) REVERT: A 3178 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7967 (mp) REVERT: A 3632 PHE cc_start: 0.4522 (OUTLIER) cc_final: 0.4224 (m-10) REVERT: A 3665 MET cc_start: 0.7416 (ppp) cc_final: 0.6567 (ptt) REVERT: A 3974 MET cc_start: 0.7850 (mpp) cc_final: 0.7593 (mmm) outliers start: 32 outliers final: 27 residues processed: 153 average time/residue: 0.2205 time to fit residues: 49.1017 Evaluate side-chains 155 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2881 LEU Chi-restraints excluded: chain A residue 2980 ASP Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3079 GLU Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3178 ILE Chi-restraints excluded: chain A residue 3268 THR Chi-restraints excluded: chain A residue 3303 THR Chi-restraints excluded: chain A residue 3410 ILE Chi-restraints excluded: chain A residue 3490 VAL Chi-restraints excluded: chain A residue 3599 THR Chi-restraints excluded: chain A residue 3632 PHE Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3687 MET Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3719 ILE Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3743 HIS Chi-restraints excluded: chain A residue 3747 GLU Chi-restraints excluded: chain A residue 3888 VAL Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3929 MET Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4028 ILE Chi-restraints excluded: chain A residue 4066 LEU Chi-restraints excluded: chain A residue 4102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3590 ASN A3679 ASN ** A3924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4068 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10218 Z= 0.273 Angle : 0.644 9.394 13801 Z= 0.331 Chirality : 0.043 0.162 1528 Planarity : 0.005 0.045 1767 Dihedral : 5.174 50.049 1352 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.71 % Favored : 89.21 % Rotamer: Outliers : 2.65 % Allowed : 21.77 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.53 (0.24), residues: 1242 helix: -0.03 (0.19), residues: 794 sheet: -1.35 (0.98), residues: 26 loop : -2.90 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A4027 HIS 0.004 0.001 HIS A3743 PHE 0.029 0.002 PHE A3110 TYR 0.016 0.001 TYR A3705 ARG 0.007 0.000 ARG A3159 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 2835 LYS cc_start: 0.7407 (ttmt) cc_final: 0.7057 (mtpt) REVERT: A 3178 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.8034 (mp) REVERT: A 3632 PHE cc_start: 0.4594 (OUTLIER) cc_final: 0.4248 (m-10) REVERT: A 3974 MET cc_start: 0.7943 (mpp) cc_final: 0.7646 (mmm) outliers start: 29 outliers final: 23 residues processed: 147 average time/residue: 0.2161 time to fit residues: 46.2180 Evaluate side-chains 149 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2881 LEU Chi-restraints excluded: chain A residue 2980 ASP Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3079 GLU Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3178 ILE Chi-restraints excluded: chain A residue 3268 THR Chi-restraints excluded: chain A residue 3303 THR Chi-restraints excluded: chain A residue 3410 ILE Chi-restraints excluded: chain A residue 3490 VAL Chi-restraints excluded: chain A residue 3599 THR Chi-restraints excluded: chain A residue 3632 PHE Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3687 MET Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3719 ILE Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3747 GLU Chi-restraints excluded: chain A residue 3888 VAL Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 3918 LEU Chi-restraints excluded: chain A residue 3933 GLU Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 4102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.2980 chunk 91 optimal weight: 0.0020 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3679 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.171659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143144 restraints weight = 13099.355| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.80 r_work: 0.3593 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10218 Z= 0.165 Angle : 0.571 9.072 13801 Z= 0.292 Chirality : 0.040 0.146 1528 Planarity : 0.004 0.046 1767 Dihedral : 4.824 47.809 1352 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.02 % Favored : 90.90 % Rotamer: Outliers : 2.56 % Allowed : 21.68 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.19 (0.24), residues: 1242 helix: 0.25 (0.19), residues: 794 sheet: -1.21 (0.97), residues: 26 loop : -2.80 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A4027 HIS 0.003 0.001 HIS A3924 PHE 0.025 0.001 PHE A3110 TYR 0.013 0.001 TYR A3040 ARG 0.006 0.000 ARG A3159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2430.85 seconds wall clock time: 44 minutes 7.32 seconds (2647.32 seconds total)