Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 5 14:28:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k11_22620/07_2023/7k11_22620.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k11_22620/07_2023/7k11_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_2023/7k11_22620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k11_22620/07_2023/7k11_22620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k11_22620/07_2023/7k11_22620.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k11_22620/07_2023/7k11_22620.pdb" } resolution = 3.21 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 ------------------------------------------------------------------------------- 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-1.21rc1-5013/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: 5.08, per 1000 atoms: 0.51 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: 3.63 Conformation dependent library (CDL) restraints added in 1.5 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: 0.61 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: 3.07 Time building geometry restraints manager: 3.96 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: 2.140 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: 9.380 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 27.170 Find NCS groups from input model: 0.260 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.820 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 166 average time/residue: 0.2622 time to fit residues: 59.6998 Evaluate side-chains 118 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0877 time to fit residues: 1.7864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 A3590 ASN A3602 ASN A3679 ASN A4088 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 10218 Z= 0.205 Angle : 0.590 7.917 13801 Z= 0.313 Chirality : 0.041 0.153 1528 Planarity : 0.005 0.059 1767 Dihedral : 5.277 21.409 1349 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.34 % Favored : 90.58 % Rotamer Outliers : 1.83 % 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: -3.26 (0.21), residues: 1242 helix: -1.40 (0.17), residues: 805 sheet: -2.39 (0.90), residues: 26 loop : -3.56 (0.25), residues: 411 *********************** 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 158 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 1.113 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 151 average time/residue: 0.2310 time to fit residues: 49.1076 Evaluate side-chains 132 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0918 time to fit residues: 3.3204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.0270 chunk 94 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 101 optimal weight: 0.0980 chunk 112 optimal weight: 0.9980 chunk 38 optimal weight: 0.0070 chunk 91 optimal weight: 0.9990 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3643 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 10218 Z= 0.152 Angle : 0.542 7.751 13801 Z= 0.284 Chirality : 0.039 0.162 1528 Planarity : 0.005 0.046 1767 Dihedral : 4.780 19.470 1349 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.34 % Favored : 90.58 % Rotamer Outliers : 1.37 % 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: -2.29 (0.23), residues: 1242 helix: -0.59 (0.19), residues: 798 sheet: -1.95 (0.92), residues: 26 loop : -3.29 (0.26), residues: 418 *********************** 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 160 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 1.115 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 156 average time/residue: 0.2567 time to fit residues: 54.9930 Evaluate side-chains 139 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0974 time to fit residues: 3.0883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.0770 chunk 85 optimal weight: 0.0970 chunk 59 optimal weight: 0.2980 chunk 12 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 108 optimal weight: 0.0470 chunk 32 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.2034 ------------------------------------------------------------------------------- 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: 0.7367 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 10218 Z= 0.138 Angle : 0.522 7.515 13801 Z= 0.272 Chirality : 0.038 0.145 1528 Planarity : 0.004 0.046 1767 Dihedral : 4.474 18.523 1349 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer Outliers : 0.91 % 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: -1.77 (0.24), residues: 1242 helix: -0.16 (0.19), residues: 798 sheet: -1.75 (0.93), residues: 26 loop : -3.13 (0.26), residues: 418 *********************** 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 150 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 1.020 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 148 average time/residue: 0.2259 time to fit residues: 48.0988 Evaluate side-chains 134 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.192 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1030 time to fit residues: 2.6473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.0970 chunk 1 optimal weight: 0.6980 chunk 89 optimal weight: 0.0770 chunk 49 optimal weight: 0.0770 chunk 103 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 108 optimal weight: 0.0670 chunk 30 optimal weight: 0.0060 chunk 40 optimal weight: 0.8980 overall best weight: 0.0648 ------------------------------------------------------------------------------- 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: 0.7299 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 10218 Z= 0.129 Angle : 0.520 9.384 13801 Z= 0.267 Chirality : 0.038 0.134 1528 Planarity : 0.004 0.046 1767 Dihedral : 4.212 18.101 1349 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer Outliers : 1.10 % 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: -1.25 (0.24), residues: 1242 helix: 0.25 (0.20), residues: 786 sheet: -1.46 (0.84), residues: 31 loop : -2.85 (0.27), residues: 425 *********************** 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 161 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 1.172 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 158 average time/residue: 0.2487 time to fit residues: 54.8439 Evaluate side-chains 135 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1097 time to fit residues: 2.5615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3154 GLN ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1863 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= 0.260 Angle : 0.624 7.289 13801 Z= 0.322 Chirality : 0.043 0.156 1528 Planarity : 0.005 0.045 1767 Dihedral : 4.721 19.156 1349 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer Outliers : 1.65 % 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: -1.54 (0.24), residues: 1242 helix: 0.02 (0.19), residues: 788 sheet: -1.55 (0.92), residues: 26 loop : -2.97 (0.27), residues: 428 *********************** 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 156 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 1.035 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 152 average time/residue: 0.2356 time to fit residues: 51.2550 Evaluate side-chains 139 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1045 time to fit residues: 3.4212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3154 GLN ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 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 : 0.003 0.049 10218 Z= 0.204 Angle : 0.586 7.131 13801 Z= 0.304 Chirality : 0.041 0.152 1528 Planarity : 0.004 0.045 1767 Dihedral : 4.642 18.781 1349 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer Outliers : 0.82 % 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: -1.41 (0.24), residues: 1242 helix: 0.10 (0.19), residues: 787 sheet: -1.34 (0.96), residues: 26 loop : -2.89 (0.27), residues: 429 *********************** 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 146 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 145 average time/residue: 0.2255 time to fit residues: 47.0168 Evaluate side-chains 134 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0965 time to fit residues: 2.5433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 76 optimal weight: 0.0070 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 0.0470 chunk 11 optimal weight: 0.9990 chunk 94 optimal weight: 0.0050 chunk 109 optimal weight: 0.5980 chunk 115 optimal weight: 0.0770 chunk 105 optimal weight: 0.0870 overall best weight: 0.0446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3037 GLN A3154 GLN A3501 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 10218 Z= 0.132 Angle : 0.531 7.315 13801 Z= 0.272 Chirality : 0.038 0.133 1528 Planarity : 0.004 0.047 1767 Dihedral : 4.106 18.248 1349 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer Outliers : 0.27 % 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: -0.89 (0.25), residues: 1242 helix: 0.54 (0.20), residues: 788 sheet: -1.13 (0.89), residues: 31 loop : -2.78 (0.28), residues: 423 *********************** 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 147 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 146 average time/residue: 0.2355 time to fit residues: 49.3818 Evaluate side-chains 129 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1180 time to fit residues: 2.0698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 0.0470 chunk 106 optimal weight: 0.0670 chunk 111 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10218 Z= 0.170 Angle : 0.561 9.329 13801 Z= 0.287 Chirality : 0.040 0.144 1528 Planarity : 0.004 0.045 1767 Dihedral : 4.216 17.849 1349 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer Outliers : 0.27 % 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: -0.83 (0.25), residues: 1242 helix: 0.55 (0.20), residues: 783 sheet: -1.04 (0.88), residues: 31 loop : -2.63 (0.28), residues: 428 *********************** 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 132 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 130 average time/residue: 0.2453 time to fit residues: 45.3394 Evaluate side-chains 127 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1081 time to fit residues: 2.2840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.0050 chunk 56 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3154 GLN A3590 ASN A4068 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 10218 Z= 0.227 Angle : 0.609 9.296 13801 Z= 0.313 Chirality : 0.042 0.155 1528 Planarity : 0.004 0.046 1767 Dihedral : 4.517 18.793 1349 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer Outliers : 0.27 % 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: -1.09 (0.24), residues: 1242 helix: 0.34 (0.19), residues: 788 sheet: -0.89 (1.00), residues: 26 loop : -2.78 (0.28), residues: 428 ********************** 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 133 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 132 average time/residue: 0.2393 time to fit residues: 44.9276 Evaluate side-chains 128 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.083 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0969 time to fit residues: 1.7319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 0.0020 chunk 12 optimal weight: 0.0170 chunk 18 optimal weight: 0.0570 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3154 GLN A3590 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.174099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.146693 restraints weight = 13069.810| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.88 r_work: 0.3624 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 10218 Z= 0.149 Angle : 0.553 9.349 13801 Z= 0.283 Chirality : 0.039 0.142 1528 Planarity : 0.004 0.046 1767 Dihedral : 4.271 18.105 1349 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer Outliers : 0.27 % 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: -0.83 (0.25), residues: 1242 helix: 0.53 (0.20), residues: 786 sheet: -0.82 (0.90), residues: 31 loop : -2.63 (0.28), residues: 425 =============================================================================== Job complete usr+sys time: 2345.70 seconds wall clock time: 43 minutes 3.90 seconds (2583.90 seconds total)