Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 5 14:02:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k10_22619/07_2023/7k10_22619.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k10_22619/07_2023/7k10_22619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k10_22619/07_2023/7k10_22619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k10_22619/07_2023/7k10_22619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k10_22619/07_2023/7k10_22619.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k10_22619/07_2023/7k10_22619.pdb" } resolution = 3.3 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 6396 2.51 5 N 1714 2.21 5 O 1870 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 ASP 2860": "OD1" <-> "OD2" Residue "A ARG 2899": "NH1" <-> "NH2" Residue "A PHE 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2983": "OD1" <-> "OD2" Residue "A GLU 2990": "OE1" <-> "OE2" Residue "A GLU 3007": "OE1" <-> "OE2" Residue "A ASP 3020": "OD1" <-> "OD2" Residue "A GLU 3022": "OE1" <-> "OE2" Residue "A ASP 3026": "OD1" <-> "OD2" Residue "A TYR 3040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3125": "NH1" <-> "NH2" Residue "A ARG 3159": "NH1" <-> "NH2" Residue "A GLU 3194": "OE1" <-> "OE2" Residue "A ARG 3232": "NH1" <-> "NH2" Residue "A ARG 3287": "NH1" <-> "NH2" Residue "A ARG 3289": "NH1" <-> "NH2" Residue "A ASP 3308": "OD1" <-> "OD2" Residue "A GLU 3309": "OE1" <-> "OE2" Residue "A ARG 3335": "NH1" <-> "NH2" Residue "A GLU 3371": "OE1" <-> "OE2" Residue "A GLU 3429": "OE1" <-> "OE2" Residue "A ARG 3462": "NH1" <-> "NH2" Residue "A ARG 3467": "NH1" <-> "NH2" Residue "A ARG 3474": "NH1" <-> "NH2" Residue "A TYR 3475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3509": "OD1" <-> "OD2" Residue "A GLU 3520": "OE1" <-> "OE2" Residue "A PHE 3542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3595": "OE1" <-> "OE2" Residue "A PHE 3628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3629": "NH1" <-> "NH2" Residue "A ARG 3630": "NH1" <-> "NH2" Residue "A GLU 3639": "OE1" <-> "OE2" Residue "A ARG 3653": "NH1" <-> "NH2" Residue "A ASP 3689": "OD1" <-> "OD2" Residue "A ARG 3696": "NH1" <-> "NH2" Residue "A ASP 3706": "OD1" <-> "OD2" Residue "A ARG 3708": "NH1" <-> "NH2" Residue "A GLU 3714": "OE1" <-> "OE2" Residue "A TYR 3715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3718": "NH1" <-> "NH2" Residue "A PHE 3722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3723": "OD1" <-> "OD2" Residue "A ARG 3733": "NH1" <-> "NH2" Residue "A ARG 3734": "NH1" <-> "NH2" Residue "A GLU 3745": "OE1" <-> "OE2" Residue "A PHE 3750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3756": "OE1" <-> "OE2" Residue "A ASP 3761": "OD1" <-> "OD2" Residue "A ARG 3799": "NH1" <-> "NH2" Residue "A ASP 3831": "OD1" <-> "OD2" Residue "A TYR 3855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3864": "NH1" <-> "NH2" Residue "A ARG 3874": "NH1" <-> "NH2" Residue "A ARG 3889": "NH1" <-> "NH2" Residue "A ARG 3923": "NH1" <-> "NH2" Residue "A GLU 3933": "OE1" <-> "OE2" Residue "A GLU 3957": "OE1" <-> "OE2" Residue "A PHE 3961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3962": "NH1" <-> "NH2" Residue "A ARG 3965": "NH1" <-> "NH2" Residue "A GLU 4030": "OE1" <-> "OE2" Residue "A ASP 4076": "OD1" <-> "OD2" 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: 10037 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1259, 10037 Classifications: {'peptide': 1259} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1205} Chain breaks: 5 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 60 Time building chain proxies: 5.02, per 1000 atoms: 0.50 Number of scatterers: 10037 At special positions: 0 Unit cell: (107.88, 96.28, 131.08, 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 1870 8.00 N 1714 7.00 C 6396 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: 4.14 Conformation dependent library (CDL) restraints added in 1.5 seconds 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 3 sheets defined 61.0% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 2801 through 2820 removed outlier: 3.796A pdb=" N SER A2814 " --> pdb=" O SER A2810 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2847 removed outlier: 3.896A pdb=" N ASN A2830 " --> pdb=" O LEU A2826 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN A2831 " --> pdb=" O SER A2827 " (cutoff:3.500A) Processing helix chain 'A' and resid 2851 through 2863 removed outlier: 4.295A pdb=" N CYS A2857 " --> pdb=" O PRO A2853 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A2858 " --> pdb=" O PHE A2854 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN A2859 " --> pdb=" O VAL A2855 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP A2860 " --> pdb=" O SER A2856 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A2861 " --> pdb=" O CYS A2857 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS A2863 " --> pdb=" O GLN A2859 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2884 removed outlier: 3.935A pdb=" N SER A2877 " --> pdb=" O PRO A2873 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A2878 " --> pdb=" O ALA A2874 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A2882 " --> pdb=" O ALA A2878 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2897 removed outlier: 3.793A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A2891 " --> pdb=" O PRO A2887 " (cutoff:3.500A) Processing helix chain 'A' and resid 2919 through 2932 removed outlier: 3.754A pdb=" N ALA A2927 " --> pdb=" O TRP A2923 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) Processing helix chain 'A' and resid 2953 through 2962 removed outlier: 3.826A pdb=" N ALA A2959 " --> pdb=" O SER A2955 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A2960 " --> pdb=" O ALA A2956 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2969 through 2977 removed outlier: 3.938A pdb=" N ASP A2973 " --> pdb=" O ALA A2969 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A2975 " --> pdb=" O GLN A2971 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN A2977 " --> pdb=" O ASP A2973 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3004 Processing helix chain 'A' and resid 3039 through 3053 removed outlier: 4.481A pdb=" N TYR A3043 " --> pdb=" O THR A3039 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A3044 " --> pdb=" O TYR A3040 " (cutoff:3.500A) Processing helix chain 'A' and resid 3061 through 3069 Processing helix chain 'A' and resid 3083 through 3093 removed outlier: 3.619A pdb=" N GLN A3093 " --> pdb=" O LEU A3089 " (cutoff:3.500A) Processing helix chain 'A' and resid 3096 through 3115 removed outlier: 3.646A pdb=" N TYR A3101 " --> pdb=" O ASP A3097 " (cutoff:3.500A) Processing helix chain 'A' and resid 3123 through 3130 Processing helix chain 'A' and resid 3131 through 3147 removed outlier: 3.927A pdb=" N LYS A3147 " --> pdb=" O SER A3143 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3165 removed outlier: 3.642A pdb=" N ARG A3159 " --> pdb=" O VAL A3155 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A3160 " --> pdb=" O PRO A3156 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A3165 " --> pdb=" O LEU A3161 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3197 removed outlier: 3.644A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU A3195 " --> pdb=" O SER A3191 " (cutoff:3.500A) Processing helix chain 'A' and resid 3231 through 3249 removed outlier: 4.064A pdb=" N SER A3237 " --> pdb=" O SER A3233 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A3241 " --> pdb=" O SER A3237 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET A3242 " --> pdb=" O MET A3238 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A3248 " --> pdb=" O ASP A3244 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN A3249 " --> pdb=" O SER A3245 " (cutoff:3.500A) Processing helix chain 'A' and resid 3251 through 3262 removed outlier: 4.081A pdb=" N LYS A3257 " --> pdb=" O SER A3253 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A3258 " --> pdb=" O LEU A3254 " (cutoff:3.500A) Processing helix chain 'A' and resid 3272 through 3288 Processing helix chain 'A' and resid 3295 through 3303 removed outlier: 3.701A pdb=" N VAL A3300 " --> pdb=" O GLN A3296 " (cutoff:3.500A) Processing helix chain 'A' and resid 3320 through 3341 removed outlier: 4.013A pdb=" N GLN A3326 " --> pdb=" O ALA A3322 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A3327 " --> pdb=" O PHE A3323 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A3332 " --> pdb=" O ILE A3328 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A3334 " --> pdb=" O LEU A3330 " (cutoff:3.500A) Processing helix chain 'A' and resid 3344 through 3349 removed outlier: 4.075A pdb=" N LEU A3348 " --> pdb=" O GLU A3344 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A3349 " --> pdb=" O PRO A3345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3344 through 3349' Processing helix chain 'A' and resid 3354 through 3361 Processing helix chain 'A' and resid 3371 through 3391 removed outlier: 4.563A pdb=" N LEU A3377 " --> pdb=" O VAL A3373 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS A3384 " --> pdb=" O ARG A3380 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA A3388 " --> pdb=" O HIS A3384 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL A3389 " --> pdb=" O LEU A3385 " (cutoff:3.500A) Processing helix chain 'A' and resid 3409 through 3429 removed outlier: 3.890A pdb=" N LEU A3416 " --> pdb=" O ALA A3412 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU A3429 " --> pdb=" O ARG A3425 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 4.074A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A3448 " --> pdb=" O ALA A3444 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A3449 " --> pdb=" O LEU A3445 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A3453 " --> pdb=" O LYS A3449 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) Processing helix chain 'A' and resid 3464 through 3475 removed outlier: 3.971A pdb=" N LEU A3468 " --> pdb=" O LYS A3464 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) Processing helix chain 'A' and resid 3479 through 3488 removed outlier: 3.982A pdb=" N THR A3484 " --> pdb=" O LEU A3480 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS A3485 " --> pdb=" O SER A3481 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A3486 " --> pdb=" O LEU A3482 " (cutoff:3.500A) Processing helix chain 'A' and resid 3498 through 3503 Processing helix chain 'A' and resid 3514 through 3525 Processing helix chain 'A' and resid 3530 through 3538 removed outlier: 3.632A pdb=" N ILE A3534 " --> pdb=" O VAL A3530 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE A3535 " --> pdb=" O TYR A3531 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A3536 " --> pdb=" O PRO A3532 " (cutoff:3.500A) Processing helix chain 'A' and resid 3545 through 3562 removed outlier: 3.605A pdb=" N LYS A3550 " --> pdb=" O SER A3546 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A3552 " --> pdb=" O GLY A3548 " (cutoff:3.500A) Processing helix chain 'A' and resid 3568 through 3577 Processing helix chain 'A' and resid 3580 through 3594 removed outlier: 4.323A pdb=" N LEU A3584 " --> pdb=" O ASN A3580 " (cutoff:3.500A) Processing helix chain 'A' and resid 3604 through 3616 removed outlier: 4.173A pdb=" N GLU A3611 " --> pdb=" O GLU A3607 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET A3613 " --> pdb=" O MET A3609 " (cutoff:3.500A) Processing helix chain 'A' and resid 3621 through 3627 removed outlier: 3.810A pdb=" N GLY A3626 " --> pdb=" O ALA A3622 " (cutoff:3.500A) Processing helix chain 'A' and resid 3632 through 3637 Processing helix chain 'A' and resid 3644 through 3651 Processing helix chain 'A' and resid 3660 through 3670 removed outlier: 3.636A pdb=" N LEU A3666 " --> pdb=" O ILE A3662 " (cutoff:3.500A) Processing helix chain 'A' and resid 3680 through 3684 removed outlier: 4.048A pdb=" N CYS A3683 " --> pdb=" O LEU A3680 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A3684 " --> pdb=" O LYS A3681 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3680 through 3684' Processing helix chain 'A' and resid 3758 through 3776 removed outlier: 3.758A pdb=" N GLN A3762 " --> pdb=" O LEU A3758 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A3776 " --> pdb=" O ASN A3772 " (cutoff:3.500A) Processing helix chain 'A' and resid 3778 through 3783 removed outlier: 3.532A pdb=" N GLN A3783 " --> pdb=" O SER A3779 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3820 removed outlier: 4.032A pdb=" N MET A3820 " --> pdb=" O LEU A3816 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3830 removed outlier: 3.635A pdb=" N ALA A3826 " --> pdb=" O GLN A3822 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A3827 " --> pdb=" O GLU A3823 " (cutoff:3.500A) Processing helix chain 'A' and resid 3834 through 3848 removed outlier: 3.612A pdb=" N TYR A3839 " --> pdb=" O PRO A3835 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3860 removed outlier: 3.848A pdb=" N TYR A3859 " --> pdb=" O TYR A3855 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3876 removed outlier: 3.751A pdb=" N THR A3867 " --> pdb=" O ASN A3863 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A3868 " --> pdb=" O ARG A3864 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N THR A3869 " --> pdb=" O THR A3865 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A3873 " --> pdb=" O THR A3869 " (cutoff:3.500A) Processing helix chain 'A' and resid 3882 through 3889 Processing helix chain 'A' and resid 3893 through 3918 removed outlier: 3.971A pdb=" N LEU A3898 " --> pdb=" O PRO A3894 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER A3902 " --> pdb=" O LEU A3898 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP A3916 " --> pdb=" O CYS A3912 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A3917 " --> pdb=" O ILE A3913 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU A3918 " --> pdb=" O SER A3914 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3970 removed outlier: 3.625A pdb=" N ILE A3968 " --> pdb=" O THR A3964 " (cutoff:3.500A) Processing helix chain 'A' and resid 3978 through 3992 removed outlier: 3.832A pdb=" N SER A3982 " --> pdb=" O GLY A3978 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A3983 " --> pdb=" O LEU A3979 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N MET A3984 " --> pdb=" O MET A3980 " (cutoff:3.500A) Processing helix chain 'A' and resid 3995 through 4002 removed outlier: 4.252A pdb=" N THR A3999 " --> pdb=" O PRO A3995 " (cutoff:3.500A) Processing helix chain 'A' and resid 4003 through 4008 Processing helix chain 'A' and resid 4010 through 4014 Processing helix chain 'A' and resid 4016 through 4023 Processing helix chain 'A' and resid 4038 through 4052 removed outlier: 3.535A pdb=" N GLN A4042 " --> pdb=" O TRP A4038 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4069 removed outlier: 3.845A pdb=" N THR A4060 " --> pdb=" O PRO A4056 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A4067 " --> pdb=" O GLU A4063 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A4069 " --> pdb=" O LEU A4065 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4081 Processing helix chain 'A' and resid 4088 through 4092 removed outlier: 3.712A pdb=" N ALA A4091 " --> pdb=" O ASN A4088 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4112 removed outlier: 3.594A pdb=" N THR A4112 " --> pdb=" O MET A4108 " (cutoff:3.500A) Processing helix chain 'A' and resid 4113 through 4118 Processing sheet with id=AA1, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 3.802A pdb=" N GLY A3721 " --> pdb=" O ARG A3741 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 3.802A pdb=" N GLY A3721 " --> pdb=" O ARG A3741 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY A3801 " --> pdb=" O LYS A3753 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3809 through 3811 437 hydrogen bonds defined for protein. 1296 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: 3.10 Time building geometry restraints manager: 4.51 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: 3195 1.34 - 1.46: 2035 1.46 - 1.58: 4922 1.58 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 10246 Sorted by residual: bond pdb=" CB ASP A3563 " pdb=" CG ASP A3563 " ideal model delta sigma weight residual 1.516 1.572 -0.056 2.50e-02 1.60e+03 4.95e+00 bond pdb=" C LEU A3041 " pdb=" N PRO A3042 " ideal model delta sigma weight residual 1.335 1.364 -0.028 1.36e-02 5.41e+03 4.29e+00 bond pdb=" C TYR A4039 " pdb=" N PRO A4040 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.01e+00 bond pdb=" C ILE A3701 " pdb=" N PRO A3702 " ideal model delta sigma weight residual 1.326 1.354 -0.028 1.44e-02 4.82e+03 3.74e+00 bond pdb=" CA ASP A3563 " pdb=" CB ASP A3563 " ideal model delta sigma weight residual 1.530 1.562 -0.032 1.69e-02 3.50e+03 3.52e+00 ... (remaining 10241 not shown) Histogram of bond angle deviations from ideal: 97.20 - 104.72: 178 104.72 - 112.24: 4839 112.24 - 119.76: 4139 119.76 - 127.28: 4564 127.28 - 134.80: 124 Bond angle restraints: 13844 Sorted by residual: angle pdb=" C LEU A3562 " pdb=" N ASP A3563 " pdb=" CA ASP A3563 " ideal model delta sigma weight residual 121.54 132.05 -10.51 1.91e+00 2.74e-01 3.03e+01 angle pdb=" C SER A3891 " pdb=" N THR A3892 " pdb=" CA THR A3892 " ideal model delta sigma weight residual 121.54 131.02 -9.48 1.91e+00 2.74e-01 2.46e+01 angle pdb=" C HIS A3122 " pdb=" N GLN A3123 " pdb=" CA GLN A3123 " ideal model delta sigma weight residual 121.54 130.34 -8.80 1.91e+00 2.74e-01 2.12e+01 angle pdb=" C GLY A3678 " pdb=" N ASN A3679 " pdb=" CA ASN A3679 " ideal model delta sigma weight residual 121.54 130.06 -8.52 1.91e+00 2.74e-01 1.99e+01 angle pdb=" C GLU A3807 " pdb=" N ASN A3808 " pdb=" CA ASN A3808 " ideal model delta sigma weight residual 122.61 129.38 -6.77 1.56e+00 4.11e-01 1.88e+01 ... (remaining 13839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5487 17.93 - 35.86: 639 35.86 - 53.79: 97 53.79 - 71.72: 16 71.72 - 89.65: 12 Dihedral angle restraints: 6251 sinusoidal: 2552 harmonic: 3699 Sorted by residual: dihedral pdb=" CA GLU A3698 " pdb=" C GLU A3698 " pdb=" N LEU A3699 " pdb=" CA LEU A3699 " ideal model delta harmonic sigma weight residual 180.00 -145.36 -34.64 0 5.00e+00 4.00e-02 4.80e+01 dihedral pdb=" CA LEU A3699 " pdb=" C LEU A3699 " pdb=" N GLU A3700 " pdb=" CA GLU A3700 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA LEU A3918 " pdb=" C LEU A3918 " pdb=" N GLY A3919 " pdb=" CA GLY A3919 " ideal model delta harmonic sigma weight residual -180.00 -153.51 -26.49 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 6248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1164 0.059 - 0.117: 307 0.117 - 0.176: 53 0.176 - 0.235: 6 0.235 - 0.293: 3 Chirality restraints: 1533 Sorted by residual: chirality pdb=" CB ILE A3701 " pdb=" CA ILE A3701 " pdb=" CG1 ILE A3701 " pdb=" CG2 ILE A3701 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ASN A3808 " pdb=" N ASN A3808 " pdb=" C ASN A3808 " pdb=" CB ASN A3808 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ASP A3563 " pdb=" N ASP A3563 " pdb=" C ASP A3563 " pdb=" CB ASP A3563 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1530 not shown) Planarity restraints: 1774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A3835 " 0.057 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO A3836 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO A3836 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A3836 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A3083 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C SER A3083 " 0.058 2.00e-02 2.50e+03 pdb=" O SER A3083 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN A3084 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A3676 " -0.051 5.00e-02 4.00e+02 7.56e-02 9.15e+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 " -0.043 5.00e-02 4.00e+02 ... (remaining 1771 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2996 2.82 - 3.34: 8778 3.34 - 3.86: 15246 3.86 - 4.38: 17624 4.38 - 4.90: 31241 Nonbonded interactions: 75885 Sorted by model distance: nonbonded pdb=" OH TYR A3855 " pdb=" OE1 GLU A4122 " model vdw 2.300 2.440 nonbonded pdb=" O TYR A3043 " pdb=" OG SER A3047 " model vdw 2.304 2.440 nonbonded pdb=" O SER A3657 " pdb=" OG SER A3657 " model vdw 2.315 2.440 nonbonded pdb=" O SER A3228 " pdb=" OG SER A3228 " model vdw 2.316 2.440 nonbonded pdb=" O LEU A3011 " pdb=" OG SER A3015 " model vdw 2.316 2.440 ... (remaining 75880 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: 4.260 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: 9.540 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.210 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: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 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 : 0.006 0.085 10246 Z= 0.375 Angle : 0.978 13.419 13844 Z= 0.522 Chirality : 0.055 0.293 1533 Planarity : 0.007 0.085 1774 Dihedral : 15.434 89.646 3843 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.59 % Favored : 89.33 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -5.28 (0.17), residues: 1247 helix: -3.20 (0.13), residues: 763 sheet: -1.30 (0.78), residues: 39 loop : -4.03 (0.22), residues: 445 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 1.260 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 153 average time/residue: 0.2605 time to fit residues: 54.6723 Evaluate side-chains 120 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0892 time to fit residues: 1.7838 ------------------------------------------------------------------------------- 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: 0.5980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 50 optimal weight: 0.0040 chunk 97 optimal weight: 0.0970 chunk 37 optimal weight: 0.2980 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2886 GLN A2971 GLN A3113 ASN A3459 ASN A3590 ASN A3605 ASN A3743 HIS A3760 GLN A3787 GLN A3924 HIS A3969 ASN A4088 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10246 Z= 0.169 Angle : 0.616 9.164 13844 Z= 0.314 Chirality : 0.040 0.199 1533 Planarity : 0.005 0.061 1774 Dihedral : 5.303 28.368 1353 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.66 % Favored : 91.26 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -3.68 (0.21), residues: 1247 helix: -1.78 (0.17), residues: 769 sheet: -0.94 (0.80), residues: 37 loop : -3.65 (0.24), residues: 441 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 148 average time/residue: 0.2290 time to fit residues: 48.0869 Evaluate side-chains 125 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.155 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0983 time to fit residues: 3.0716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.2812 > 50: distance: 53 - 59: 27.921 distance: 59 - 60: 37.648 distance: 60 - 61: 7.341 distance: 60 - 63: 13.027 distance: 61 - 62: 18.210 distance: 61 - 67: 19.683 distance: 62 - 83: 7.925 distance: 63 - 64: 13.481 distance: 63 - 65: 20.329 distance: 64 - 66: 12.242 distance: 67 - 68: 16.723 distance: 68 - 69: 23.589 distance: 68 - 71: 15.541 distance: 69 - 70: 44.743 distance: 69 - 78: 23.966 distance: 71 - 72: 27.021 distance: 72 - 73: 13.381 distance: 73 - 74: 18.398 distance: 74 - 75: 32.801 distance: 75 - 76: 21.006 distance: 75 - 77: 30.852 distance: 78 - 79: 26.867 distance: 79 - 80: 28.932 distance: 79 - 82: 50.731 distance: 80 - 81: 30.629 distance: 80 - 83: 27.543 distance: 83 - 84: 8.597 distance: 84 - 85: 14.810 distance: 84 - 87: 38.022 distance: 85 - 86: 22.863 distance: 85 - 92: 32.217 distance: 87 - 88: 44.928 distance: 88 - 89: 21.627 distance: 89 - 90: 11.995 distance: 89 - 91: 3.093 distance: 92 - 93: 14.033 distance: 93 - 94: 19.469 distance: 93 - 96: 9.912 distance: 94 - 95: 9.477 distance: 94 - 101: 12.656 distance: 96 - 97: 17.845 distance: 97 - 98: 17.917 distance: 98 - 99: 6.832 distance: 98 - 100: 5.811 distance: 101 - 102: 19.021 distance: 101 - 107: 22.221 distance: 102 - 103: 16.206 distance: 102 - 105: 27.118 distance: 103 - 104: 4.421 distance: 103 - 108: 5.628 distance: 105 - 106: 8.294 distance: 106 - 107: 37.810 distance: 108 - 109: 19.306 distance: 109 - 110: 14.652 distance: 109 - 112: 31.193 distance: 110 - 111: 4.916 distance: 110 - 117: 30.041 distance: 112 - 113: 13.453 distance: 113 - 114: 14.435 distance: 114 - 115: 11.968 distance: 114 - 116: 8.710 distance: 117 - 118: 18.803 distance: 118 - 119: 18.807 distance: 118 - 121: 10.750 distance: 119 - 120: 17.097 distance: 119 - 123: 25.192 distance: 121 - 122: 7.631 distance: 123 - 124: 19.165 distance: 124 - 125: 41.276 distance: 125 - 126: 31.422 distance: 125 - 127: 31.426 distance: 127 - 128: 26.262 distance: 128 - 129: 50.910 distance: 129 - 130: 13.373 distance: 129 - 135: 27.191 distance: 131 - 132: 43.251 distance: 132 - 133: 26.211 distance: 132 - 134: 43.607