Starting phenix.real_space_refine on Sat Sep 28 04:01:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1t_14452/09_2024/7z1t_14452.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1t_14452/09_2024/7z1t_14452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1t_14452/09_2024/7z1t_14452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1t_14452/09_2024/7z1t_14452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1t_14452/09_2024/7z1t_14452.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1t_14452/09_2024/7z1t_14452.cif" } resolution = 2.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 96 5.16 5 C 12396 2.51 5 N 2892 2.21 5 O 3108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18492 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 6.28, per 1000 atoms: 0.34 Number of scatterers: 18492 At special positions: 0 Unit cell: (100.062, 98.754, 158.922, 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 96 16.00 O 3108 8.00 N 2892 7.00 C 12396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.69 Conformation dependent library (CDL) restraints added in 2.2 seconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 75.7% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 105 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 152 through 177 Processing helix chain 'A' and resid 202 through 235 Processing helix chain 'B' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 105 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 152 through 177 Processing helix chain 'B' and resid 202 through 235 Processing helix chain 'C' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 105 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 152 through 177 Processing helix chain 'C' and resid 202 through 235 Processing helix chain 'D' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU D 7 " --> pdb=" O ASP D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 43 " --> pdb=" O THR D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 105 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 152 through 177 Processing helix chain 'D' and resid 202 through 235 Processing helix chain 'E' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 45 removed outlier: 4.391A pdb=" N VAL E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU E 42 " --> pdb=" O GLY E 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER E 43 " --> pdb=" O THR E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 105 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 152 through 177 Processing helix chain 'E' and resid 202 through 235 Processing helix chain 'F' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU F 42 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER F 43 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 105 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 152 through 177 Processing helix chain 'F' and resid 202 through 235 Processing helix chain 'G' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU G 42 " --> pdb=" O GLY G 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER G 43 " --> pdb=" O THR G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 73 through 105 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 152 through 177 Processing helix chain 'G' and resid 202 through 235 Processing helix chain 'H' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU H 7 " --> pdb=" O ASP H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL H 41 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU H 42 " --> pdb=" O GLY H 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER H 43 " --> pdb=" O THR H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 73 through 105 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 152 through 177 Processing helix chain 'H' and resid 202 through 235 Processing helix chain 'I' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU I 7 " --> pdb=" O ASP I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU I 42 " --> pdb=" O GLY I 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER I 43 " --> pdb=" O THR I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 70 Processing helix chain 'I' and resid 73 through 105 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 152 through 177 Processing helix chain 'I' and resid 202 through 235 Processing helix chain 'J' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU J 7 " --> pdb=" O ASP J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL J 41 " --> pdb=" O LEU J 37 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU J 42 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER J 43 " --> pdb=" O THR J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 73 through 105 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 152 through 177 Processing helix chain 'J' and resid 202 through 235 Processing helix chain 'K' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU K 7 " --> pdb=" O ASP K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL K 41 " --> pdb=" O LEU K 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU K 42 " --> pdb=" O GLY K 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER K 43 " --> pdb=" O THR K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 70 Processing helix chain 'K' and resid 73 through 105 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 152 through 177 Processing helix chain 'K' and resid 202 through 235 Processing helix chain 'L' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU L 7 " --> pdb=" O ASP L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL L 41 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU L 42 " --> pdb=" O GLY L 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER L 43 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 70 Processing helix chain 'L' and resid 73 through 105 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 152 through 177 Processing helix chain 'L' and resid 202 through 235 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 1416 hydrogen bonds defined for protein. 4176 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: 5.38 Time building geometry restraints manager: 5.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5391 1.34 - 1.46: 4689 1.46 - 1.58: 8808 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 19008 Sorted by residual: bond pdb=" C ASP G 190 " pdb=" N PRO G 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.76e+00 bond pdb=" C ASP A 190 " pdb=" N PRO A 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.76e+00 bond pdb=" C ASP E 190 " pdb=" N PRO E 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.69e+00 bond pdb=" C ASP K 190 " pdb=" N PRO K 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.69e+00 bond pdb=" C ASP B 190 " pdb=" N PRO B 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.69e+00 ... (remaining 19003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 24699 1.16 - 2.32: 879 2.32 - 3.48: 132 3.48 - 4.64: 54 4.64 - 5.80: 36 Bond angle restraints: 25800 Sorted by residual: angle pdb=" C VAL C 87 " pdb=" CA VAL C 87 " pdb=" CB VAL C 87 " ideal model delta sigma weight residual 113.70 110.61 3.09 9.50e-01 1.11e+00 1.05e+01 angle pdb=" C VAL I 87 " pdb=" CA VAL I 87 " pdb=" CB VAL I 87 " ideal model delta sigma weight residual 113.70 110.61 3.09 9.50e-01 1.11e+00 1.05e+01 angle pdb=" C VAL F 87 " pdb=" CA VAL F 87 " pdb=" CB VAL F 87 " ideal model delta sigma weight residual 113.70 110.61 3.09 9.50e-01 1.11e+00 1.05e+01 angle pdb=" C VAL L 87 " pdb=" CA VAL L 87 " pdb=" CB VAL L 87 " ideal model delta sigma weight residual 113.70 110.61 3.09 9.50e-01 1.11e+00 1.05e+01 angle pdb=" C VAL B 87 " pdb=" CA VAL B 87 " pdb=" CB VAL B 87 " ideal model delta sigma weight residual 113.70 110.62 3.08 9.50e-01 1.11e+00 1.05e+01 ... (remaining 25795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 9784 17.21 - 34.42: 918 34.42 - 51.63: 227 51.63 - 68.83: 12 68.83 - 86.04: 24 Dihedral angle restraints: 10965 sinusoidal: 4293 harmonic: 6672 Sorted by residual: dihedral pdb=" CA TYR E 177 " pdb=" C TYR E 177 " pdb=" N GLY E 178 " pdb=" CA GLY E 178 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA TYR D 177 " pdb=" C TYR D 177 " pdb=" N GLY D 178 " pdb=" CA GLY D 178 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA TYR A 177 " pdb=" C TYR A 177 " pdb=" N GLY A 178 " pdb=" CA GLY A 178 " ideal model delta harmonic sigma weight residual 180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 10962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1976 0.027 - 0.054: 598 0.054 - 0.080: 275 0.080 - 0.107: 79 0.107 - 0.134: 24 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CA ARG D 202 " pdb=" N ARG D 202 " pdb=" C ARG D 202 " pdb=" CB ARG D 202 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ARG H 202 " pdb=" N ARG H 202 " pdb=" C ARG H 202 " pdb=" CB ARG H 202 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ARG J 202 " pdb=" N ARG J 202 " pdb=" C ARG J 202 " pdb=" CB ARG J 202 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 2949 not shown) Planarity restraints: 3096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU K 205 " 0.004 2.00e-02 2.50e+03 9.14e-03 8.36e-01 pdb=" CD GLU K 205 " -0.016 2.00e-02 2.50e+03 pdb=" OE1 GLU K 205 " 0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU K 205 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 205 " -0.004 2.00e-02 2.50e+03 9.12e-03 8.31e-01 pdb=" CD GLU H 205 " 0.016 2.00e-02 2.50e+03 pdb=" OE1 GLU H 205 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU H 205 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 205 " -0.004 2.00e-02 2.50e+03 9.06e-03 8.20e-01 pdb=" CD GLU B 205 " 0.016 2.00e-02 2.50e+03 pdb=" OE1 GLU B 205 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU B 205 " -0.006 2.00e-02 2.50e+03 ... (remaining 3093 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 57 2.61 - 3.18: 15675 3.18 - 3.75: 30774 3.75 - 4.33: 38935 4.33 - 4.90: 64325 Nonbonded interactions: 149766 Sorted by model distance: nonbonded pdb=" SG CYS J 65 " pdb=" SG CYS J 187 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS E 65 " pdb=" SG CYS E 187 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS F 65 " pdb=" SG CYS F 187 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS I 65 " pdb=" SG CYS I 187 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS C 65 " pdb=" SG CYS C 187 " model vdw 2.032 3.760 ... (remaining 149761 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 2.400 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 35.050 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 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:11.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.003 0.025 19008 Z= 0.177 Angle : 0.552 5.799 25800 Z= 0.307 Chirality : 0.034 0.134 2952 Planarity : 0.003 0.019 3096 Dihedral : 15.039 86.044 6636 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.17), residues: 2220 helix: 3.20 (0.11), residues: 1680 sheet: -0.64 (0.35), residues: 204 loop : -2.06 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 78 HIS 0.002 0.000 HIS G 74 PHE 0.012 0.001 PHE K 32 TYR 0.010 0.002 TYR A 66 ARG 0.003 0.000 ARG K 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 2.397 Fit side-chains outliers start: 0 outliers final: 6 residues processed: 372 average time/residue: 1.3367 time to fit residues: 553.2856 Evaluate side-chains 329 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 323 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain L residue 12 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 1.9990 chunk 163 optimal weight: 0.0870 chunk 90 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 169 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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: 0.8277 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 19008 Z= 0.170 Angle : 0.515 6.196 25800 Z= 0.261 Chirality : 0.035 0.109 2952 Planarity : 0.003 0.017 3096 Dihedral : 3.864 40.385 2448 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.09 % Allowed : 16.08 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.17), residues: 2220 helix: 3.37 (0.11), residues: 1692 sheet: -0.41 (0.36), residues: 204 loop : -2.30 (0.26), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 4 HIS 0.001 0.000 HIS E 74 PHE 0.014 0.001 PHE F 32 TYR 0.019 0.001 TYR B 98 ARG 0.002 0.000 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 346 time to evaluate : 2.058 Fit side-chains REVERT: A 4 TRP cc_start: 0.7126 (OUTLIER) cc_final: 0.5340 (t-100) REVERT: C 4 TRP cc_start: 0.7162 (OUTLIER) cc_final: 0.6026 (t-100) REVERT: D 4 TRP cc_start: 0.7120 (OUTLIER) cc_final: 0.5336 (t-100) REVERT: D 101 ARG cc_start: 0.8005 (mmm160) cc_final: 0.7801 (mtt90) REVERT: F 4 TRP cc_start: 0.7133 (OUTLIER) cc_final: 0.6012 (t-100) REVERT: G 4 TRP cc_start: 0.7125 (OUTLIER) cc_final: 0.5339 (t-100) REVERT: I 4 TRP cc_start: 0.7176 (OUTLIER) cc_final: 0.6047 (t-100) REVERT: J 4 TRP cc_start: 0.7117 (OUTLIER) cc_final: 0.5326 (t-100) REVERT: J 101 ARG cc_start: 0.8017 (mmm160) cc_final: 0.7814 (mtt90) REVERT: L 4 TRP cc_start: 0.7136 (OUTLIER) cc_final: 0.6006 (t-100) outliers start: 63 outliers final: 26 residues processed: 393 average time/residue: 1.4817 time to fit residues: 645.0390 Evaluate side-chains 342 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 308 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TRP Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 4 TRP Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 4 TRP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 4 TRP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 4 TRP Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 4 TRP Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain L residue 4 TRP Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 163 optimal weight: 0.0670 chunk 133 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 chunk 175 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN C 49 GLN E 49 GLN F 49 GLN H 49 GLN I 49 GLN K 49 GLN L 49 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 19008 Z= 0.179 Angle : 0.468 5.124 25800 Z= 0.239 Chirality : 0.035 0.107 2952 Planarity : 0.003 0.017 3096 Dihedral : 3.303 17.739 2436 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.60 % Allowed : 17.94 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.17), residues: 2220 helix: 3.40 (0.11), residues: 1692 sheet: -0.23 (0.36), residues: 204 loop : -2.28 (0.27), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 4 HIS 0.001 0.001 HIS G 74 PHE 0.013 0.001 PHE I 32 TYR 0.017 0.001 TYR B 98 ARG 0.005 0.001 ARG L 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 308 time to evaluate : 2.691 Fit side-chains outliers start: 53 outliers final: 26 residues processed: 355 average time/residue: 1.3830 time to fit residues: 547.3079 Evaluate side-chains 326 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 300 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 197 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.8350 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 19008 Z= 0.229 Angle : 0.498 6.534 25800 Z= 0.253 Chirality : 0.036 0.114 2952 Planarity : 0.003 0.019 3096 Dihedral : 3.386 18.950 2436 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 4.36 % Allowed : 15.25 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.17), residues: 2220 helix: 3.43 (0.11), residues: 1692 sheet: -0.17 (0.37), residues: 204 loop : -2.16 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 4 HIS 0.002 0.001 HIS H 74 PHE 0.015 0.002 PHE D 32 TYR 0.017 0.001 TYR E 98 ARG 0.003 0.001 ARG L 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 324 time to evaluate : 2.222 Fit side-chains REVERT: B 98 TYR cc_start: 0.8688 (m-80) cc_final: 0.8479 (m-80) REVERT: E 7 LEU cc_start: 0.9016 (mp) cc_final: 0.8815 (tp) REVERT: E 98 TYR cc_start: 0.8682 (m-80) cc_final: 0.8473 (m-80) REVERT: F 13 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8823 (tptp) REVERT: H 98 TYR cc_start: 0.8688 (m-80) cc_final: 0.8476 (m-80) REVERT: K 7 LEU cc_start: 0.9023 (mp) cc_final: 0.8820 (tp) REVERT: K 98 TYR cc_start: 0.8683 (m-80) cc_final: 0.8476 (m-80) outliers start: 89 outliers final: 42 residues processed: 400 average time/residue: 1.3201 time to fit residues: 589.6430 Evaluate side-chains 356 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 313 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 178 optimal weight: 0.5980 chunk 144 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 106 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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: 0.8345 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 19008 Z= 0.213 Angle : 0.477 6.189 25800 Z= 0.243 Chirality : 0.035 0.118 2952 Planarity : 0.003 0.019 3096 Dihedral : 3.407 18.577 2436 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.33 % Allowed : 16.47 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.17), residues: 2220 helix: 3.50 (0.11), residues: 1692 sheet: -0.21 (0.37), residues: 204 loop : -1.99 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 174 HIS 0.002 0.000 HIS H 74 PHE 0.021 0.002 PHE J 232 TYR 0.016 0.001 TYR B 98 ARG 0.003 0.000 ARG L 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 312 time to evaluate : 2.301 Fit side-chains REVERT: B 98 TYR cc_start: 0.8690 (m-80) cc_final: 0.8466 (m-80) REVERT: E 98 TYR cc_start: 0.8695 (m-80) cc_final: 0.8471 (m-80) REVERT: F 13 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8812 (tptp) REVERT: H 98 TYR cc_start: 0.8704 (m-80) cc_final: 0.8479 (m-80) REVERT: K 98 TYR cc_start: 0.8699 (m-80) cc_final: 0.8474 (m-80) outliers start: 68 outliers final: 44 residues processed: 367 average time/residue: 1.3726 time to fit residues: 561.5518 Evaluate side-chains 354 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 309 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.9990 chunk 188 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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: 0.8358 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 19008 Z= 0.239 Angle : 0.493 6.463 25800 Z= 0.251 Chirality : 0.036 0.116 2952 Planarity : 0.003 0.019 3096 Dihedral : 3.416 18.758 2436 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.58 % Allowed : 16.52 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.17), residues: 2220 helix: 3.46 (0.11), residues: 1692 sheet: -0.20 (0.37), residues: 204 loop : -2.01 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 174 HIS 0.002 0.000 HIS I 74 PHE 0.025 0.002 PHE H 232 TYR 0.016 0.001 TYR K 98 ARG 0.003 0.000 ARG F 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 308 time to evaluate : 2.355 Fit side-chains REVERT: A 7 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8897 (tp) REVERT: D 7 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8895 (tp) REVERT: F 13 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8793 (tptp) REVERT: G 7 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8900 (tp) REVERT: J 7 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8894 (tp) outliers start: 73 outliers final: 50 residues processed: 364 average time/residue: 1.3938 time to fit residues: 567.0892 Evaluate side-chains 359 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 304 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 5.9990 chunk 23 optimal weight: 0.0270 chunk 119 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 overall best weight: 1.2842 ------------------------------------------------------------------------------- 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: 0.8318 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19008 Z= 0.159 Angle : 0.451 6.586 25800 Z= 0.227 Chirality : 0.034 0.105 2952 Planarity : 0.002 0.017 3096 Dihedral : 3.278 17.842 2436 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.16 % Allowed : 18.14 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.82 (0.17), residues: 2220 helix: 3.60 (0.11), residues: 1692 sheet: -0.18 (0.36), residues: 204 loop : -2.04 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 174 HIS 0.001 0.000 HIS H 74 PHE 0.011 0.001 PHE J 32 TYR 0.010 0.001 TYR E 98 ARG 0.005 0.000 ARG C 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 317 time to evaluate : 2.355 Fit side-chains REVERT: F 13 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8797 (tptp) outliers start: 44 outliers final: 34 residues processed: 349 average time/residue: 1.3980 time to fit residues: 546.0979 Evaluate side-chains 340 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 305 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 160 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 13 LYS Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 160 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 141 optimal weight: 0.2980 chunk 102 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 163 optimal weight: 0.9990 chunk 189 optimal weight: 0.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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: 0.8294 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19008 Z= 0.130 Angle : 0.439 6.167 25800 Z= 0.221 Chirality : 0.033 0.099 2952 Planarity : 0.002 0.018 3096 Dihedral : 3.196 16.894 2436 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.96 % Allowed : 18.04 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.82 (0.17), residues: 2220 helix: 3.60 (0.11), residues: 1692 sheet: -0.22 (0.35), residues: 204 loop : -2.05 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 174 HIS 0.001 0.000 HIS K 74 PHE 0.011 0.001 PHE G 32 TYR 0.013 0.001 TYR B 98 ARG 0.004 0.000 ARG C 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 322 time to evaluate : 2.147 Fit side-chains outliers start: 40 outliers final: 30 residues processed: 354 average time/residue: 1.3532 time to fit residues: 533.7235 Evaluate side-chains 340 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 310 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 24 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 10.0000 chunk 181 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 175 optimal weight: 0.0020 chunk 183 optimal weight: 10.0000 chunk 193 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN D 49 GLN G 49 GLN H 49 GLN J 49 GLN K 49 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 19008 Z= 0.120 Angle : 0.423 5.345 25800 Z= 0.211 Chirality : 0.033 0.099 2952 Planarity : 0.002 0.018 3096 Dihedral : 3.105 16.032 2436 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.67 % Allowed : 18.04 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.17), residues: 2220 helix: 3.64 (0.11), residues: 1692 sheet: -0.18 (0.35), residues: 204 loop : -2.11 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 45 HIS 0.001 0.000 HIS H 74 PHE 0.010 0.001 PHE G 32 TYR 0.012 0.001 TYR E 98 ARG 0.004 0.000 ARG C 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 328 time to evaluate : 2.230 Fit side-chains outliers start: 34 outliers final: 28 residues processed: 357 average time/residue: 1.3861 time to fit residues: 549.1435 Evaluate side-chains 340 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 312 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 171 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 81 GLN H 49 GLN K 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 19008 Z= 0.199 Angle : 0.471 6.248 25800 Z= 0.237 Chirality : 0.034 0.109 2952 Planarity : 0.003 0.020 3096 Dihedral : 3.255 17.704 2436 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.52 % Allowed : 18.63 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.17), residues: 2220 helix: 3.58 (0.11), residues: 1692 sheet: -0.12 (0.35), residues: 204 loop : -2.04 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 45 HIS 0.001 0.000 HIS A 74 PHE 0.012 0.001 PHE D 32 TYR 0.013 0.001 TYR E 98 ARG 0.004 0.000 ARG C 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 328 time to evaluate : 2.337 Fit side-chains REVERT: F 13 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8770 (tptp) outliers start: 31 outliers final: 29 residues processed: 357 average time/residue: 1.4265 time to fit residues: 562.8883 Evaluate side-chains 353 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 323 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 158 optimal weight: 0.0060 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 171 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 176 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.096844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.067568 restraints weight = 28925.702| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.65 r_work: 0.2752 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 19008 Z= 0.221 Angle : 0.481 6.440 25800 Z= 0.244 Chirality : 0.035 0.113 2952 Planarity : 0.003 0.018 3096 Dihedral : 3.343 18.419 2436 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.67 % Allowed : 18.19 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.17), residues: 2220 helix: 3.54 (0.11), residues: 1692 sheet: -0.18 (0.36), residues: 204 loop : -1.99 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 4 HIS 0.001 0.000 HIS A 74 PHE 0.013 0.001 PHE D 32 TYR 0.012 0.001 TYR D 155 ARG 0.004 0.001 ARG A 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8710.71 seconds wall clock time: 153 minutes 30.44 seconds (9210.44 seconds total)