Starting phenix.real_space_refine on Sat Mar 16 03:52:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbn_16546/03_2024/8cbn_16546_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbn_16546/03_2024/8cbn_16546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbn_16546/03_2024/8cbn_16546.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbn_16546/03_2024/8cbn_16546.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbn_16546/03_2024/8cbn_16546_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbn_16546/03_2024/8cbn_16546_updated.pdb" } resolution = 3.34 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= 0.001 sd= 0.024 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: 5 Type Number sf(0) Gaussians P 300 5.49 5 S 15 5.16 5 C 7698 2.51 5 N 2540 2.21 5 O 3116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 24": "OD1" <-> "OD2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "F ARG 17": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "K ARG 3": "NH1" <-> "NH2" Residue "K GLU 66": "OE1" <-> "OE2" Residue "K ARG 74": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "L ARG 3": "NH1" <-> "NH2" Residue "L GLU 66": "OE1" <-> "OE2" Residue "L ARG 74": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13669 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3055 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "J" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3095 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "K" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "A" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 829 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "L" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Time building chain proxies: 7.29, per 1000 atoms: 0.53 Number of scatterers: 13669 At special positions: 0 Unit cell: (81.144, 139.104, 129.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 300 15.00 O 3116 8.00 N 2540 7.00 C 7698 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: 6.48 Conformation dependent library (CDL) restraints added in 1.3 seconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 4 sheets defined 50.9% alpha, 2.6% beta 125 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 7.44 Creating SS restraints... Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.520A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 75 removed outlier: 3.790A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.542A pdb=" N TYR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 87 Processing helix chain 'C' and resid 93 through 96 No H-bonds generated for 'chain 'C' and resid 93 through 96' Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.957A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 80 removed outlier: 3.734A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 103 through 121 removed outlier: 3.965A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 28 Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 removed outlier: 3.943A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 removed outlier: 3.516A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 72 removed outlier: 3.542A pdb=" N TYR G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 87 Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'H' and resid 35 through 45 removed outlier: 3.956A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 80 removed outlier: 3.734A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 103 through 121 removed outlier: 3.966A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 86 removed outlier: 5.137A pdb=" N ASP K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN K 86 " --> pdb=" O TRP K 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 86 through 113 removed outlier: 3.505A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'E' and resid 45 through 54 removed outlier: 3.621A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 86 through 113 removed outlier: 3.684A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 removed outlier: 3.545A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 86 removed outlier: 5.136A pdb=" N ASP L 85 " --> pdb=" O LEU L 81 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN L 86 " --> pdb=" O TRP L 82 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 10 through 14 removed outlier: 3.685A pdb=" N ILE K 11 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA K 23 " --> pdb=" O ILE K 11 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA K 13 " --> pdb=" O TRP K 21 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 42 through 44 removed outlier: 3.538A pdb=" N PHE K 44 " --> pdb=" O GLU K 49 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU K 49 " --> pdb=" O PHE K 44 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L' and resid 10 through 14 removed outlier: 3.685A pdb=" N ILE L 11 " --> pdb=" O ALA L 23 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA L 23 " --> pdb=" O ILE L 11 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA L 13 " --> pdb=" O TRP L 21 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 42 through 44 removed outlier: 3.539A pdb=" N PHE L 44 " --> pdb=" O GLU L 49 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU L 49 " --> pdb=" O PHE L 44 " (cutoff:3.500A) 299 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 307 hydrogen bonds 602 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 4.64 Time building geometry restraints manager: 6.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2357 1.33 - 1.45: 4911 1.45 - 1.57: 6654 1.57 - 1.69: 598 1.69 - 1.81: 30 Bond restraints: 14550 Sorted by residual: bond pdb=" SG ML3 A 36 " pdb=" CD ML3 A 36 " ideal model delta sigma weight residual 1.815 1.757 0.058 2.00e-02 2.50e+03 8.48e+00 bond pdb=" CB ML3 A 36 " pdb=" SG ML3 A 36 " ideal model delta sigma weight residual 1.817 1.763 0.054 2.00e-02 2.50e+03 7.38e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.499 -0.077 3.00e-02 1.11e+03 6.52e+00 bond pdb=" C3' DT I 34 " pdb=" O3' DT I 34 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 2.99e+00 bond pdb=" CB ARG F 78 " pdb=" CG ARG F 78 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.49e+00 ... (remaining 14545 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.58: 1560 105.58 - 112.66: 7991 112.66 - 119.74: 4834 119.74 - 126.81: 5670 126.81 - 133.89: 880 Bond angle restraints: 20935 Sorted by residual: angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sigma weight residual 120.20 125.90 -5.70 1.50e+00 4.44e-01 1.45e+01 angle pdb=" C SER L 62 " pdb=" N GLU L 63 " pdb=" CA GLU L 63 " ideal model delta sigma weight residual 122.61 128.15 -5.54 1.56e+00 4.11e-01 1.26e+01 angle pdb=" C SER K 62 " pdb=" N GLU K 63 " pdb=" CA GLU K 63 " ideal model delta sigma weight residual 122.61 128.14 -5.53 1.56e+00 4.11e-01 1.26e+01 angle pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sigma weight residual 120.20 125.02 -4.82 1.50e+00 4.44e-01 1.03e+01 angle pdb=" C3' DT I 34 " pdb=" O3' DT I 34 " pdb=" P DC I 35 " ideal model delta sigma weight residual 120.20 124.97 -4.77 1.50e+00 4.44e-01 1.01e+01 ... (remaining 20930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.29: 6580 34.29 - 68.57: 1388 68.57 - 102.86: 15 102.86 - 137.15: 2 137.15 - 171.44: 1 Dihedral angle restraints: 7986 sinusoidal: 5267 harmonic: 2719 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sinusoidal sigma weight residual 220.00 48.56 171.44 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA LEU K 53 " pdb=" C LEU K 53 " pdb=" N GLY K 54 " pdb=" CA GLY K 54 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1293 0.035 - 0.070: 832 0.070 - 0.105: 172 0.105 - 0.140: 40 0.140 - 0.175: 10 Chirality restraints: 2347 Sorted by residual: chirality pdb=" P DC I 21 " pdb=" OP1 DC I 21 " pdb=" OP2 DC I 21 " pdb=" O5' DC I 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.52 -0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA LEU A 65 " pdb=" N LEU A 65 " pdb=" C LEU A 65 " pdb=" CB LEU A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CB VAL L 90 " pdb=" CA VAL L 90 " pdb=" CG1 VAL L 90 " pdb=" CG2 VAL L 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 2344 not shown) Planarity restraints: 1614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 65 " -0.046 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO E 66 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 66 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 66 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.045 5.00e-02 4.00e+02 6.71e-02 7.21e+00 pdb=" N PRO G 80 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.045 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO C 80 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.037 5.00e-02 4.00e+02 ... (remaining 1611 not shown) Histogram of nonbonded interaction distances: 0.88 - 1.68: 2 1.68 - 2.49: 54 2.49 - 3.29: 12998 3.29 - 4.10: 39196 4.10 - 4.90: 66154 Warning: very small nonbonded interaction distances. Nonbonded interactions: 118404 Sorted by model distance: nonbonded pdb=" OP1 DA I -69 " pdb=" NZ LYS L 73 " model vdw 0.876 2.520 nonbonded pdb=" OP1 DA I -69 " pdb=" CE LYS L 73 " model vdw 0.936 3.440 nonbonded pdb=" OP1 DG I -68 " pdb=" CD PRO L 19 " model vdw 1.751 3.440 nonbonded pdb=" O3' DA I -69 " pdb=" NH2 ARG L 74 " model vdw 1.840 2.520 nonbonded pdb=" P DA I -69 " pdb=" CE LYS L 73 " model vdw 1.967 3.800 ... (remaining 118399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = 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=0.00 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: 2.230 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: 0.000 Extract box with map and model: 6.310 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 41.980 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 : 0.008 0.077 14550 Z= 0.470 Angle : 0.720 7.960 20935 Z= 0.424 Chirality : 0.044 0.175 2347 Planarity : 0.007 0.069 1614 Dihedral : 25.785 171.435 6230 Min Nonbonded Distance : 0.876 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.28 % Allowed : 8.75 % Favored : 88.97 % 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: -5.72 (0.17), residues: 913 helix: -4.46 (0.09), residues: 538 sheet: -4.09 (0.69), residues: 34 loop : -2.16 (0.26), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP L 82 HIS 0.004 0.001 HIS L 20 PHE 0.013 0.002 PHE K 45 TYR 0.012 0.002 TYR B 72 ARG 0.004 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 310 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.8817 (mttt) cc_final: 0.8467 (mttp) REVERT: B 98 TYR cc_start: 0.8973 (m-10) cc_final: 0.8159 (m-10) REVERT: C 34 LEU cc_start: 0.8953 (mt) cc_final: 0.8726 (mm) REVERT: C 110 ASN cc_start: 0.8654 (t0) cc_final: 0.8437 (t0) REVERT: C 115 LEU cc_start: 0.8384 (mt) cc_final: 0.7998 (mp) REVERT: D 59 MET cc_start: 0.8367 (mmm) cc_final: 0.8047 (mmm) REVERT: D 91 ILE cc_start: 0.8561 (mm) cc_final: 0.8306 (mt) REVERT: D 103 LEU cc_start: 0.8637 (mt) cc_final: 0.8277 (mt) REVERT: F 43 VAL cc_start: 0.9461 (t) cc_final: 0.9260 (t) REVERT: F 73 THR cc_start: 0.7936 (m) cc_final: 0.7699 (m) REVERT: H 87 THR cc_start: 0.8808 (p) cc_final: 0.8441 (t) REVERT: A 90 MET cc_start: 0.8080 (mmm) cc_final: 0.7870 (mmt) REVERT: A 120 MET cc_start: 0.7883 (mtp) cc_final: 0.7414 (mtt) REVERT: A 126 LEU cc_start: 0.9415 (tp) cc_final: 0.9168 (tp) REVERT: E 41 TYR cc_start: 0.8515 (m-80) cc_final: 0.8265 (m-10) REVERT: E 60 LEU cc_start: 0.8938 (mt) cc_final: 0.8699 (mt) REVERT: E 119 ILE cc_start: 0.9261 (pt) cc_final: 0.9011 (pt) REVERT: E 125 GLN cc_start: 0.8627 (mt0) cc_final: 0.8360 (mt0) outliers start: 18 outliers final: 7 residues processed: 323 average time/residue: 0.3976 time to fit residues: 163.3941 Evaluate side-chains 240 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 233 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 73 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.9980 chunk 90 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 68 ASN C 73 ASN D 44 GLN D 92 GLN F 18 HIS F 75 HIS G 31 HIS G 73 ASN H 81 ASN H 92 GLN K 64 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 HIS A 68 GLN A 108 ASN A 113 HIS L 64 ASN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14550 Z= 0.258 Angle : 0.647 9.358 20935 Z= 0.378 Chirality : 0.038 0.192 2347 Planarity : 0.006 0.053 1614 Dihedral : 29.679 155.158 4342 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.53 % Allowed : 17.74 % Favored : 79.72 % 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: -2.52 (0.24), residues: 913 helix: -1.65 (0.19), residues: 535 sheet: -3.77 (0.97), residues: 24 loop : -1.25 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 82 HIS 0.008 0.001 HIS E 39 PHE 0.014 0.002 PHE A 67 TYR 0.014 0.002 TYR D 80 ARG 0.006 0.001 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 264 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9296 (mttt) cc_final: 0.8962 (mttp) REVERT: B 79 LYS cc_start: 0.8534 (mptt) cc_final: 0.8230 (mmtm) REVERT: B 93 GLN cc_start: 0.8515 (mt0) cc_final: 0.8271 (mt0) REVERT: B 98 TYR cc_start: 0.8895 (m-10) cc_final: 0.8133 (m-10) REVERT: C 73 ASN cc_start: 0.8613 (t0) cc_final: 0.7430 (t0) REVERT: C 94 ASN cc_start: 0.8913 (t0) cc_final: 0.8618 (t0) REVERT: C 115 LEU cc_start: 0.8763 (mt) cc_final: 0.8560 (mp) REVERT: D 59 MET cc_start: 0.8753 (mmm) cc_final: 0.8267 (mmt) REVERT: D 80 TYR cc_start: 0.8937 (m-10) cc_final: 0.8706 (m-10) REVERT: D 91 ILE cc_start: 0.8779 (mm) cc_final: 0.8503 (mt) REVERT: F 73 THR cc_start: 0.8361 (m) cc_final: 0.8118 (m) REVERT: F 78 ARG cc_start: 0.8950 (mtt90) cc_final: 0.8669 (mtp180) REVERT: G 92 GLU cc_start: 0.8081 (pm20) cc_final: 0.7784 (pm20) REVERT: H 51 ILE cc_start: 0.9125 (tt) cc_final: 0.8911 (tt) REVERT: H 87 THR cc_start: 0.9070 (p) cc_final: 0.8805 (t) REVERT: H 110 GLU cc_start: 0.8898 (tp30) cc_final: 0.8518 (tp30) REVERT: H 113 LYS cc_start: 0.9294 (ttmm) cc_final: 0.9048 (ttpp) REVERT: H 117 LYS cc_start: 0.8955 (tppp) cc_final: 0.8628 (ttpp) REVERT: K 15 MET cc_start: 0.7077 (mtt) cc_final: 0.6818 (mtt) REVERT: A 41 TYR cc_start: 0.8850 (m-80) cc_final: 0.8558 (m-80) REVERT: A 55 GLN cc_start: 0.9217 (mt0) cc_final: 0.8901 (mt0) REVERT: A 79 LYS cc_start: 0.8959 (tttm) cc_final: 0.8369 (tttp) REVERT: A 90 MET cc_start: 0.8124 (mmm) cc_final: 0.7798 (mmt) REVERT: A 120 MET cc_start: 0.7903 (mtp) cc_final: 0.7670 (mtp) REVERT: E 115 LYS cc_start: 0.8877 (mtpp) cc_final: 0.8611 (mttm) REVERT: E 119 ILE cc_start: 0.9319 (pt) cc_final: 0.9106 (pt) REVERT: E 126 LEU cc_start: 0.8719 (tp) cc_final: 0.8499 (tt) outliers start: 20 outliers final: 12 residues processed: 277 average time/residue: 0.3223 time to fit residues: 119.4394 Evaluate side-chains 253 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 241 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 30.0000 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 116 optimal weight: 40.0000 chunk 96 optimal weight: 0.0030 chunk 107 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 HIS E 93 GLN E 125 GLN L 78 ASN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14550 Z= 0.294 Angle : 0.615 8.228 20935 Z= 0.358 Chirality : 0.037 0.159 2347 Planarity : 0.005 0.054 1614 Dihedral : 29.568 149.140 4325 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.44 % Allowed : 20.53 % Favored : 75.03 % 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: -0.88 (0.26), residues: 913 helix: -0.05 (0.22), residues: 530 sheet: -3.83 (0.96), residues: 24 loop : -0.99 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 82 HIS 0.008 0.001 HIS A 39 PHE 0.012 0.001 PHE F 100 TYR 0.017 0.002 TYR D 80 ARG 0.013 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 268 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9480 (mttt) cc_final: 0.9109 (mttp) REVERT: B 84 MET cc_start: 0.8233 (mmt) cc_final: 0.7428 (mmt) REVERT: B 88 TYR cc_start: 0.9065 (m-10) cc_final: 0.8606 (m-80) REVERT: B 98 TYR cc_start: 0.8908 (m-10) cc_final: 0.8190 (m-10) REVERT: C 73 ASN cc_start: 0.9065 (t0) cc_final: 0.7916 (t0) REVERT: D 80 TYR cc_start: 0.9177 (m-10) cc_final: 0.8524 (m-10) REVERT: D 98 LEU cc_start: 0.9047 (mt) cc_final: 0.8781 (mt) REVERT: D 102 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7067 (mm-30) REVERT: D 117 LYS cc_start: 0.9258 (tppp) cc_final: 0.8967 (ttmm) REVERT: F 43 VAL cc_start: 0.9257 (t) cc_final: 0.9032 (m) REVERT: F 47 SER cc_start: 0.9421 (t) cc_final: 0.9164 (t) REVERT: F 52 GLU cc_start: 0.8674 (tp30) cc_final: 0.8353 (mm-30) REVERT: F 74 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7828 (tm-30) REVERT: F 88 TYR cc_start: 0.8960 (m-10) cc_final: 0.8626 (m-80) REVERT: G 33 LEU cc_start: 0.9029 (mt) cc_final: 0.8780 (mt) REVERT: G 73 ASN cc_start: 0.9193 (t160) cc_final: 0.8616 (t0) REVERT: G 75 LYS cc_start: 0.9228 (mmtp) cc_final: 0.8819 (mmtm) REVERT: G 90 ASP cc_start: 0.8402 (t70) cc_final: 0.8183 (t0) REVERT: G 92 GLU cc_start: 0.8225 (pm20) cc_final: 0.7871 (pm20) REVERT: G 93 LEU cc_start: 0.8886 (mt) cc_final: 0.8536 (mt) REVERT: H 52 SER cc_start: 0.9296 (p) cc_final: 0.9027 (t) REVERT: H 57 SER cc_start: 0.9001 (m) cc_final: 0.8613 (t) REVERT: H 64 ASN cc_start: 0.9102 (m-40) cc_final: 0.8865 (m-40) REVERT: H 68 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7946 (mm-30) REVERT: H 84 SER cc_start: 0.9100 (OUTLIER) cc_final: 0.8553 (p) REVERT: A 42 ARG cc_start: 0.7415 (mmm-85) cc_final: 0.6836 (mmm-85) REVERT: A 57 SER cc_start: 0.8839 (p) cc_final: 0.8125 (t) REVERT: A 59 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6947 (mp0) REVERT: A 79 LYS cc_start: 0.9038 (tttm) cc_final: 0.8743 (tttm) REVERT: A 120 MET cc_start: 0.8179 (mtp) cc_final: 0.7908 (mtp) REVERT: E 105 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8332 (mm-30) REVERT: E 115 LYS cc_start: 0.8968 (mtpp) cc_final: 0.8746 (mttm) outliers start: 35 outliers final: 24 residues processed: 283 average time/residue: 0.3240 time to fit residues: 122.5740 Evaluate side-chains 277 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 250 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 115 optimal weight: 20.0000 chunk 102 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 112 GLN D 81 ASN F 25 ASN F 93 GLN K 78 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN E 76 GLN E 93 GLN E 108 ASN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14550 Z= 0.214 Angle : 0.573 8.202 20935 Z= 0.334 Chirality : 0.035 0.128 2347 Planarity : 0.004 0.045 1614 Dihedral : 29.308 150.889 4323 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.93 % Allowed : 25.48 % Favored : 70.60 % 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: -0.00 (0.27), residues: 913 helix: 0.81 (0.23), residues: 526 sheet: -3.75 (0.99), residues: 24 loop : -0.85 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 82 HIS 0.011 0.001 HIS A 39 PHE 0.008 0.001 PHE E 67 TYR 0.013 0.001 TYR D 39 ARG 0.008 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 268 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9467 (mttt) cc_final: 0.9189 (mttp) REVERT: B 84 MET cc_start: 0.8252 (mmt) cc_final: 0.7463 (mmt) REVERT: B 88 TYR cc_start: 0.9139 (m-10) cc_final: 0.8763 (m-80) REVERT: B 98 TYR cc_start: 0.9022 (m-10) cc_final: 0.8254 (m-10) REVERT: C 73 ASN cc_start: 0.9011 (t0) cc_final: 0.7786 (t0) REVERT: C 90 ASP cc_start: 0.8465 (t0) cc_final: 0.7306 (t0) REVERT: C 92 GLU cc_start: 0.8262 (pm20) cc_final: 0.7825 (pm20) REVERT: D 80 TYR cc_start: 0.9085 (m-10) cc_final: 0.8608 (m-10) REVERT: D 102 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7020 (mm-30) REVERT: D 117 LYS cc_start: 0.9232 (tppp) cc_final: 0.8981 (ttmm) REVERT: F 74 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: G 33 LEU cc_start: 0.8997 (mt) cc_final: 0.8745 (mt) REVERT: G 73 ASN cc_start: 0.9053 (t160) cc_final: 0.8660 (t0) REVERT: H 57 SER cc_start: 0.8954 (m) cc_final: 0.8640 (t) REVERT: H 64 ASN cc_start: 0.9098 (m-40) cc_final: 0.8849 (m-40) REVERT: H 84 SER cc_start: 0.9143 (m) cc_final: 0.8588 (p) REVERT: K 14 LYS cc_start: 0.4783 (tppt) cc_final: 0.3164 (mmtt) REVERT: K 16 LYS cc_start: 0.8513 (tppt) cc_final: 0.7962 (tptp) REVERT: A 42 ARG cc_start: 0.7527 (mmm-85) cc_final: 0.7311 (mmm-85) REVERT: A 79 LYS cc_start: 0.9019 (tttm) cc_final: 0.8760 (tttm) REVERT: A 120 MET cc_start: 0.8004 (mtp) cc_final: 0.7754 (mtp) REVERT: E 90 MET cc_start: 0.8574 (tpp) cc_final: 0.8232 (mmm) REVERT: E 105 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8492 (mm-30) REVERT: E 108 ASN cc_start: 0.9384 (t0) cc_final: 0.9125 (t0) REVERT: E 115 LYS cc_start: 0.8906 (mtpp) cc_final: 0.8676 (mttm) outliers start: 31 outliers final: 22 residues processed: 280 average time/residue: 0.3342 time to fit residues: 124.0248 Evaluate side-chains 274 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 250 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 0.0070 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 81 ASN F 93 GLN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 93 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14550 Z= 0.283 Angle : 0.601 8.278 20935 Z= 0.346 Chirality : 0.037 0.144 2347 Planarity : 0.004 0.042 1614 Dihedral : 29.416 146.699 4323 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 6.21 % Allowed : 24.71 % Favored : 69.07 % 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: 0.35 (0.27), residues: 913 helix: 1.13 (0.23), residues: 525 sheet: -3.67 (1.02), residues: 24 loop : -0.76 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 82 HIS 0.004 0.001 HIS G 31 PHE 0.009 0.001 PHE F 100 TYR 0.034 0.002 TYR H 80 ARG 0.006 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 265 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8064 (mm-30) REVERT: B 84 MET cc_start: 0.8242 (mmt) cc_final: 0.7351 (mmt) REVERT: B 88 TYR cc_start: 0.9173 (m-10) cc_final: 0.8736 (m-80) REVERT: B 98 TYR cc_start: 0.9001 (m-10) cc_final: 0.8397 (m-10) REVERT: C 15 LYS cc_start: 0.8297 (mtmm) cc_final: 0.8069 (mtmm) REVERT: C 73 ASN cc_start: 0.9164 (t0) cc_final: 0.8282 (t0) REVERT: C 75 LYS cc_start: 0.9403 (mmtp) cc_final: 0.9107 (mmmm) REVERT: C 90 ASP cc_start: 0.8481 (t0) cc_final: 0.7149 (t0) REVERT: C 92 GLU cc_start: 0.8099 (pm20) cc_final: 0.7651 (pm20) REVERT: C 100 VAL cc_start: 0.9112 (OUTLIER) cc_final: 0.8790 (p) REVERT: D 80 TYR cc_start: 0.9235 (m-10) cc_final: 0.8616 (m-10) REVERT: D 117 LYS cc_start: 0.9273 (tppp) cc_final: 0.9015 (ttmm) REVERT: F 47 SER cc_start: 0.9492 (t) cc_final: 0.9291 (t) REVERT: F 74 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7769 (tm-30) REVERT: G 33 LEU cc_start: 0.9142 (mt) cc_final: 0.8890 (mt) REVERT: G 73 ASN cc_start: 0.9087 (t160) cc_final: 0.8587 (t0) REVERT: G 90 ASP cc_start: 0.8588 (t0) cc_final: 0.8380 (t0) REVERT: G 112 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8356 (mm110) REVERT: H 52 SER cc_start: 0.9200 (p) cc_final: 0.8973 (t) REVERT: H 57 SER cc_start: 0.9065 (m) cc_final: 0.8756 (t) REVERT: H 64 ASN cc_start: 0.9015 (m-40) cc_final: 0.8596 (m-40) REVERT: H 80 TYR cc_start: 0.9021 (m-80) cc_final: 0.8809 (m-80) REVERT: H 84 SER cc_start: 0.9226 (m) cc_final: 0.8701 (p) REVERT: H 110 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8473 (tp30) REVERT: H 117 LYS cc_start: 0.8922 (tttt) cc_final: 0.8573 (tttt) REVERT: K 14 LYS cc_start: 0.5444 (tppt) cc_final: 0.3612 (mptt) REVERT: K 16 LYS cc_start: 0.8661 (tppt) cc_final: 0.8208 (tptm) REVERT: A 42 ARG cc_start: 0.7611 (mmm-85) cc_final: 0.7165 (mmm160) REVERT: A 79 LYS cc_start: 0.8944 (tttm) cc_final: 0.8630 (tttp) REVERT: A 120 MET cc_start: 0.8138 (mtp) cc_final: 0.7629 (mtp) REVERT: A 123 ASP cc_start: 0.8751 (m-30) cc_final: 0.8431 (m-30) REVERT: E 41 TYR cc_start: 0.8931 (m-10) cc_final: 0.8717 (m-10) REVERT: E 73 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8314 (tt0) REVERT: E 90 MET cc_start: 0.8606 (tpp) cc_final: 0.8274 (mmm) REVERT: E 105 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8354 (mm-30) outliers start: 49 outliers final: 43 residues processed: 286 average time/residue: 0.3112 time to fit residues: 119.7693 Evaluate side-chains 303 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 257 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 115 optimal weight: 50.0000 chunk 95 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 111 optimal weight: 30.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 93 GLN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 76 GLN E 93 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14550 Z= 0.213 Angle : 0.567 8.762 20935 Z= 0.329 Chirality : 0.035 0.157 2347 Planarity : 0.004 0.044 1614 Dihedral : 29.138 147.151 4323 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.58 % Allowed : 25.60 % Favored : 68.82 % 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: 0.71 (0.28), residues: 913 helix: 1.49 (0.23), residues: 524 sheet: -3.69 (1.02), residues: 24 loop : -0.70 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.003 0.001 HIS G 31 PHE 0.008 0.001 PHE E 67 TYR 0.018 0.001 TYR H 80 ARG 0.013 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 260 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7893 (mm-30) REVERT: B 84 MET cc_start: 0.8243 (mmt) cc_final: 0.7556 (mmt) REVERT: B 88 TYR cc_start: 0.9153 (m-10) cc_final: 0.8769 (m-80) REVERT: B 98 TYR cc_start: 0.8984 (m-10) cc_final: 0.8310 (m-10) REVERT: C 73 ASN cc_start: 0.9256 (t0) cc_final: 0.8384 (t0) REVERT: C 75 LYS cc_start: 0.9379 (mmtp) cc_final: 0.9091 (mmmm) REVERT: C 84 GLN cc_start: 0.9332 (tp-100) cc_final: 0.9111 (tp-100) REVERT: C 90 ASP cc_start: 0.8543 (t0) cc_final: 0.7263 (t0) REVERT: C 92 GLU cc_start: 0.8156 (pm20) cc_final: 0.7730 (pm20) REVERT: D 80 TYR cc_start: 0.9163 (m-10) cc_final: 0.8627 (m-10) REVERT: D 105 LYS cc_start: 0.8238 (ptpp) cc_final: 0.8028 (ptpp) REVERT: D 117 LYS cc_start: 0.9256 (tppp) cc_final: 0.9006 (ttmm) REVERT: F 22 LEU cc_start: 0.8514 (mt) cc_final: 0.8027 (mm) REVERT: F 74 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: F 88 TYR cc_start: 0.8893 (m-10) cc_final: 0.8465 (m-10) REVERT: G 33 LEU cc_start: 0.9126 (mt) cc_final: 0.8877 (mt) REVERT: G 73 ASN cc_start: 0.9150 (t160) cc_final: 0.8615 (t0) REVERT: G 90 ASP cc_start: 0.8495 (t0) cc_final: 0.8231 (t70) REVERT: H 57 SER cc_start: 0.9013 (m) cc_final: 0.8730 (t) REVERT: H 64 ASN cc_start: 0.9005 (m-40) cc_final: 0.8643 (m-40) REVERT: H 80 TYR cc_start: 0.8965 (m-80) cc_final: 0.8567 (m-80) REVERT: H 84 SER cc_start: 0.9195 (m) cc_final: 0.8633 (p) REVERT: H 117 LYS cc_start: 0.8924 (tttt) cc_final: 0.8479 (ttpp) REVERT: K 14 LYS cc_start: 0.5331 (tppt) cc_final: 0.3714 (mmtt) REVERT: K 16 LYS cc_start: 0.8507 (tppt) cc_final: 0.8161 (tptp) REVERT: A 42 ARG cc_start: 0.7692 (mmm-85) cc_final: 0.7288 (mmm160) REVERT: A 79 LYS cc_start: 0.9139 (tttm) cc_final: 0.8662 (tttp) REVERT: A 120 MET cc_start: 0.8048 (mtp) cc_final: 0.7554 (mtp) REVERT: A 123 ASP cc_start: 0.8752 (m-30) cc_final: 0.8458 (m-30) REVERT: E 73 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8353 (tt0) REVERT: E 90 MET cc_start: 0.8573 (tpp) cc_final: 0.8211 (mmm) REVERT: E 105 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8382 (mm-30) outliers start: 44 outliers final: 35 residues processed: 275 average time/residue: 0.3206 time to fit residues: 119.6129 Evaluate side-chains 290 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 253 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 40.0000 chunk 96 optimal weight: 0.0570 chunk 64 optimal weight: 2.9990 chunk 114 optimal weight: 30.0000 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 52 optimal weight: 0.0870 chunk 70 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.9278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN F 25 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 93 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14550 Z= 0.248 Angle : 0.581 9.164 20935 Z= 0.336 Chirality : 0.036 0.148 2347 Planarity : 0.004 0.042 1614 Dihedral : 29.121 146.027 4323 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 6.21 % Allowed : 26.11 % Favored : 67.68 % 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: 0.78 (0.28), residues: 913 helix: 1.61 (0.23), residues: 526 sheet: -3.69 (0.99), residues: 24 loop : -0.80 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.010 0.001 HIS E 39 PHE 0.007 0.001 PHE E 67 TYR 0.018 0.001 TYR G 39 ARG 0.013 0.001 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 259 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7798 (mm-30) REVERT: B 88 TYR cc_start: 0.9171 (m-10) cc_final: 0.8768 (m-80) REVERT: B 98 TYR cc_start: 0.8995 (m-10) cc_final: 0.8382 (m-10) REVERT: C 73 ASN cc_start: 0.9196 (t0) cc_final: 0.8640 (t0) REVERT: C 84 GLN cc_start: 0.9349 (tp-100) cc_final: 0.9051 (tp-100) REVERT: C 90 ASP cc_start: 0.8510 (t0) cc_final: 0.7146 (t0) REVERT: C 92 GLU cc_start: 0.8151 (pm20) cc_final: 0.7726 (pm20) REVERT: C 100 VAL cc_start: 0.9150 (t) cc_final: 0.8682 (p) REVERT: D 80 TYR cc_start: 0.9220 (m-10) cc_final: 0.8655 (m-10) REVERT: D 117 LYS cc_start: 0.9270 (tppp) cc_final: 0.8974 (ttmm) REVERT: F 74 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: F 88 TYR cc_start: 0.8912 (m-10) cc_final: 0.8342 (m-10) REVERT: G 33 LEU cc_start: 0.9141 (mt) cc_final: 0.8883 (mt) REVERT: G 73 ASN cc_start: 0.9202 (t160) cc_final: 0.8749 (t0) REVERT: H 57 SER cc_start: 0.9058 (m) cc_final: 0.8781 (t) REVERT: H 64 ASN cc_start: 0.8902 (m-40) cc_final: 0.8546 (m-40) REVERT: H 80 TYR cc_start: 0.9026 (m-80) cc_final: 0.8358 (m-80) REVERT: H 84 SER cc_start: 0.9229 (m) cc_final: 0.8669 (p) REVERT: H 117 LYS cc_start: 0.8908 (tttt) cc_final: 0.8605 (tttt) REVERT: K 14 LYS cc_start: 0.5399 (tppt) cc_final: 0.3777 (mmtt) REVERT: K 16 LYS cc_start: 0.8620 (tppt) cc_final: 0.8295 (tptp) REVERT: A 42 ARG cc_start: 0.7721 (mmm-85) cc_final: 0.7339 (mmm160) REVERT: A 79 LYS cc_start: 0.9140 (tttm) cc_final: 0.8650 (tttp) REVERT: A 120 MET cc_start: 0.8127 (mtp) cc_final: 0.7629 (mtp) REVERT: A 123 ASP cc_start: 0.8775 (m-30) cc_final: 0.8449 (m-30) REVERT: E 90 MET cc_start: 0.8564 (tpp) cc_final: 0.8235 (mmm) REVERT: E 105 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8275 (mm-30) outliers start: 49 outliers final: 43 residues processed: 276 average time/residue: 0.3117 time to fit residues: 115.6858 Evaluate side-chains 303 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 258 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 0.0370 overall best weight: 0.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 93 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14550 Z= 0.205 Angle : 0.566 8.936 20935 Z= 0.328 Chirality : 0.034 0.144 2347 Planarity : 0.004 0.044 1614 Dihedral : 28.990 145.564 4323 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.32 % Allowed : 27.88 % Favored : 66.79 % 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: 1.00 (0.28), residues: 913 helix: 1.81 (0.23), residues: 523 sheet: -3.70 (0.96), residues: 24 loop : -0.70 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.003 0.001 HIS G 31 PHE 0.008 0.001 PHE E 67 TYR 0.014 0.001 TYR G 39 ARG 0.006 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 268 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7733 (mm-30) REVERT: B 84 MET cc_start: 0.8259 (mmt) cc_final: 0.7558 (mmt) REVERT: B 88 TYR cc_start: 0.9148 (m-10) cc_final: 0.8801 (m-80) REVERT: B 98 TYR cc_start: 0.9009 (m-10) cc_final: 0.8316 (m-10) REVERT: C 73 ASN cc_start: 0.9190 (t0) cc_final: 0.8647 (t0) REVERT: C 84 GLN cc_start: 0.9356 (tp-100) cc_final: 0.9068 (tp-100) REVERT: C 90 ASP cc_start: 0.8548 (t0) cc_final: 0.7344 (t0) REVERT: C 92 GLU cc_start: 0.8138 (pm20) cc_final: 0.7725 (pm20) REVERT: C 100 VAL cc_start: 0.9164 (t) cc_final: 0.8691 (p) REVERT: D 80 TYR cc_start: 0.9125 (m-10) cc_final: 0.8616 (m-10) REVERT: D 117 LYS cc_start: 0.9265 (tppp) cc_final: 0.9002 (ttmm) REVERT: F 74 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: F 88 TYR cc_start: 0.8907 (m-10) cc_final: 0.8274 (m-10) REVERT: G 33 LEU cc_start: 0.9113 (mt) cc_final: 0.8852 (mt) REVERT: G 73 ASN cc_start: 0.9200 (t160) cc_final: 0.8767 (t0) REVERT: H 57 SER cc_start: 0.9020 (m) cc_final: 0.8753 (t) REVERT: H 64 ASN cc_start: 0.8870 (m-40) cc_final: 0.8525 (m-40) REVERT: H 80 TYR cc_start: 0.8979 (m-80) cc_final: 0.8296 (m-80) REVERT: H 84 SER cc_start: 0.9208 (m) cc_final: 0.8663 (p) REVERT: H 117 LYS cc_start: 0.8908 (tttt) cc_final: 0.8608 (tttt) REVERT: K 14 LYS cc_start: 0.5368 (tppt) cc_final: 0.3797 (mmtt) REVERT: K 16 LYS cc_start: 0.8538 (tppt) cc_final: 0.8052 (tptm) REVERT: A 42 ARG cc_start: 0.7660 (mmm-85) cc_final: 0.7304 (mmm160) REVERT: A 79 LYS cc_start: 0.9148 (tttm) cc_final: 0.8651 (tttp) REVERT: A 120 MET cc_start: 0.8077 (mtp) cc_final: 0.7596 (mtp) REVERT: A 123 ASP cc_start: 0.8764 (m-30) cc_final: 0.8445 (m-30) REVERT: E 90 MET cc_start: 0.8543 (tpp) cc_final: 0.8206 (mmm) REVERT: E 105 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8353 (mm-30) outliers start: 42 outliers final: 36 residues processed: 281 average time/residue: 0.3252 time to fit residues: 121.8881 Evaluate side-chains 299 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 261 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 1.9990 chunk 109 optimal weight: 0.0980 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 0.0370 chunk 101 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 113 optimal weight: 30.0000 chunk 68 optimal weight: 5.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN F 25 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 93 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.6487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14550 Z= 0.189 Angle : 0.565 8.528 20935 Z= 0.326 Chirality : 0.034 0.220 2347 Planarity : 0.004 0.042 1614 Dihedral : 28.918 144.752 4323 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.56 % Allowed : 28.26 % Favored : 67.17 % 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: 1.19 (0.28), residues: 913 helix: 1.94 (0.23), residues: 525 sheet: -3.69 (0.94), residues: 24 loop : -0.60 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.004 0.001 HIS H 106 PHE 0.008 0.001 PHE E 67 TYR 0.013 0.001 TYR H 37 ARG 0.011 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 268 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7906 (mm-30) REVERT: B 84 MET cc_start: 0.8246 (mmt) cc_final: 0.7571 (mmt) REVERT: B 88 TYR cc_start: 0.9148 (m-10) cc_final: 0.8809 (m-80) REVERT: B 92 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8308 (tmm-80) REVERT: B 98 TYR cc_start: 0.9007 (m-10) cc_final: 0.8302 (m-10) REVERT: C 73 ASN cc_start: 0.9141 (t0) cc_final: 0.8654 (t0) REVERT: C 84 GLN cc_start: 0.9348 (tp-100) cc_final: 0.9067 (tp-100) REVERT: C 90 ASP cc_start: 0.8556 (t0) cc_final: 0.7276 (t0) REVERT: C 92 GLU cc_start: 0.8129 (pm20) cc_final: 0.7704 (pm20) REVERT: C 100 VAL cc_start: 0.9140 (t) cc_final: 0.8652 (p) REVERT: D 80 TYR cc_start: 0.9076 (m-10) cc_final: 0.8592 (m-10) REVERT: D 105 LYS cc_start: 0.8449 (ptpp) cc_final: 0.8050 (pttm) REVERT: D 117 LYS cc_start: 0.9261 (tppp) cc_final: 0.8960 (ttmm) REVERT: F 25 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8185 (t0) REVERT: F 45 ARG cc_start: 0.9088 (mtp85) cc_final: 0.8748 (mtp85) REVERT: F 74 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: F 88 TYR cc_start: 0.8938 (m-10) cc_final: 0.8264 (m-10) REVERT: G 33 LEU cc_start: 0.9102 (mt) cc_final: 0.8857 (mt) REVERT: G 73 ASN cc_start: 0.9233 (t160) cc_final: 0.8808 (t0) REVERT: H 57 SER cc_start: 0.8909 (m) cc_final: 0.8612 (t) REVERT: H 64 ASN cc_start: 0.8901 (m-40) cc_final: 0.8515 (m-40) REVERT: H 80 TYR cc_start: 0.8937 (m-80) cc_final: 0.8258 (m-80) REVERT: H 84 SER cc_start: 0.9204 (m) cc_final: 0.8655 (p) REVERT: H 117 LYS cc_start: 0.8950 (tttt) cc_final: 0.8641 (tttt) REVERT: K 14 LYS cc_start: 0.5356 (tppt) cc_final: 0.3814 (mmtt) REVERT: K 16 LYS cc_start: 0.8443 (tppt) cc_final: 0.7956 (tptm) REVERT: A 42 ARG cc_start: 0.7601 (mmm-85) cc_final: 0.7273 (mmm160) REVERT: A 79 LYS cc_start: 0.9157 (tttm) cc_final: 0.8800 (tttp) REVERT: A 120 MET cc_start: 0.7927 (mtp) cc_final: 0.7427 (mtp) REVERT: A 123 ASP cc_start: 0.8763 (m-30) cc_final: 0.8454 (m-30) REVERT: E 73 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8244 (tt0) REVERT: E 90 MET cc_start: 0.8524 (tpp) cc_final: 0.8190 (mmm) REVERT: E 105 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8383 (mm-30) outliers start: 36 outliers final: 29 residues processed: 279 average time/residue: 0.3303 time to fit residues: 122.4167 Evaluate side-chains 297 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 264 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 68 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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: 70.2022 > 50: distance: 43 - 61: 29.263 distance: 53 - 74: 28.295 distance: 58 - 61: 32.025 distance: 59 - 83: 29.417 distance: 61 - 62: 25.953 distance: 62 - 63: 43.509 distance: 62 - 65: 8.570 distance: 63 - 64: 16.387 distance: 63 - 68: 30.456 distance: 64 - 87: 57.372 distance: 65 - 66: 44.793 distance: 65 - 67: 60.927 distance: 68 - 69: 26.419 distance: 69 - 70: 3.627 distance: 69 - 72: 16.898 distance: 70 - 71: 27.297 distance: 70 - 74: 9.681 distance: 71 - 94: 45.691 distance: 72 - 73: 20.727 distance: 74 - 75: 58.654 distance: 75 - 78: 28.637 distance: 76 - 77: 40.188 distance: 76 - 83: 41.986 distance: 78 - 79: 19.776 distance: 79 - 80: 19.636 distance: 80 - 81: 37.405 distance: 80 - 82: 39.318 distance: 83 - 84: 20.514 distance: 84 - 85: 8.000 distance: 85 - 86: 20.235 distance: 85 - 87: 21.338 distance: 86 - 108: 12.242 distance: 87 - 88: 15.107 distance: 88 - 89: 28.968 distance: 88 - 91: 6.604 distance: 89 - 94: 3.208 distance: 90 - 115: 31.852 distance: 91 - 92: 31.421 distance: 91 - 93: 51.961 distance: 94 - 95: 37.818 distance: 95 - 96: 8.624 distance: 95 - 98: 14.050 distance: 96 - 97: 33.427 distance: 96 - 103: 38.407 distance: 97 - 122: 40.195 distance: 98 - 99: 43.601 distance: 99 - 100: 18.761 distance: 100 - 101: 52.416 distance: 101 - 102: 31.106 distance: 103 - 104: 37.147 distance: 104 - 105: 14.771 distance: 104 - 107: 37.694 distance: 105 - 106: 48.015 distance: 105 - 108: 40.171 distance: 106 - 131: 29.700 distance: 108 - 109: 20.162 distance: 109 - 110: 33.928 distance: 109 - 112: 13.373 distance: 110 - 115: 8.679 distance: 111 - 138: 32.763 distance: 112 - 113: 15.161 distance: 112 - 114: 18.185 distance: 115 - 116: 57.078 distance: 116 - 119: 56.720 distance: 117 - 122: 13.392 distance: 119 - 120: 19.886 distance: 119 - 121: 40.452 distance: 122 - 123: 46.504 distance: 123 - 124: 10.789 distance: 123 - 126: 18.020 distance: 124 - 125: 17.162 distance: 124 - 131: 23.559 distance: 125 - 150: 36.265 distance: 126 - 127: 10.990 distance: 127 - 128: 49.548 distance: 128 - 129: 42.313 distance: 129 - 130: 40.762