Starting phenix.real_space_refine on Fri Apr 12 12:51:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9f_31030/04_2024/7e9f_31030_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9f_31030/04_2024/7e9f_31030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9f_31030/04_2024/7e9f_31030.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9f_31030/04_2024/7e9f_31030.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9f_31030/04_2024/7e9f_31030_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9f_31030/04_2024/7e9f_31030_updated.pdb" } resolution = 4.0 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12591 atoms to isotropic. 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 249 5.49 5 S 4 5.16 5 C 7588 2.51 5 N 2468 2.21 5 O 2970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "G ARG 36": "NH1" <-> "NH2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "K ARG 148": "NH1" <-> "NH2" Residue "L ARG 148": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13279 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 734 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 88} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 659 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 776 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 714 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 710 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 781 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 714 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2506 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain: "J" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2600 Classifications: {'DNA': 126} Link IDs: {'rna3p': 125} Chain: "K" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1221 Unusual residues: {'ACE': 1} Classifications: {'peptide': 163, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 160} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "L" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1221 Unusual residues: {'ACE': 1} Classifications: {'peptide': 163, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 160} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 67 Time building chain proxies: 7.39, per 1000 atoms: 0.56 Number of scatterers: 13279 At special positions: 0 Unit cell: (113, 116, 116, 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 4 16.00 P 249 15.00 O 2970 8.00 N 2468 7.00 C 7588 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: 7.37 Conformation dependent library (CDL) restraints added in 1.7 seconds 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 2 sheets defined 48.8% alpha, 4.5% beta 117 base pairs and 202 stacking pairs defined. Time for finding SS restraints: 7.21 Creating SS restraints... Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 4.398A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 removed outlier: 3.596A pdb=" N GLY A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 51 through 75 removed outlier: 3.623A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.308A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 93 through 97 Processing helix chain 'D' and resid 41 through 48 Processing helix chain 'D' and resid 59 through 86 removed outlier: 3.542A pdb=" N LYS D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 104 Processing helix chain 'D' and resid 107 through 126 removed outlier: 3.531A pdb=" N ALA D 110 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL D 114 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR D 118 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR D 122 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER D 125 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER D 126 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 54 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.284A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 114 removed outlier: 3.871A pdb=" N GLY E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 129 Processing helix chain 'F' and resid 25 through 27 No H-bonds generated for 'chain 'F' and resid 25 through 27' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 28 through 37 Processing helix chain 'G' and resid 46 through 72 removed outlier: 4.336A pdb=" N VAL G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 90 removed outlier: 3.617A pdb=" N ASN G 90 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 41 through 49 Processing helix chain 'H' and resid 59 through 85 Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 108 through 125 Processing helix chain 'K' and resid 27 through 29 No H-bonds generated for 'chain 'K' and resid 27 through 29' Processing helix chain 'K' and resid 190 through 198 removed outlier: 4.403A pdb=" N ALA K 194 " --> pdb=" O GLU K 190 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 211 removed outlier: 4.446A pdb=" N GLU K 206 " --> pdb=" O ARG K 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 29 No H-bonds generated for 'chain 'L' and resid 27 through 29' Processing helix chain 'L' and resid 190 through 198 removed outlier: 4.402A pdb=" N ALA L 194 " --> pdb=" O GLU L 190 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR L 195 " --> pdb=" O ASP L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 201 through 211 removed outlier: 4.446A pdb=" N GLU L 206 " --> pdb=" O ARG L 202 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 146 through 149 removed outlier: 6.800A pdb=" N VAL K 57 " --> pdb=" O ILE K 147 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL K 149 " --> pdb=" O SER K 55 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N SER K 55 " --> pdb=" O VAL K 149 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TRP K 86 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU K 74 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU K 84 " --> pdb=" O LEU K 74 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'L' and resid 146 through 149 removed outlier: 6.801A pdb=" N VAL L 57 " --> pdb=" O ILE L 147 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL L 149 " --> pdb=" O SER L 55 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N SER L 55 " --> pdb=" O VAL L 149 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TRP L 86 " --> pdb=" O GLN L 72 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU L 74 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU L 84 " --> pdb=" O LEU L 74 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 1017 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 304 hydrogen bonds 600 hydrogen bond angles 0 basepair planarities 117 basepair parallelities 202 stacking parallelities Total time for adding SS restraints: 4.40 Time building geometry restraints manager: 7.68 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: 2644 1.33 - 1.45: 4127 1.45 - 1.57: 6732 1.57 - 1.69: 496 1.69 - 1.81: 6 Bond restraints: 14005 Sorted by residual: bond pdb=" C PHE G 26 " pdb=" N PRO G 27 " ideal model delta sigma weight residual 1.333 1.356 -0.022 1.01e-02 9.80e+03 4.86e+00 bond pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.80e+00 bond pdb=" C3' DG I 63 " pdb=" O3' DG I 63 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.20e+00 bond pdb=" C LEU A 65 " pdb=" N PRO A 66 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.20e-02 6.94e+03 2.05e+00 bond pdb=" C ACE K 1 " pdb=" O ACE K 1 " ideal model delta sigma weight residual 1.199 1.228 -0.029 2.00e-02 2.50e+03 2.03e+00 ... (remaining 14000 not shown) Histogram of bond angle deviations from ideal: 97.41 - 104.73: 1052 104.73 - 112.05: 7484 112.05 - 119.36: 4314 119.36 - 126.68: 6412 126.68 - 133.99: 745 Bond angle restraints: 20007 Sorted by residual: angle pdb=" C LYS L 28 " pdb=" N ARG L 29 " pdb=" CA ARG L 29 " ideal model delta sigma weight residual 121.54 128.73 -7.19 1.91e+00 2.74e-01 1.42e+01 angle pdb=" C LYS K 28 " pdb=" N ARG K 29 " pdb=" CA ARG K 29 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C TRP K 93 " pdb=" N PHE K 94 " pdb=" CA PHE K 94 " ideal model delta sigma weight residual 121.70 127.84 -6.14 1.80e+00 3.09e-01 1.16e+01 angle pdb=" C TRP L 93 " pdb=" N PHE L 94 " pdb=" CA PHE L 94 " ideal model delta sigma weight residual 121.70 127.81 -6.11 1.80e+00 3.09e-01 1.15e+01 angle pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " pdb=" P DG I 25 " ideal model delta sigma weight residual 120.20 124.49 -4.29 1.50e+00 4.44e-01 8.20e+00 ... (remaining 20002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.38: 5977 29.38 - 58.77: 1609 58.77 - 88.15: 137 88.15 - 117.54: 1 117.54 - 146.92: 2 Dihedral angle restraints: 7726 sinusoidal: 4661 harmonic: 3065 Sorted by residual: dihedral pdb=" C4' DC I 24 " pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " pdb=" P DG I 25 " ideal model delta sinusoidal sigma weight residual 220.00 73.08 146.92 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" C4' DG I 63 " pdb=" C3' DG I 63 " pdb=" O3' DG I 63 " pdb=" P DC I 64 " ideal model delta sinusoidal sigma weight residual 220.00 77.94 142.06 1 3.50e+01 8.16e-04 1.40e+01 dihedral pdb=" CA GLU B 74 " pdb=" C GLU B 74 " pdb=" N HIS B 75 " pdb=" CA HIS B 75 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 7723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1566 0.038 - 0.077: 523 0.077 - 0.115: 181 0.115 - 0.153: 38 0.153 - 0.191: 8 Chirality restraints: 2316 Sorted by residual: chirality pdb=" CB ILE F 29 " pdb=" CA ILE F 29 " pdb=" CG1 ILE F 29 " pdb=" CG2 ILE F 29 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" P DG I 25 " pdb=" OP1 DG I 25 " pdb=" OP2 DG I 25 " pdb=" O5' DG I 25 " both_signs ideal model delta sigma weight residual True 2.35 -2.54 -0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" CA ILE B 46 " pdb=" N ILE B 46 " pdb=" C ILE B 46 " pdb=" CB ILE B 46 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.84e-01 ... (remaining 2313 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 31 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO F 32 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO F 32 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 32 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 65 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO E 66 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 66 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 66 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 80 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO G 81 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO G 81 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 81 " -0.028 5.00e-02 4.00e+02 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3036 2.79 - 3.32: 10835 3.32 - 3.85: 26788 3.85 - 4.37: 29099 4.37 - 4.90: 42930 Nonbonded interactions: 112688 Sorted by model distance: nonbonded pdb=" O2 DC I 130 " pdb=" N2 DG J 18 " model vdw 2.264 2.496 nonbonded pdb=" N2 DG I 126 " pdb=" O2 DC J 22 " model vdw 2.319 2.496 nonbonded pdb=" OG SER H 93 " pdb=" OE1 GLU H 96 " model vdw 2.369 2.440 nonbonded pdb=" OE1 GLN G 42 " pdb=" OG SER H 90 " model vdw 2.376 2.440 nonbonded pdb=" OG SER D 67 " pdb=" O GLY F 101 " model vdw 2.387 2.440 ... (remaining 112683 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 46 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 132)) selection = (chain 'E' and (resid 46 through 80 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 132)) } ncs_group { reference = (chain 'B' and (resid 21 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 16 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 99 or (resid 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 116)) selection = (chain 'G' and (resid 16 through 113 or (resid 114 and (name N or name CA or nam \ e C or name O or name CB )) or resid 115 through 116)) } ncs_group { reference = (chain 'D' and (resid 35 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 127)) selection = (chain 'H' and (resid 35 through 107 or (resid 108 and (name N or name CA or nam \ e C or name O or name CB )) or resid 109 through 127)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 2.270 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 44.500 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 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 : 0.004 0.059 14005 Z= 0.212 Angle : 0.739 9.548 20007 Z= 0.436 Chirality : 0.044 0.191 2316 Planarity : 0.005 0.066 1668 Dihedral : 28.022 146.923 5742 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.36 % Allowed : 6.89 % Favored : 92.74 % 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: -4.61 (0.18), residues: 1029 helix: -2.87 (0.14), residues: 567 sheet: -3.24 (0.54), residues: 44 loop : -3.14 (0.22), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 93 HIS 0.003 0.001 HIS F 75 PHE 0.024 0.002 PHE H 68 TYR 0.009 0.001 TYR K 40 ARG 0.003 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 377 time to evaluate : 1.103 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: A 62 ILE cc_start: 0.8660 (mt) cc_final: 0.7930 (mp) REVERT: A 79 LYS cc_start: 0.8434 (tptm) cc_final: 0.8182 (tptp) REVERT: A 92 LEU cc_start: 0.9163 (mt) cc_final: 0.8861 (tp) REVERT: B 25 ASN cc_start: 0.8257 (m-40) cc_final: 0.8037 (m110) REVERT: B 35 ARG cc_start: 0.8578 (mtp-110) cc_final: 0.8008 (ttm110) REVERT: B 37 LEU cc_start: 0.9502 (mt) cc_final: 0.9119 (mt) REVERT: B 52 GLU cc_start: 0.8229 (tp30) cc_final: 0.7969 (tp30) REVERT: B 77 LYS cc_start: 0.8849 (mttt) cc_final: 0.8512 (mttm) REVERT: C 26 PHE cc_start: 0.8908 (m-80) cc_final: 0.8344 (m-10) REVERT: C 43 ARG cc_start: 0.8717 (mtp180) cc_final: 0.8452 (mtp-110) REVERT: C 53 THR cc_start: 0.8791 (m) cc_final: 0.8570 (m) REVERT: C 96 LYS cc_start: 0.8854 (mmtm) cc_final: 0.8555 (ttmt) REVERT: D 46 LYS cc_start: 0.9348 (ttmt) cc_final: 0.9125 (ttmm) REVERT: D 79 GLU cc_start: 0.8327 (tp30) cc_final: 0.7725 (tp30) REVERT: E 54 PHE cc_start: 0.7397 (m-80) cc_final: 0.6547 (m-10) REVERT: E 69 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7828 (ptp90) REVERT: F 40 ARG cc_start: 0.8054 (ttm170) cc_final: 0.7776 (ttt180) REVERT: F 83 SER cc_start: 0.8232 (p) cc_final: 0.8021 (m) REVERT: G 39 ASN cc_start: 0.8404 (m-40) cc_final: 0.8088 (p0) REVERT: H 43 TYR cc_start: 0.7620 (m-80) cc_final: 0.7174 (m-80) REVERT: H 46 LYS cc_start: 0.9330 (ttmt) cc_final: 0.9120 (ttmm) REVERT: H 86 TYR cc_start: 0.7918 (m-10) cc_final: 0.7561 (m-10) REVERT: K 49 LYS cc_start: 0.6236 (mtmt) cc_final: 0.5394 (mmtp) REVERT: L 49 LYS cc_start: 0.6371 (mtmt) cc_final: 0.5668 (mmtp) REVERT: L 79 LEU cc_start: 0.7380 (mt) cc_final: 0.6588 (mp) REVERT: L 134 LEU cc_start: 0.7157 (mt) cc_final: 0.6932 (tt) outliers start: 3 outliers final: 0 residues processed: 380 average time/residue: 0.3860 time to fit residues: 187.4588 Evaluate side-chains 231 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 6.9990 chunk 96 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 0.0980 chunk 74 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 32 HIS C 39 ASN C 74 ASN D 52 HIS F 25 ASN G 74 ASN K 27 GLN K 145 ASN L 27 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14005 Z= 0.223 Angle : 0.621 7.784 20007 Z= 0.352 Chirality : 0.038 0.184 2316 Planarity : 0.005 0.043 1668 Dihedral : 31.400 147.275 3864 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 5.56 % Allowed : 20.56 % Favored : 73.88 % 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: -2.53 (0.23), residues: 1029 helix: -0.99 (0.19), residues: 570 sheet: -2.46 (0.66), residues: 42 loop : -2.51 (0.26), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 86 HIS 0.006 0.001 HIS F 75 PHE 0.009 0.001 PHE D 68 TYR 0.017 0.001 TYR K 40 ARG 0.006 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 264 time to evaluate : 1.036 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.7765 (mttt) cc_final: 0.7438 (mttm) REVERT: A 79 LYS cc_start: 0.8570 (tptm) cc_final: 0.8370 (tptp) REVERT: B 25 ASN cc_start: 0.8313 (m-40) cc_final: 0.7934 (m-40) REVERT: B 35 ARG cc_start: 0.8558 (mtp-110) cc_final: 0.8083 (ttm110) REVERT: B 40 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8230 (mtp85) REVERT: B 52 GLU cc_start: 0.8068 (tp30) cc_final: 0.7590 (tp30) REVERT: B 55 ARG cc_start: 0.7808 (ptp-110) cc_final: 0.7570 (mtt90) REVERT: B 90 LEU cc_start: 0.8962 (mt) cc_final: 0.8698 (mt) REVERT: B 95 ARG cc_start: 0.8733 (ttm-80) cc_final: 0.8097 (ttm-80) REVERT: C 43 ARG cc_start: 0.8848 (mtp180) cc_final: 0.8478 (mtp-110) REVERT: C 96 LYS cc_start: 0.8894 (mmtm) cc_final: 0.8616 (ttmt) REVERT: C 100 ASN cc_start: 0.6914 (p0) cc_final: 0.6449 (p0) REVERT: C 101 VAL cc_start: 0.9381 (t) cc_final: 0.9051 (p) REVERT: D 86 TYR cc_start: 0.8010 (m-10) cc_final: 0.7505 (m-10) REVERT: E 54 PHE cc_start: 0.7575 (m-80) cc_final: 0.6833 (m-10) REVERT: E 59 GLU cc_start: 0.8548 (pm20) cc_final: 0.8180 (pm20) REVERT: E 69 ARG cc_start: 0.8514 (mtm-85) cc_final: 0.7963 (ptp90) REVERT: F 25 ASN cc_start: 0.8434 (m-40) cc_final: 0.8232 (m110) REVERT: F 52 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7551 (tp30) REVERT: F 83 SER cc_start: 0.8269 (p) cc_final: 0.7711 (t) REVERT: H 71 ASP cc_start: 0.7843 (t70) cc_final: 0.7630 (t0) REVERT: H 86 TYR cc_start: 0.8199 (m-10) cc_final: 0.7617 (m-10) REVERT: K 49 LYS cc_start: 0.6363 (mtmt) cc_final: 0.5576 (mmtp) REVERT: K 79 LEU cc_start: 0.7424 (mt) cc_final: 0.6792 (mp) REVERT: L 49 LYS cc_start: 0.6484 (mtmt) cc_final: 0.5830 (mmtp) REVERT: L 134 LEU cc_start: 0.7082 (mt) cc_final: 0.6822 (tt) REVERT: L 148 ARG cc_start: 0.6429 (ptt-90) cc_final: 0.5999 (pmt170) outliers start: 46 outliers final: 34 residues processed: 292 average time/residue: 0.3735 time to fit residues: 141.2777 Evaluate side-chains 266 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 231 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 0.1980 chunk 78 optimal weight: 10.0000 chunk 31 optimal weight: 0.0570 chunk 115 optimal weight: 40.0000 chunk 124 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 overall best weight: 2.4504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14005 Z= 0.226 Angle : 0.613 8.497 20007 Z= 0.348 Chirality : 0.038 0.187 2316 Planarity : 0.004 0.042 1668 Dihedral : 31.236 146.655 3864 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 6.53 % Allowed : 23.46 % Favored : 70.01 % 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: -1.48 (0.25), residues: 1029 helix: -0.02 (0.21), residues: 572 sheet: -1.78 (0.78), residues: 42 loop : -2.25 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 11 HIS 0.005 0.001 HIS B 75 PHE 0.010 0.001 PHE D 68 TYR 0.016 0.001 TYR L 40 ARG 0.011 0.001 ARG K 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 248 time to evaluate : 1.208 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.7690 (mttt) cc_final: 0.7229 (mttp) REVERT: B 25 ASN cc_start: 0.8309 (m-40) cc_final: 0.7848 (m110) REVERT: B 35 ARG cc_start: 0.8646 (mtp-110) cc_final: 0.8207 (ttm110) REVERT: B 53 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7993 (tm-30) REVERT: B 77 LYS cc_start: 0.9094 (mttt) cc_final: 0.8714 (mttp) REVERT: C 43 ARG cc_start: 0.8828 (mtp180) cc_final: 0.8396 (mtp-110) REVERT: C 96 LYS cc_start: 0.8916 (mmtm) cc_final: 0.8641 (ttmt) REVERT: C 100 ASN cc_start: 0.7128 (p0) cc_final: 0.6708 (p0) REVERT: D 86 TYR cc_start: 0.8114 (m-10) cc_final: 0.7629 (m-10) REVERT: D 95 ARG cc_start: 0.8280 (ttt90) cc_final: 0.8033 (ttt90) REVERT: E 54 PHE cc_start: 0.7527 (m-80) cc_final: 0.7081 (m-10) REVERT: E 64 LYS cc_start: 0.7739 (mtpt) cc_final: 0.7402 (mttp) REVERT: E 69 ARG cc_start: 0.8506 (mtm-85) cc_final: 0.8111 (mtp180) REVERT: F 25 ASN cc_start: 0.8282 (m-40) cc_final: 0.8046 (m-40) REVERT: F 52 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7761 (tp30) REVERT: F 83 SER cc_start: 0.8142 (p) cc_final: 0.7542 (t) REVERT: G 26 PHE cc_start: 0.8498 (m-10) cc_final: 0.8201 (m-10) REVERT: G 59 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8444 (tp) REVERT: H 72 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8848 (tp) REVERT: H 74 GLU cc_start: 0.7602 (tt0) cc_final: 0.7330 (tt0) REVERT: K 49 LYS cc_start: 0.6210 (mtmt) cc_final: 0.5366 (mmtp) REVERT: L 40 TYR cc_start: 0.5014 (p90) cc_final: 0.4731 (p90) REVERT: L 148 ARG cc_start: 0.6409 (ptt-90) cc_final: 0.5935 (pmt170) REVERT: L 193 LYS cc_start: 0.8893 (mtpp) cc_final: 0.8546 (mmtp) outliers start: 54 outliers final: 39 residues processed: 281 average time/residue: 0.3505 time to fit residues: 129.0193 Evaluate side-chains 249 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 208 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 115 optimal weight: 50.0000 chunk 122 optimal weight: 30.0000 chunk 60 optimal weight: 6.9990 chunk 109 optimal weight: 0.0770 chunk 33 optimal weight: 0.7980 overall best weight: 2.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14005 Z= 0.243 Angle : 0.622 8.931 20007 Z= 0.351 Chirality : 0.038 0.198 2316 Planarity : 0.004 0.043 1668 Dihedral : 31.165 146.958 3864 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 7.38 % Allowed : 25.03 % Favored : 67.59 % 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: -1.13 (0.26), residues: 1029 helix: 0.23 (0.21), residues: 577 sheet: -1.47 (0.81), residues: 42 loop : -2.10 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 86 HIS 0.005 0.001 HIS B 75 PHE 0.010 0.001 PHE D 68 TYR 0.046 0.002 TYR H 86 ARG 0.007 0.001 ARG L 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 222 time to evaluate : 1.136 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7639 (mm-30) REVERT: B 25 ASN cc_start: 0.8263 (m-40) cc_final: 0.7984 (m-40) REVERT: B 35 ARG cc_start: 0.8787 (mtp-110) cc_final: 0.8304 (mtp85) REVERT: B 44 LYS cc_start: 0.8806 (mttt) cc_final: 0.8423 (mttt) REVERT: B 77 LYS cc_start: 0.9069 (mttt) cc_final: 0.8726 (mttp) REVERT: C 43 ARG cc_start: 0.8830 (mtp180) cc_final: 0.8352 (mtp-110) REVERT: C 96 LYS cc_start: 0.8900 (mmtm) cc_final: 0.8596 (ttmt) REVERT: C 100 ASN cc_start: 0.6813 (p0) cc_final: 0.6420 (p0) REVERT: D 86 TYR cc_start: 0.8247 (m-10) cc_final: 0.7661 (m-10) REVERT: D 88 LYS cc_start: 0.8837 (mppt) cc_final: 0.8442 (mmtt) REVERT: E 69 ARG cc_start: 0.8494 (mtm-85) cc_final: 0.8177 (mtp180) REVERT: E 79 LYS cc_start: 0.8553 (tmtt) cc_final: 0.8278 (tptp) REVERT: F 52 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7785 (tp30) REVERT: F 77 LYS cc_start: 0.8291 (mmtt) cc_final: 0.8023 (mmmt) REVERT: F 83 SER cc_start: 0.8122 (p) cc_final: 0.7343 (t) REVERT: F 84 LEU cc_start: 0.8684 (tp) cc_final: 0.8430 (tp) REVERT: F 90 LEU cc_start: 0.8989 (mt) cc_final: 0.8647 (mt) REVERT: G 26 PHE cc_start: 0.8604 (m-10) cc_final: 0.8110 (m-10) REVERT: G 59 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8424 (tp) REVERT: H 72 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8839 (tp) REVERT: K 40 TYR cc_start: 0.5042 (p90) cc_final: 0.4752 (p90) REVERT: K 86 TRP cc_start: 0.6752 (OUTLIER) cc_final: 0.6419 (m-90) REVERT: L 40 TYR cc_start: 0.5131 (p90) cc_final: 0.4650 (p90) REVERT: L 193 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8563 (mmtp) outliers start: 61 outliers final: 44 residues processed: 264 average time/residue: 0.3380 time to fit residues: 118.9553 Evaluate side-chains 250 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 203 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 86 TRP Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 81 ASN Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN E 113 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 14005 Z= 0.395 Angle : 0.736 10.979 20007 Z= 0.406 Chirality : 0.043 0.209 2316 Planarity : 0.005 0.043 1668 Dihedral : 31.363 149.426 3864 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 7.98 % Allowed : 26.60 % Favored : 65.42 % 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: -1.30 (0.26), residues: 1029 helix: 0.08 (0.22), residues: 573 sheet: -1.37 (0.82), residues: 42 loop : -2.15 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 11 HIS 0.008 0.001 HIS B 75 PHE 0.016 0.002 PHE A 78 TYR 0.056 0.002 TYR H 86 ARG 0.010 0.001 ARG H 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 210 time to evaluate : 1.049 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: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8358 (tp) REVERT: A 83 ARG cc_start: 0.8287 (ptp-110) cc_final: 0.8073 (ptp-110) REVERT: B 25 ASN cc_start: 0.8312 (m-40) cc_final: 0.8108 (m-40) REVERT: B 35 ARG cc_start: 0.8861 (mtp-110) cc_final: 0.8287 (mtp-110) REVERT: B 44 LYS cc_start: 0.8842 (mttt) cc_final: 0.8447 (mttt) REVERT: B 53 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8211 (tm-30) REVERT: C 96 LYS cc_start: 0.8966 (mmtm) cc_final: 0.8671 (ttmt) REVERT: C 100 ASN cc_start: 0.7142 (p0) cc_final: 0.6658 (p0) REVERT: D 88 LYS cc_start: 0.8799 (mppt) cc_final: 0.8361 (mmtt) REVERT: D 116 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8507 (tm-30) REVERT: E 69 ARG cc_start: 0.8759 (mtm-85) cc_final: 0.8328 (mtp180) REVERT: E 81 ASP cc_start: 0.7875 (m-30) cc_final: 0.7649 (m-30) REVERT: E 129 ARG cc_start: 0.8112 (tpp80) cc_final: 0.7841 (tpp80) REVERT: F 25 ASN cc_start: 0.8260 (m-40) cc_final: 0.7932 (m-40) REVERT: F 52 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8094 (tp30) REVERT: F 83 SER cc_start: 0.8042 (p) cc_final: 0.7278 (t) REVERT: F 84 LEU cc_start: 0.8766 (tp) cc_final: 0.8510 (tp) REVERT: G 26 PHE cc_start: 0.9094 (m-10) cc_final: 0.8477 (m-10) REVERT: G 59 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8512 (tp) REVERT: H 75 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7803 (ttm170) REVERT: K 86 TRP cc_start: 0.7031 (OUTLIER) cc_final: 0.6600 (m-90) REVERT: L 86 TRP cc_start: 0.7073 (m-90) cc_final: 0.6486 (m-90) outliers start: 66 outliers final: 51 residues processed: 261 average time/residue: 0.3239 time to fit residues: 114.4771 Evaluate side-chains 252 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 198 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 86 TRP Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 81 ASN Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.9980 chunk 110 optimal weight: 30.0000 chunk 24 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 122 optimal weight: 30.0000 chunk 102 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN L 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14005 Z= 0.177 Angle : 0.609 10.881 20007 Z= 0.346 Chirality : 0.038 0.221 2316 Planarity : 0.004 0.049 1668 Dihedral : 31.047 148.457 3864 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 5.08 % Allowed : 31.20 % Favored : 63.72 % 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: -0.73 (0.26), residues: 1029 helix: 0.56 (0.22), residues: 571 sheet: -0.96 (0.86), residues: 42 loop : -1.93 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP K 11 HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE E 84 TYR 0.039 0.002 TYR H 86 ARG 0.005 0.001 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 244 time to evaluate : 1.065 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: symmetry clash REVERT: A 79 LYS cc_start: 0.8622 (tmtt) cc_final: 0.8385 (tptp) REVERT: A 83 ARG cc_start: 0.8153 (ptp-110) cc_final: 0.7871 (ptp-110) REVERT: B 25 ASN cc_start: 0.8244 (m-40) cc_final: 0.7832 (m110) REVERT: B 35 ARG cc_start: 0.8775 (mtp-110) cc_final: 0.8304 (mtt90) REVERT: B 44 LYS cc_start: 0.8744 (mttt) cc_final: 0.8466 (mttt) REVERT: B 46 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8449 (mt) REVERT: B 77 LYS cc_start: 0.8940 (mttt) cc_final: 0.8514 (mmtm) REVERT: C 96 LYS cc_start: 0.8929 (mmtm) cc_final: 0.8588 (ttmt) REVERT: C 100 ASN cc_start: 0.7028 (p0) cc_final: 0.6540 (p0) REVERT: D 46 LYS cc_start: 0.9216 (ttmm) cc_final: 0.9004 (ttmm) REVERT: D 86 TYR cc_start: 0.8246 (m-10) cc_final: 0.7773 (m-10) REVERT: D 88 LYS cc_start: 0.8788 (mppt) cc_final: 0.8418 (mmtt) REVERT: D 116 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8440 (tm-30) REVERT: E 69 ARG cc_start: 0.8559 (mtm-85) cc_final: 0.8178 (mtp180) REVERT: E 70 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8056 (tp) REVERT: E 79 LYS cc_start: 0.8658 (tmtt) cc_final: 0.8412 (tptp) REVERT: E 83 ARG cc_start: 0.8452 (mtp85) cc_final: 0.8235 (mtp85) REVERT: E 105 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: F 83 SER cc_start: 0.7965 (p) cc_final: 0.7259 (t) REVERT: F 84 LEU cc_start: 0.8583 (tp) cc_final: 0.8317 (tp) REVERT: G 26 PHE cc_start: 0.8606 (m-10) cc_final: 0.8138 (m-10) REVERT: G 59 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8439 (tp) outliers start: 42 outliers final: 26 residues processed: 270 average time/residue: 0.3091 time to fit residues: 113.3635 Evaluate side-chains 254 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 224 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 103 optimal weight: 30.0000 chunk 68 optimal weight: 2.9990 chunk 122 optimal weight: 30.0000 chunk 76 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14005 Z= 0.281 Angle : 0.663 9.283 20007 Z= 0.369 Chirality : 0.040 0.220 2316 Planarity : 0.004 0.049 1668 Dihedral : 31.147 148.924 3864 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 7.26 % Allowed : 31.32 % Favored : 61.43 % 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: -0.79 (0.26), residues: 1029 helix: 0.53 (0.22), residues: 572 sheet: -1.08 (0.71), residues: 60 loop : -2.01 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 11 HIS 0.009 0.001 HIS F 75 PHE 0.011 0.001 PHE H 73 TYR 0.030 0.002 TYR H 86 ARG 0.007 0.001 ARG K 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 228 time to evaluate : 1.038 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8250 (tp) REVERT: A 79 LYS cc_start: 0.8739 (tmtt) cc_final: 0.8327 (tptp) REVERT: A 83 ARG cc_start: 0.8145 (ptp-110) cc_final: 0.7874 (ptp-110) REVERT: B 44 LYS cc_start: 0.8803 (mttt) cc_final: 0.8356 (mttt) REVERT: B 46 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8581 (mm) REVERT: B 53 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8071 (tm-30) REVERT: B 77 LYS cc_start: 0.9078 (mttt) cc_final: 0.8676 (mmtp) REVERT: C 96 LYS cc_start: 0.9008 (mmtm) cc_final: 0.8663 (ttmt) REVERT: C 100 ASN cc_start: 0.7514 (p0) cc_final: 0.7183 (p0) REVERT: D 88 LYS cc_start: 0.8784 (mppt) cc_final: 0.8409 (mmtt) REVERT: D 116 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8512 (tm-30) REVERT: E 69 ARG cc_start: 0.8666 (mtm-85) cc_final: 0.8276 (mtp180) REVERT: E 70 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8189 (tp) REVERT: E 79 LYS cc_start: 0.8653 (tmtt) cc_final: 0.8375 (tptp) REVERT: E 105 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: E 129 ARG cc_start: 0.8190 (tpp80) cc_final: 0.7802 (tpp80) REVERT: F 52 GLU cc_start: 0.8058 (tp30) cc_final: 0.7822 (tp30) REVERT: F 83 SER cc_start: 0.8002 (p) cc_final: 0.7310 (t) REVERT: F 84 LEU cc_start: 0.8578 (tp) cc_final: 0.8357 (tp) REVERT: G 26 PHE cc_start: 0.8928 (m-10) cc_final: 0.8315 (m-10) outliers start: 60 outliers final: 48 residues processed: 265 average time/residue: 0.3108 time to fit residues: 111.5631 Evaluate side-chains 257 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 205 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 171 PHE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 96 optimal weight: 0.2980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14005 Z= 0.204 Angle : 0.630 9.416 20007 Z= 0.353 Chirality : 0.039 0.235 2316 Planarity : 0.004 0.052 1668 Dihedral : 31.052 148.484 3864 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 6.41 % Allowed : 33.01 % Favored : 60.58 % 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: -0.61 (0.26), residues: 1029 helix: 0.70 (0.22), residues: 570 sheet: -1.00 (0.73), residues: 60 loop : -1.94 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 11 HIS 0.007 0.001 HIS F 75 PHE 0.009 0.001 PHE H 73 TYR 0.028 0.002 TYR H 86 ARG 0.008 0.001 ARG K 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 234 time to evaluate : 1.233 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7925 (tt0) cc_final: 0.7558 (tt0) REVERT: A 79 LYS cc_start: 0.8699 (tmtt) cc_final: 0.8387 (tptp) REVERT: A 83 ARG cc_start: 0.8238 (ptp-110) cc_final: 0.7976 (ptp-110) REVERT: B 44 LYS cc_start: 0.8878 (mttt) cc_final: 0.8522 (mttt) REVERT: B 53 GLU cc_start: 0.8287 (tm-30) cc_final: 0.8054 (tm-30) REVERT: B 77 LYS cc_start: 0.8999 (mttt) cc_final: 0.8518 (mmtm) REVERT: C 96 LYS cc_start: 0.8996 (mmtm) cc_final: 0.8656 (ttmt) REVERT: C 100 ASN cc_start: 0.7407 (p0) cc_final: 0.7045 (p0) REVERT: D 86 TYR cc_start: 0.8262 (m-10) cc_final: 0.7746 (m-10) REVERT: D 88 LYS cc_start: 0.8756 (mppt) cc_final: 0.8407 (mmtt) REVERT: D 116 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8532 (tm-30) REVERT: E 69 ARG cc_start: 0.8582 (mtm-85) cc_final: 0.8185 (mtp180) REVERT: E 70 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8076 (tp) REVERT: E 79 LYS cc_start: 0.8654 (tmtt) cc_final: 0.8344 (tptp) REVERT: E 105 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: F 52 GLU cc_start: 0.7949 (tp30) cc_final: 0.7712 (tp30) REVERT: F 83 SER cc_start: 0.7954 (p) cc_final: 0.7210 (t) REVERT: F 84 LEU cc_start: 0.8534 (tp) cc_final: 0.8300 (tp) REVERT: G 26 PHE cc_start: 0.8775 (m-10) cc_final: 0.8173 (m-10) REVERT: L 48 ILE cc_start: 0.6431 (mm) cc_final: 0.6133 (mp) REVERT: L 148 ARG cc_start: 0.6372 (ptt-90) cc_final: 0.5970 (pmt170) outliers start: 53 outliers final: 41 residues processed: 266 average time/residue: 0.3116 time to fit residues: 112.2260 Evaluate side-chains 266 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 223 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 20.0000 chunk 117 optimal weight: 30.0000 chunk 106 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14005 Z= 0.305 Angle : 0.692 11.517 20007 Z= 0.382 Chirality : 0.041 0.244 2316 Planarity : 0.005 0.077 1668 Dihedral : 31.191 149.007 3864 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 6.65 % Allowed : 33.01 % Favored : 60.34 % 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: -0.70 (0.26), residues: 1029 helix: 0.51 (0.22), residues: 571 sheet: -0.68 (0.91), residues: 44 loop : -1.84 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 11 HIS 0.008 0.001 HIS F 75 PHE 0.011 0.002 PHE A 78 TYR 0.049 0.002 TYR H 86 ARG 0.015 0.001 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 218 time to evaluate : 1.191 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: symmetry clash REVERT: A 79 LYS cc_start: 0.8808 (tmtt) cc_final: 0.8480 (tptp) REVERT: A 83 ARG cc_start: 0.8245 (ptp-110) cc_final: 0.7982 (ptp-110) REVERT: B 25 ASN cc_start: 0.8407 (m-40) cc_final: 0.8016 (m110) REVERT: B 44 LYS cc_start: 0.8955 (mttt) cc_final: 0.8505 (mttt) REVERT: B 53 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8050 (tm-30) REVERT: B 77 LYS cc_start: 0.9128 (mttt) cc_final: 0.8716 (mmtp) REVERT: C 96 LYS cc_start: 0.9036 (mmtm) cc_final: 0.8716 (ttmt) REVERT: C 100 ASN cc_start: 0.7521 (p0) cc_final: 0.7145 (p0) REVERT: D 86 TYR cc_start: 0.8337 (m-10) cc_final: 0.7769 (m-10) REVERT: D 88 LYS cc_start: 0.8753 (mppt) cc_final: 0.8424 (mmtt) REVERT: D 116 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8553 (tm-30) REVERT: E 69 ARG cc_start: 0.8693 (mtm-85) cc_final: 0.8323 (mtp180) REVERT: E 70 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8191 (tp) REVERT: E 79 LYS cc_start: 0.8699 (tmtt) cc_final: 0.8484 (tptp) REVERT: E 105 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: E 129 ARG cc_start: 0.8259 (tpp80) cc_final: 0.7843 (tpp80) REVERT: F 52 GLU cc_start: 0.8165 (tp30) cc_final: 0.7941 (tp30) REVERT: F 77 LYS cc_start: 0.8942 (mmtt) cc_final: 0.8595 (mmtt) REVERT: F 83 SER cc_start: 0.8031 (p) cc_final: 0.7328 (t) REVERT: G 26 PHE cc_start: 0.9016 (m-10) cc_final: 0.8644 (m-80) REVERT: G 65 GLU cc_start: 0.8333 (pp20) cc_final: 0.8010 (pp20) outliers start: 55 outliers final: 49 residues processed: 254 average time/residue: 0.3005 time to fit residues: 104.5661 Evaluate side-chains 252 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 201 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 81 ASN Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 10.0000 chunk 120 optimal weight: 0.0270 chunk 73 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 126 optimal weight: 8.9990 chunk 116 optimal weight: 0.5980 chunk 100 optimal weight: 40.0000 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 overall best weight: 2.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14005 Z= 0.260 Angle : 0.665 11.489 20007 Z= 0.369 Chirality : 0.040 0.257 2316 Planarity : 0.004 0.049 1668 Dihedral : 31.158 148.690 3864 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 6.29 % Allowed : 33.62 % Favored : 60.10 % 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: -0.62 (0.26), residues: 1029 helix: 0.55 (0.22), residues: 568 sheet: -0.70 (0.90), residues: 44 loop : -1.74 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 11 HIS 0.006 0.001 HIS F 75 PHE 0.008 0.001 PHE A 78 TYR 0.043 0.002 TYR H 86 ARG 0.009 0.001 ARG E 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 218 time to evaluate : 1.158 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8221 (tp) REVERT: A 83 ARG cc_start: 0.8313 (ptp-110) cc_final: 0.8048 (ptp-110) REVERT: B 25 ASN cc_start: 0.8412 (m-40) cc_final: 0.8057 (m110) REVERT: B 44 LYS cc_start: 0.8912 (mttt) cc_final: 0.8426 (mttt) REVERT: B 53 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8004 (tm-30) REVERT: B 77 LYS cc_start: 0.9064 (mttt) cc_final: 0.8685 (mmtp) REVERT: C 96 LYS cc_start: 0.9032 (mmtm) cc_final: 0.8726 (ttmt) REVERT: C 100 ASN cc_start: 0.7444 (p0) cc_final: 0.7063 (p0) REVERT: D 88 LYS cc_start: 0.8740 (mppt) cc_final: 0.8407 (mmtt) REVERT: D 116 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8510 (tm-30) REVERT: E 70 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8117 (tp) REVERT: E 79 LYS cc_start: 0.8698 (tmtt) cc_final: 0.8486 (tptp) REVERT: E 105 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7371 (tt0) REVERT: F 83 SER cc_start: 0.7985 (p) cc_final: 0.7238 (t) REVERT: G 26 PHE cc_start: 0.8958 (m-10) cc_final: 0.8292 (m-10) REVERT: L 48 ILE cc_start: 0.6026 (mm) cc_final: 0.5669 (mp) REVERT: L 148 ARG cc_start: 0.6200 (ptt-90) cc_final: 0.5779 (pmt170) outliers start: 52 outliers final: 47 residues processed: 252 average time/residue: 0.2915 time to fit residues: 101.7061 Evaluate side-chains 258 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 208 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 59 HIS Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 81 ASN Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 0.0670 chunk 100 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.118183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.085533 restraints weight = 40265.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.087554 restraints weight = 23805.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.088813 restraints weight = 17869.165| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14005 Z= 0.180 Angle : 0.633 11.590 20007 Z= 0.353 Chirality : 0.038 0.239 2316 Planarity : 0.004 0.053 1668 Dihedral : 30.918 148.350 3864 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.72 % Allowed : 35.43 % Favored : 59.85 % 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: -0.32 (0.26), residues: 1029 helix: 0.85 (0.23), residues: 564 sheet: -0.10 (0.91), residues: 40 loop : -1.70 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 11 HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE B 61 TYR 0.020 0.002 TYR H 86 ARG 0.008 0.001 ARG E 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2894.48 seconds wall clock time: 53 minutes 24.31 seconds (3204.31 seconds total)