Starting phenix.real_space_refine on Wed May 8 23:03:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr0_40716/05_2024/8sr0_40716_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr0_40716/05_2024/8sr0_40716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr0_40716/05_2024/8sr0_40716.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr0_40716/05_2024/8sr0_40716.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr0_40716/05_2024/8sr0_40716_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr0_40716/05_2024/8sr0_40716_trim.pdb" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 3756 2.51 5 N 1067 2.21 5 O 1139 1.98 5 H 5426 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X GLU 223": "OE1" <-> "OE2" Residue "Z GLU 85": "OE1" <-> "OE2" Residue "L GLU 85": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 11414 Number of models: 1 Model: "" Number of chains: 8 Chain: "X" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 2479 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 20, 'TRANS': 161} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 89 Chain: "Y" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1743 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "Z" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1568 Classifications: {'peptide': 109} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 100} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2493 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 19, 'TRANS': 161} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 89 Chain: "H" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1553 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "L" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1550 Classifications: {'peptide': 109} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 100} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "X" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.34, per 1000 atoms: 0.47 Number of scatterers: 11414 At special positions: 0 Unit cell: (98.56, 101.92, 108.64, 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 26 16.00 O 1139 8.00 N 1067 7.00 C 3756 6.00 H 5426 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS X 44 " - pdb=" SG CYS X 160 " distance=2.03 Simple disulfide: pdb=" SG CYS X 189 " - pdb=" SG CYS X 241 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 44 " - pdb=" SG CYS D 160 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 241 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.04 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: 8.58 Conformation dependent library (CDL) restraints added in 1.3 seconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1486 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 22 sheets defined 1.8% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'X' and resid 232 through 236 Processing helix chain 'D' and resid 140 through 144 removed outlier: 3.604A pdb=" N ASP D 143 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 144 " --> pdb=" O ARG D 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 140 through 144' Processing helix chain 'L' and resid 63 through 67 Processing sheet with id=AA1, first strand: chain 'X' and resid 34 through 35 removed outlier: 5.999A pdb=" N ALA X 34 " --> pdb=" O GLY X 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'X' and resid 40 through 43 Processing sheet with id=AA3, first strand: chain 'X' and resid 99 through 102 removed outlier: 5.507A pdb=" N THR X 100 " --> pdb=" O HIS X 65 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N HIS X 65 " --> pdb=" O THR X 100 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU X 102 " --> pdb=" O TRP X 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 185 through 186 Processing sheet with id=AA5, first strand: chain 'X' and resid 199 through 203 Processing sheet with id=AA6, first strand: chain 'Y' and resid 3 through 4 removed outlier: 3.725A pdb=" N LEU Y 3 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER Y 25 " --> pdb=" O LEU Y 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'Y' and resid 18 through 21 removed outlier: 3.569A pdb=" N VAL Y 18 " --> pdb=" O LEU Y 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Y' and resid 46 through 51 removed outlier: 6.621A pdb=" N TRP Y 36 " --> pdb=" O ILE Y 48 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ASP Y 50 " --> pdb=" O VAL Y 34 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL Y 34 " --> pdb=" O ASP Y 50 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA Y 92 " --> pdb=" O VAL Y 115 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL Y 115 " --> pdb=" O ALA Y 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Z' and resid 5 through 7 removed outlier: 3.524A pdb=" N SER Z 7 " --> pdb=" O SER Z 22 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER Z 22 " --> pdb=" O SER Z 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Z' and resid 10 through 12 Processing sheet with id=AB2, first strand: chain 'Z' and resid 19 through 20 Processing sheet with id=AB3, first strand: chain 'Z' and resid 49 through 50 Processing sheet with id=AB4, first strand: chain 'Z' and resid 52 through 53 Processing sheet with id=AB5, first strand: chain 'D' and resid 40 through 42 Processing sheet with id=AB6, first strand: chain 'D' and resid 63 through 66 Processing sheet with id=AB7, first strand: chain 'D' and resid 171 through 173 Processing sheet with id=AB8, first strand: chain 'D' and resid 199 through 202 removed outlier: 3.583A pdb=" N SER D 199 " --> pdb=" O THR D 244 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR D 244 " --> pdb=" O SER D 199 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR D 255 " --> pdb=" O TRP D 239 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE D 253 " --> pdb=" O CYS D 241 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.539A pdb=" N SER H 25 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.914A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR H 100 " --> pdb=" O MET H 106 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N MET H 106 " --> pdb=" O TYR H 100 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.765A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.843A pdb=" N ILE L 52 " --> pdb=" O TRP L 39 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLN L 41 " --> pdb=" O LEU L 50 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU L 50 " --> pdb=" O GLN L 41 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 19 through 20 133 hydrogen bonds defined for protein. 285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.64 Time building geometry restraints manager: 8.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 5426 1.04 - 1.23: 120 1.23 - 1.43: 2534 1.43 - 1.62: 3455 1.62 - 1.82: 36 Bond restraints: 11571 Sorted by residual: bond pdb=" C SER X 216 " pdb=" N PRO X 217 " ideal model delta sigma weight residual 1.336 1.519 -0.183 1.25e-02 6.40e+03 2.15e+02 bond pdb=" C TRP D 63 " pdb=" O TRP D 63 " ideal model delta sigma weight residual 1.233 1.114 0.119 1.47e-02 4.63e+03 6.60e+01 bond pdb=" NZ LYS H 43 " pdb=" HZ1 LYS H 43 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS H 38 " pdb=" HZ2 LYS H 38 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS Y 63 " pdb=" HZ3 LYS Y 63 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 11566 not shown) Histogram of bond angle deviations from ideal: 91.12 - 106.37: 445 106.37 - 121.61: 17623 121.61 - 136.85: 2667 136.85 - 152.10: 2 152.10 - 167.34: 2 Bond angle restraints: 20739 Sorted by residual: angle pdb=" CA ARG X 129 " pdb=" N ARG X 129 " pdb=" H ARG X 129 " ideal model delta sigma weight residual 114.00 167.34 -53.34 3.00e+00 1.11e-01 3.16e+02 angle pdb=" CA SER D 90 " pdb=" N SER D 90 " pdb=" H SER D 90 " ideal model delta sigma weight residual 114.00 156.97 -42.97 3.00e+00 1.11e-01 2.05e+02 angle pdb=" CA SER X 90 " pdb=" N SER X 90 " pdb=" H SER X 90 " ideal model delta sigma weight residual 114.00 144.03 -30.03 3.00e+00 1.11e-01 1.00e+02 angle pdb=" C PRO X 94 " pdb=" N ARG X 95 " pdb=" CA ARG X 95 " ideal model delta sigma weight residual 121.80 143.84 -22.04 2.44e+00 1.68e-01 8.16e+01 angle pdb=" CA SER X 216 " pdb=" C SER X 216 " pdb=" N PRO X 217 " ideal model delta sigma weight residual 117.60 127.65 -10.05 1.20e+00 6.94e-01 7.01e+01 ... (remaining 20734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 5107 17.57 - 35.13: 382 35.13 - 52.70: 127 52.70 - 70.27: 33 70.27 - 87.83: 11 Dihedral angle restraints: 5660 sinusoidal: 2940 harmonic: 2720 Sorted by residual: dihedral pdb=" CB CYS X 44 " pdb=" SG CYS X 44 " pdb=" SG CYS X 160 " pdb=" CB CYS X 160 " ideal model delta sinusoidal sigma weight residual -86.00 -170.16 84.16 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS Z 23 " pdb=" SG CYS Z 23 " pdb=" SG CYS Z 92 " pdb=" CB CYS Z 92 " ideal model delta sinusoidal sigma weight residual 93.00 163.34 -70.34 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" CA HIS Z 80 " pdb=" C HIS Z 80 " pdb=" N PRO Z 81 " pdb=" CA PRO Z 81 " ideal model delta harmonic sigma weight residual 0.00 -27.20 27.20 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 5657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 820 0.084 - 0.168: 95 0.168 - 0.252: 1 0.252 - 0.336: 0 0.336 - 0.420: 3 Chirality restraints: 919 Sorted by residual: chirality pdb=" CA SER D 174 " pdb=" N SER D 174 " pdb=" C SER D 174 " pdb=" CB SER D 174 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CA HIS D 152 " pdb=" N HIS D 152 " pdb=" C HIS D 152 " pdb=" CB HIS D 152 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CB VAL D 61 " pdb=" CA VAL D 61 " pdb=" CG1 VAL D 61 " pdb=" CG2 VAL D 61 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 916 not shown) Planarity restraints: 1841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP D 63 " 0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C TRP D 63 " -0.073 2.00e-02 2.50e+03 pdb=" O TRP D 63 " 0.028 2.00e-02 2.50e+03 pdb=" N GLN D 64 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG X 214 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C ARG X 214 " 0.058 2.00e-02 2.50e+03 pdb=" O ARG X 214 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU X 215 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS Z 80 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.75e+00 pdb=" N PRO Z 81 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO Z 81 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO Z 81 " -0.033 5.00e-02 4.00e+02 ... (remaining 1838 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 283 2.10 - 2.72: 18428 2.72 - 3.35: 28668 3.35 - 3.97: 37457 3.97 - 4.60: 57159 Nonbonded interactions: 141995 Sorted by model distance: nonbonded pdb=" OE1 GLU L 85 " pdb=" H GLU L 85 " model vdw 1.473 1.850 nonbonded pdb=" OE1 GLU Z 85 " pdb=" H GLU Z 85 " model vdw 1.543 1.850 nonbonded pdb=" OE1 GLN Z 27 " pdb=" H GLN Z 27 " model vdw 1.588 1.850 nonbonded pdb=" O ALA L 9 " pdb=" H LYS L 107 " model vdw 1.637 1.850 nonbonded pdb=" O MET Y 106 " pdb=" HH TYR Z 40 " model vdw 1.649 1.850 ... (remaining 141990 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 'D' and (resid 27 or (resid 28 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 29 through 49 or resid 59 through 6 \ 0 or (resid 61 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 62 through 71 or (resid 90 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 91 through 104 or resid \ 130 through 140 or (resid 141 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 142 through 151 or (resid 152 through 156 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 157 or (resid 158 through 159 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 160 through 162 or (resid 163 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 164 through 167 or (resid 168 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 169 through 182 or (resid 183 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 184 th \ rough 203 or (resid 204 through 206 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 207 through 230 or (resid 231 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 232 through 245 or (resid 246 through 247 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 248 through 257 or resid 601)) selection = (chain 'X' and (resid 27 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 37 through 46 or (resid \ 47 through 48 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 49 or resid 59 through 70 or (resid 71 and (name N or name \ CA or name C or name O or name CB or name HA )) or resid 90 through 91 or (resid \ 92 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 93 through 104 or resid 130 through 134 or (resid 135 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 136 thro \ ugh 154 or (resid 155 through 156 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 157 through 158 or (resid 159 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 16 \ 0 through 195 or (resid 196 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 197 through 213 or (resid 214 through 215 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 216 through 252 or (resid 253 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 254 through 257 or resid 601)) } ncs_group { reference = (chain 'H' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 6 through 85 or (resid 86 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 87 through 117)) selection = (chain 'Y' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 8 through 10 or (resid 11 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 12 or (resid 13 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 14 through 17 or (resid 18 through 20 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 21 thr \ ough 40 or (resid 41 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 42 through 61 or (resid 62 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 63 through 64 or ( \ resid 65 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 66 or (resid 67 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 68 or (resid 69 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 70 through 73 or ( \ resid 74 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 75 through 81 or (resid 82 through 84 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 85 through 87 or (r \ esid 88 through 90 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 91 through 117)) } ncs_group { reference = chain 'L' selection = (chain 'Z' and (resid 1 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 47 through 96 or (resid 9 \ 7 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 98 through 109)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.170 Extract box with map and model: 7.440 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 38.080 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.183 6145 Z= 0.306 Angle : 0.799 22.045 8393 Z= 0.436 Chirality : 0.052 0.420 919 Planarity : 0.006 0.065 1102 Dihedral : 14.056 87.834 2139 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.34 % Allowed : 0.68 % Favored : 98.98 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 9.52 % 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: -2.68 (0.28), residues: 792 helix: None (None), residues: 0 sheet: -1.72 (0.29), residues: 300 loop : -1.85 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 63 HIS 0.014 0.001 HIS D 152 PHE 0.017 0.002 PHE Z 75 TYR 0.010 0.001 TYR D 147 ARG 0.007 0.001 ARG X 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 58 ARG cc_start: 0.5984 (OUTLIER) cc_final: 0.4277 (ptm-80) REVERT: D 254 MET cc_start: 0.7273 (tpp) cc_final: 0.6782 (tpp) REVERT: H 98 ARG cc_start: 0.8156 (ttt180) cc_final: 0.7909 (ttt180) outliers start: 2 outliers final: 1 residues processed: 95 average time/residue: 0.4375 time to fit residues: 52.6259 Evaluate side-chains 86 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 62 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6145 Z= 0.227 Angle : 0.638 5.650 8393 Z= 0.324 Chirality : 0.045 0.156 919 Planarity : 0.005 0.051 1102 Dihedral : 5.584 29.098 918 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.85 % Allowed : 8.69 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -2.67 (0.28), residues: 792 helix: None (None), residues: 0 sheet: -1.72 (0.29), residues: 309 loop : -1.83 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 63 HIS 0.004 0.001 HIS Z 80 PHE 0.014 0.002 PHE H 95 TYR 0.009 0.001 TYR D 147 ARG 0.004 0.000 ARG X 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 254 MET cc_start: 0.7247 (tpp) cc_final: 0.7042 (tpp) outliers start: 5 outliers final: 4 residues processed: 89 average time/residue: 0.4419 time to fit residues: 50.3931 Evaluate side-chains 82 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 166 LEU Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Z residue 1 ASP Chi-restraints excluded: chain D residue 247 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 0.0470 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 0.0370 chunk 70 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6145 Z= 0.164 Angle : 0.572 4.987 8393 Z= 0.290 Chirality : 0.044 0.151 919 Planarity : 0.004 0.046 1102 Dihedral : 5.019 27.139 913 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.68 % Allowed : 10.56 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -2.50 (0.28), residues: 792 helix: None (None), residues: 0 sheet: -1.63 (0.29), residues: 308 loop : -1.69 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 63 HIS 0.009 0.001 HIS X 219 PHE 0.012 0.001 PHE H 95 TYR 0.008 0.001 TYR L 31 ARG 0.003 0.000 ARG Y 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 79 average time/residue: 0.5095 time to fit residues: 50.5112 Evaluate side-chains 77 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 166 LEU Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 6 GLN D 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6145 Z= 0.249 Angle : 0.595 5.433 8393 Z= 0.305 Chirality : 0.044 0.147 919 Planarity : 0.005 0.040 1102 Dihedral : 5.236 29.706 913 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 2.39 % Allowed : 10.90 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -2.56 (0.28), residues: 792 helix: None (None), residues: 0 sheet: -1.63 (0.29), residues: 311 loop : -1.75 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 202 HIS 0.005 0.001 HIS X 219 PHE 0.015 0.002 PHE H 95 TYR 0.009 0.001 TYR Y 32 ARG 0.003 0.000 ARG X 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 LEU cc_start: 0.5573 (OUTLIER) cc_final: 0.5300 (pt) outliers start: 14 outliers final: 9 residues processed: 84 average time/residue: 0.4521 time to fit residues: 48.1323 Evaluate side-chains 81 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 166 LEU Chi-restraints excluded: chain X residue 216 SER Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 93 VAL Chi-restraints excluded: chain Z residue 1 ASP Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6145 Z= 0.237 Angle : 0.588 6.047 8393 Z= 0.302 Chirality : 0.044 0.148 919 Planarity : 0.005 0.050 1102 Dihedral : 5.182 31.802 913 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.21 % Allowed : 12.27 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.28), residues: 792 helix: None (None), residues: 0 sheet: -1.63 (0.29), residues: 311 loop : -1.71 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 63 HIS 0.005 0.001 HIS D 65 PHE 0.013 0.002 PHE H 95 TYR 0.009 0.001 TYR Y 32 ARG 0.003 0.000 ARG X 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 LEU cc_start: 0.5449 (OUTLIER) cc_final: 0.5135 (pt) outliers start: 13 outliers final: 8 residues processed: 84 average time/residue: 0.4279 time to fit residues: 45.7611 Evaluate side-chains 79 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 166 LEU Chi-restraints excluded: chain X residue 216 SER Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 93 VAL Chi-restraints excluded: chain Z residue 1 ASP Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain L residue 38 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 39 optimal weight: 0.0020 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6145 Z= 0.182 Angle : 0.551 5.487 8393 Z= 0.279 Chirality : 0.043 0.145 919 Planarity : 0.004 0.041 1102 Dihedral : 4.917 30.230 913 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.53 % Allowed : 13.97 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -2.41 (0.29), residues: 792 helix: None (None), residues: 0 sheet: -1.54 (0.30), residues: 304 loop : -1.66 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 202 HIS 0.003 0.001 HIS X 219 PHE 0.011 0.001 PHE H 95 TYR 0.010 0.001 TYR L 31 ARG 0.002 0.000 ARG X 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 45 LEU cc_start: 0.5449 (OUTLIER) cc_final: 0.5164 (pt) outliers start: 9 outliers final: 7 residues processed: 84 average time/residue: 0.4526 time to fit residues: 48.9422 Evaluate side-chains 81 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 166 LEU Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Z residue 1 ASP Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain L residue 38 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6145 Z= 0.220 Angle : 0.565 6.006 8393 Z= 0.287 Chirality : 0.044 0.150 919 Planarity : 0.004 0.042 1102 Dihedral : 4.967 31.205 913 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 2.21 % Allowed : 13.46 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -2.39 (0.29), residues: 792 helix: None (None), residues: 0 sheet: -1.52 (0.30), residues: 317 loop : -1.63 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 47 HIS 0.002 0.001 HIS D 152 PHE 0.015 0.002 PHE X 227 TYR 0.016 0.001 TYR L 40 ARG 0.003 0.000 ARG X 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 LEU cc_start: 0.5443 (OUTLIER) cc_final: 0.5132 (pt) outliers start: 13 outliers final: 8 residues processed: 87 average time/residue: 0.4538 time to fit residues: 49.9759 Evaluate side-chains 82 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 166 LEU Chi-restraints excluded: chain X residue 216 SER Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Z residue 1 ASP Chi-restraints excluded: chain D residue 230 GLN Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain L residue 38 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 65 optimal weight: 0.0040 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6145 Z= 0.163 Angle : 0.536 5.330 8393 Z= 0.271 Chirality : 0.043 0.144 919 Planarity : 0.004 0.041 1102 Dihedral : 4.684 28.941 913 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.04 % Allowed : 13.97 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.29), residues: 792 helix: None (None), residues: 0 sheet: -1.50 (0.31), residues: 292 loop : -1.55 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 63 HIS 0.002 0.001 HIS X 219 PHE 0.011 0.001 PHE H 80 TYR 0.013 0.001 TYR L 40 ARG 0.003 0.000 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 45 LEU cc_start: 0.5395 (OUTLIER) cc_final: 0.5127 (pt) outliers start: 12 outliers final: 7 residues processed: 82 average time/residue: 0.4596 time to fit residues: 47.9890 Evaluate side-chains 81 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 166 LEU Chi-restraints excluded: chain X residue 216 SER Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Z residue 1 ASP Chi-restraints excluded: chain Z residue 38 ASN Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 115 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 0.0670 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6145 Z= 0.210 Angle : 0.552 5.657 8393 Z= 0.280 Chirality : 0.043 0.145 919 Planarity : 0.004 0.039 1102 Dihedral : 4.792 29.184 913 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 1.70 % Allowed : 14.14 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -2.27 (0.29), residues: 792 helix: None (None), residues: 0 sheet: -1.44 (0.30), residues: 317 loop : -1.54 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.002 0.001 HIS D 201 PHE 0.011 0.002 PHE Y 64 TYR 0.014 0.001 TYR L 40 ARG 0.002 0.000 ARG X 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue SER 182 is missing expected H atoms. Skipping. Residue MET 234 is missing expected H atoms. Skipping. Residue ILE 253 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue VAL 18 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 LEU cc_start: 0.5502 (OUTLIER) cc_final: 0.5216 (pt) outliers start: 10 outliers final: 8 residues processed: 84 average time/residue: 0.4449 time to fit residues: 46.5850 Evaluate side-chains 84 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 166 LEU Chi-restraints excluded: chain X residue 216 SER Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Z residue 1 ASP Chi-restraints excluded: chain Z residue 38 ASN Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain L residue 38 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.0970 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -build -allalt -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: