Starting phenix.real_space_refine on Fri Apr 5 23:19:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sks_40566/04_2024/8sks_40566.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sks_40566/04_2024/8sks_40566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sks_40566/04_2024/8sks_40566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sks_40566/04_2024/8sks_40566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sks_40566/04_2024/8sks_40566.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sks_40566/04_2024/8sks_40566.pdb" } resolution = 2.91 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= 0.019 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 Mn 4 7.51 5 S 16 5.16 5 C 3992 2.51 5 N 1092 2.21 5 O 1128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 39": "OE1" <-> "OE2" Residue "A GLU 66": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D GLU 66": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6232 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1557 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 187} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1557 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 187} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1557 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 187} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1557 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 187} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.71, per 1000 atoms: 0.60 Number of scatterers: 6232 At special positions: 0 Unit cell: (71.69, 86.67, 86.67, 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) Mn 4 24.99 S 16 16.00 O 1128 8.00 N 1092 7.00 C 3992 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: 2.44 Conformation dependent library (CDL) restraints added in 1.3 seconds 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 69.2% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 34 through 39 removed outlier: 4.275A pdb=" N LEU A 38 " --> pdb=" O TYR A 35 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 39 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 76 removed outlier: 3.915A pdb=" N HIS A 55 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ALA A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 105 Proline residue: A 86 - end of helix removed outlier: 3.627A pdb=" N THR A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 196 through 205 removed outlier: 3.517A pdb=" N TYR A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 222 Processing helix chain 'B' and resid 34 through 39 removed outlier: 4.276A pdb=" N LEU B 38 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU B 39 " --> pdb=" O GLY B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 76 removed outlier: 3.914A pdb=" N HIS B 55 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 105 Proline residue: B 86 - end of helix removed outlier: 3.628A pdb=" N THR B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 126 Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'B' and resid 196 through 205 removed outlier: 3.516A pdb=" N TYR B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 222 Processing helix chain 'C' and resid 34 through 39 removed outlier: 4.276A pdb=" N LEU C 38 " --> pdb=" O TYR C 35 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 39 " --> pdb=" O GLY C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 76 removed outlier: 3.915A pdb=" N HIS C 55 " --> pdb=" O HIS C 51 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA C 56 " --> pdb=" O SER C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 105 Proline residue: C 86 - end of helix removed outlier: 3.627A pdb=" N THR C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 185 through 188 Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 196 through 205 removed outlier: 3.517A pdb=" N TYR C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 222 Processing helix chain 'D' and resid 34 through 39 removed outlier: 4.275A pdb=" N LEU D 38 " --> pdb=" O TYR D 35 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU D 39 " --> pdb=" O GLY D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 76 removed outlier: 3.915A pdb=" N HIS D 55 " --> pdb=" O HIS D 51 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 105 Proline residue: D 86 - end of helix removed outlier: 3.628A pdb=" N THR D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 126 Processing helix chain 'D' and resid 127 through 142 Processing helix chain 'D' and resid 169 through 174 Processing helix chain 'D' and resid 185 through 188 Processing helix chain 'D' and resid 189 through 194 Processing helix chain 'D' and resid 196 through 205 removed outlier: 3.517A pdb=" N TYR D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 165 removed outlier: 7.322A pdb=" N GLY A 146 " --> pdb=" O ASP A 183 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP A 183 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY A 148 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY A 181 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 150 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 158 through 165 removed outlier: 7.323A pdb=" N GLY B 146 " --> pdb=" O ASP B 183 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASP B 183 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY B 148 " --> pdb=" O GLY B 181 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY B 181 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU B 150 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 158 through 165 removed outlier: 7.323A pdb=" N GLY C 146 " --> pdb=" O ASP C 183 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP C 183 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY C 148 " --> pdb=" O GLY C 181 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY C 181 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 150 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 158 through 165 removed outlier: 7.322A pdb=" N GLY D 146 " --> pdb=" O ASP D 183 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP D 183 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY D 148 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY D 181 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU D 150 " --> pdb=" O LEU D 179 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1164 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: 1.66 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2041 1.34 - 1.46: 1253 1.46 - 1.57: 3094 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 6412 Sorted by residual: bond pdb=" CA LYS D 221 " pdb=" C LYS D 221 " ideal model delta sigma weight residual 1.524 1.508 0.016 1.28e-02 6.10e+03 1.61e+00 bond pdb=" CA VAL A 196 " pdb=" CB VAL A 196 " ideal model delta sigma weight residual 1.527 1.543 -0.016 1.31e-02 5.83e+03 1.45e+00 bond pdb=" CA LYS C 221 " pdb=" C LYS C 221 " ideal model delta sigma weight residual 1.524 1.509 0.015 1.28e-02 6.10e+03 1.45e+00 bond pdb=" CA LYS B 221 " pdb=" C LYS B 221 " ideal model delta sigma weight residual 1.524 1.509 0.015 1.28e-02 6.10e+03 1.45e+00 bond pdb=" CA VAL B 196 " pdb=" CB VAL B 196 " ideal model delta sigma weight residual 1.527 1.542 -0.016 1.31e-02 5.83e+03 1.41e+00 ... (remaining 6407 not shown) Histogram of bond angle deviations from ideal: 101.24 - 107.82: 350 107.82 - 114.40: 3525 114.40 - 120.97: 3098 120.97 - 127.55: 1632 127.55 - 134.13: 119 Bond angle restraints: 8724 Sorted by residual: angle pdb=" C VAL A 196 " pdb=" N ARG A 197 " pdb=" CA ARG A 197 " ideal model delta sigma weight residual 120.09 124.62 -4.53 1.25e+00 6.40e-01 1.31e+01 angle pdb=" C VAL B 196 " pdb=" N ARG B 197 " pdb=" CA ARG B 197 " ideal model delta sigma weight residual 120.09 124.61 -4.52 1.25e+00 6.40e-01 1.31e+01 angle pdb=" C VAL D 196 " pdb=" N ARG D 197 " pdb=" CA ARG D 197 " ideal model delta sigma weight residual 120.09 124.61 -4.52 1.25e+00 6.40e-01 1.31e+01 angle pdb=" C VAL C 196 " pdb=" N ARG C 197 " pdb=" CA ARG C 197 " ideal model delta sigma weight residual 120.09 124.58 -4.49 1.25e+00 6.40e-01 1.29e+01 angle pdb=" N VAL C 184 " pdb=" CA VAL C 184 " pdb=" C VAL C 184 " ideal model delta sigma weight residual 112.29 109.52 2.77 9.40e-01 1.13e+00 8.66e+00 ... (remaining 8719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 3408 16.49 - 32.99: 256 32.99 - 49.48: 28 49.48 - 65.98: 8 65.98 - 82.47: 4 Dihedral angle restraints: 3704 sinusoidal: 1448 harmonic: 2256 Sorted by residual: dihedral pdb=" CA TRP B 149 " pdb=" C TRP B 149 " pdb=" N LEU B 150 " pdb=" CA LEU B 150 " ideal model delta harmonic sigma weight residual 180.00 161.65 18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TRP C 149 " pdb=" C TRP C 149 " pdb=" N LEU C 150 " pdb=" CA LEU C 150 " ideal model delta harmonic sigma weight residual 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA TRP D 149 " pdb=" C TRP D 149 " pdb=" N LEU D 150 " pdb=" CA LEU D 150 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 3701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 467 0.026 - 0.052: 286 0.052 - 0.078: 111 0.078 - 0.104: 24 0.104 - 0.131: 16 Chirality restraints: 904 Sorted by residual: chirality pdb=" CA ILE A 182 " pdb=" N ILE A 182 " pdb=" C ILE A 182 " pdb=" CB ILE A 182 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE C 182 " pdb=" N ILE C 182 " pdb=" C ILE C 182 " pdb=" CB ILE C 182 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE D 182 " pdb=" N ILE D 182 " pdb=" C ILE D 182 " pdb=" CB ILE D 182 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 901 not shown) Planarity restraints: 1140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 197 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO D 198 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 198 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 198 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 197 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO B 198 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 198 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 198 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 197 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO C 198 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 198 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 198 " -0.022 5.00e-02 4.00e+02 ... (remaining 1137 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 36 2.48 - 3.09: 4537 3.09 - 3.69: 9955 3.69 - 4.30: 15215 4.30 - 4.90: 25365 Nonbonded interactions: 55108 Sorted by model distance: nonbonded pdb=" OD2 ASP C 183 " pdb="MN MN C 301 " model vdw 1.880 2.320 nonbonded pdb=" OD2 ASP B 183 " pdb="MN MN B 301 " model vdw 1.881 2.320 nonbonded pdb=" OD2 ASP D 183 " pdb="MN MN D 301 " model vdw 1.881 2.320 nonbonded pdb=" OD2 ASP A 183 " pdb="MN MN A 301 " model vdw 1.881 2.320 nonbonded pdb=" NE2 HIS D 50 " pdb="MN MN D 301 " model vdw 2.017 2.400 ... (remaining 55103 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.780 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 20.650 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 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:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 0.028 6412 Z= 0.246 Angle : 0.551 4.917 8724 Z= 0.324 Chirality : 0.039 0.131 904 Planarity : 0.004 0.039 1140 Dihedral : 11.977 82.471 2272 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.81 (0.29), residues: 784 helix: 0.78 (0.23), residues: 504 sheet: 1.20 (0.52), residues: 72 loop : -0.02 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 147 HIS 0.004 0.001 HIS D 187 PHE 0.005 0.001 PHE B 90 TYR 0.023 0.002 TYR C 69 ARG 0.002 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.703 Fit side-chains REVERT: A 70 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7843 (tm-30) REVERT: A 124 ASP cc_start: 0.8531 (m-30) cc_final: 0.8160 (m-30) REVERT: A 200 TYR cc_start: 0.9364 (t80) cc_final: 0.9120 (t80) REVERT: B 70 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7815 (tm-30) REVERT: B 124 ASP cc_start: 0.8508 (m-30) cc_final: 0.8105 (m-30) REVERT: B 200 TYR cc_start: 0.9356 (t80) cc_final: 0.9143 (t80) REVERT: C 70 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7924 (tm-30) REVERT: C 124 ASP cc_start: 0.8491 (m-30) cc_final: 0.8071 (m-30) REVERT: C 200 TYR cc_start: 0.9358 (t80) cc_final: 0.9097 (t80) REVERT: D 70 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7850 (tm-30) REVERT: D 124 ASP cc_start: 0.8481 (m-30) cc_final: 0.8072 (m-30) REVERT: D 200 TYR cc_start: 0.9355 (t80) cc_final: 0.9142 (t80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 1.2277 time to fit residues: 167.2577 Evaluate side-chains 105 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.8173 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6412 Z= 0.240 Angle : 0.532 4.999 8724 Z= 0.286 Chirality : 0.039 0.121 904 Planarity : 0.004 0.039 1140 Dihedral : 7.243 85.873 844 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.90 % Allowed : 8.39 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.12 (0.30), residues: 784 helix: 0.88 (0.23), residues: 508 sheet: 1.97 (0.61), residues: 72 loop : 0.21 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 147 HIS 0.004 0.001 HIS D 187 PHE 0.006 0.001 PHE B 101 TYR 0.008 0.001 TYR A 33 ARG 0.001 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 0.727 Fit side-chains REVERT: A 48 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7930 (tm-30) REVERT: A 70 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7824 (tm-30) REVERT: A 200 TYR cc_start: 0.9388 (t80) cc_final: 0.9138 (t80) REVERT: B 48 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7947 (tm-30) REVERT: B 70 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7828 (tm-30) REVERT: B 124 ASP cc_start: 0.8766 (m-30) cc_final: 0.8563 (m-30) REVERT: B 200 TYR cc_start: 0.9384 (t80) cc_final: 0.9139 (t80) REVERT: C 48 GLN cc_start: 0.8385 (tm-30) cc_final: 0.7943 (tm-30) REVERT: C 70 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7838 (tm-30) REVERT: C 200 TYR cc_start: 0.9385 (t80) cc_final: 0.9131 (t80) REVERT: D 48 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7937 (tm-30) REVERT: D 70 GLN cc_start: 0.8313 (tm-30) cc_final: 0.7745 (tm-30) REVERT: D 200 TYR cc_start: 0.9383 (t80) cc_final: 0.9124 (t80) outliers start: 12 outliers final: 8 residues processed: 137 average time/residue: 1.3153 time to fit residues: 188.5122 Evaluate side-chains 117 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 106 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN C 206 ASN D 206 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6412 Z= 0.194 Angle : 0.492 4.945 8724 Z= 0.262 Chirality : 0.039 0.121 904 Planarity : 0.004 0.038 1140 Dihedral : 7.045 83.914 844 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.32 % Allowed : 10.60 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.29), residues: 784 helix: 0.93 (0.22), residues: 508 sheet: 2.16 (0.63), residues: 72 loop : 0.17 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 147 HIS 0.003 0.001 HIS C 187 PHE 0.006 0.001 PHE A 101 TYR 0.007 0.001 TYR D 33 ARG 0.001 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 0.766 Fit side-chains REVERT: A 70 GLN cc_start: 0.8286 (tm-30) cc_final: 0.7738 (tm-30) REVERT: A 200 TYR cc_start: 0.9383 (t80) cc_final: 0.9154 (t80) REVERT: A 211 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7790 (tp30) REVERT: B 48 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7877 (tm-30) REVERT: B 70 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7747 (tm-30) REVERT: B 155 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8317 (mm-30) REVERT: B 200 TYR cc_start: 0.9378 (t80) cc_final: 0.9149 (t80) REVERT: B 211 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7761 (tp30) REVERT: C 70 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7753 (tm-30) REVERT: C 200 TYR cc_start: 0.9378 (t80) cc_final: 0.9149 (t80) REVERT: C 211 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7755 (tp30) REVERT: D 70 GLN cc_start: 0.8314 (tm-30) cc_final: 0.7734 (tm-30) REVERT: D 155 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8296 (mm-30) REVERT: D 200 TYR cc_start: 0.9376 (t80) cc_final: 0.9139 (t80) REVERT: D 211 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7761 (tp30) outliers start: 21 outliers final: 9 residues processed: 138 average time/residue: 1.2760 time to fit residues: 184.3853 Evaluate side-chains 111 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 106 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6412 Z= 0.204 Angle : 0.495 4.976 8724 Z= 0.262 Chirality : 0.038 0.118 904 Planarity : 0.004 0.037 1140 Dihedral : 7.038 83.640 844 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.11 % Allowed : 11.55 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.29), residues: 784 helix: 0.95 (0.22), residues: 508 sheet: 2.01 (0.60), residues: 72 loop : 0.17 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 147 HIS 0.003 0.001 HIS D 187 PHE 0.006 0.001 PHE A 101 TYR 0.008 0.001 TYR B 33 ARG 0.001 0.000 ARG C 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 0.728 Fit side-chains REVERT: A 70 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7765 (tm-30) REVERT: A 155 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8323 (mm-30) REVERT: A 200 TYR cc_start: 0.9382 (t80) cc_final: 0.9173 (t80) REVERT: A 211 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7836 (tp30) REVERT: A 218 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7829 (mpp) REVERT: B 70 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 119 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8282 (mp0) REVERT: B 155 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8315 (mm-30) REVERT: B 200 TYR cc_start: 0.9380 (t80) cc_final: 0.9176 (t80) REVERT: B 211 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7784 (tp30) REVERT: B 218 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7860 (mpp) REVERT: C 70 GLN cc_start: 0.8292 (tm-30) cc_final: 0.7760 (tm-30) REVERT: C 119 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8264 (mp0) REVERT: C 155 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8313 (mm-30) REVERT: C 200 TYR cc_start: 0.9381 (t80) cc_final: 0.9128 (t80) REVERT: C 211 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7782 (tp30) REVERT: C 218 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7867 (mpp) REVERT: D 70 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7712 (tm-30) REVERT: D 119 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8272 (mp0) REVERT: D 155 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8315 (mm-30) REVERT: D 200 TYR cc_start: 0.9378 (t80) cc_final: 0.9169 (t80) REVERT: D 211 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7781 (tp30) REVERT: D 218 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7824 (mpp) outliers start: 26 outliers final: 21 residues processed: 131 average time/residue: 1.2456 time to fit residues: 171.0632 Evaluate side-chains 127 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 218 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.8198 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6412 Z= 0.271 Angle : 0.520 5.087 8724 Z= 0.275 Chirality : 0.040 0.122 904 Planarity : 0.004 0.036 1140 Dihedral : 7.013 82.481 844 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.06 % Allowed : 11.87 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.18 (0.29), residues: 784 helix: 0.97 (0.23), residues: 508 sheet: 1.97 (0.57), residues: 72 loop : 0.13 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 147 HIS 0.003 0.001 HIS D 187 PHE 0.006 0.001 PHE C 101 TYR 0.009 0.001 TYR B 33 ARG 0.001 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 101 time to evaluate : 0.686 Fit side-chains REVERT: A 70 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7665 (tm-30) REVERT: A 155 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8291 (mm-30) REVERT: A 200 TYR cc_start: 0.9388 (t80) cc_final: 0.9170 (t80) REVERT: A 211 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7823 (tp30) REVERT: B 70 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7689 (tm-30) REVERT: B 155 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8298 (mm-30) REVERT: B 200 TYR cc_start: 0.9391 (t80) cc_final: 0.9176 (t80) REVERT: B 211 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7796 (tp30) REVERT: C 70 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7695 (tm-30) REVERT: C 155 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8294 (mm-30) REVERT: C 200 TYR cc_start: 0.9390 (t80) cc_final: 0.9174 (t80) REVERT: C 211 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7769 (tp30) REVERT: D 70 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7657 (tm-30) REVERT: D 155 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8296 (mm-30) REVERT: D 200 TYR cc_start: 0.9387 (t80) cc_final: 0.9169 (t80) REVERT: D 211 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7788 (tp30) outliers start: 32 outliers final: 20 residues processed: 116 average time/residue: 1.2610 time to fit residues: 153.0268 Evaluate side-chains 114 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.8194 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6412 Z= 0.254 Angle : 0.525 5.161 8724 Z= 0.276 Chirality : 0.040 0.121 904 Planarity : 0.004 0.036 1140 Dihedral : 6.990 82.506 844 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.64 % Allowed : 15.35 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.18 (0.29), residues: 784 helix: 1.01 (0.22), residues: 508 sheet: 1.67 (0.55), residues: 72 loop : 0.11 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 147 HIS 0.003 0.001 HIS D 187 PHE 0.006 0.001 PHE A 101 TYR 0.009 0.001 TYR A 33 ARG 0.001 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 0.771 Fit side-chains REVERT: A 70 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7689 (tm-30) REVERT: A 155 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8300 (mm-30) REVERT: A 200 TYR cc_start: 0.9382 (t80) cc_final: 0.9161 (t80) REVERT: A 211 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7881 (tp30) REVERT: B 70 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7685 (tm-30) REVERT: B 155 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8303 (mm-30) REVERT: B 200 TYR cc_start: 0.9384 (t80) cc_final: 0.9167 (t80) REVERT: B 211 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7799 (tp30) REVERT: C 70 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7693 (tm-30) REVERT: C 155 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8306 (mm-30) REVERT: C 200 TYR cc_start: 0.9383 (t80) cc_final: 0.9166 (t80) REVERT: C 211 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7791 (tp30) REVERT: D 70 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7675 (tm-30) REVERT: D 155 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8300 (mm-30) REVERT: D 200 TYR cc_start: 0.9381 (t80) cc_final: 0.9161 (t80) REVERT: D 211 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7790 (tp30) outliers start: 23 outliers final: 19 residues processed: 103 average time/residue: 1.4201 time to fit residues: 152.8698 Evaluate side-chains 111 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8177 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6412 Z= 0.193 Angle : 0.507 6.007 8724 Z= 0.266 Chirality : 0.039 0.119 904 Planarity : 0.004 0.036 1140 Dihedral : 6.972 82.974 844 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.27 % Allowed : 14.24 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.33 (0.29), residues: 784 helix: 1.05 (0.22), residues: 508 sheet: 2.35 (0.58), residues: 64 loop : 0.23 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 147 HIS 0.002 0.001 HIS D 187 PHE 0.005 0.001 PHE C 101 TYR 0.007 0.001 TYR D 190 ARG 0.000 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 110 time to evaluate : 0.734 Fit side-chains REVERT: A 70 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7662 (tm-30) REVERT: A 155 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8303 (mm-30) REVERT: A 200 TYR cc_start: 0.9371 (t80) cc_final: 0.9156 (t80) REVERT: A 211 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7884 (tp30) REVERT: B 70 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7663 (tm-30) REVERT: B 119 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8263 (mp0) REVERT: B 155 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8342 (mm-30) REVERT: B 200 TYR cc_start: 0.9373 (t80) cc_final: 0.9164 (t80) REVERT: B 211 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7760 (tp30) REVERT: C 70 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7662 (tm-30) REVERT: C 119 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8265 (mp0) REVERT: C 155 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8293 (mm-30) REVERT: C 200 TYR cc_start: 0.9373 (t80) cc_final: 0.9163 (t80) REVERT: C 211 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7784 (tp30) REVERT: D 70 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7647 (tm-30) REVERT: D 119 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8265 (mp0) REVERT: D 155 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8344 (mm-30) REVERT: D 200 TYR cc_start: 0.9370 (t80) cc_final: 0.9157 (t80) REVERT: D 211 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7754 (tp30) outliers start: 27 outliers final: 18 residues processed: 118 average time/residue: 1.2454 time to fit residues: 153.9919 Evaluate side-chains 119 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 133 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8179 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6412 Z= 0.194 Angle : 0.515 6.828 8724 Z= 0.268 Chirality : 0.039 0.121 904 Planarity : 0.004 0.036 1140 Dihedral : 6.956 82.916 844 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.80 % Allowed : 15.51 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.36 (0.29), residues: 784 helix: 1.09 (0.22), residues: 508 sheet: 2.33 (0.58), residues: 64 loop : 0.22 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 147 HIS 0.002 0.001 HIS D 187 PHE 0.005 0.001 PHE A 101 TYR 0.008 0.001 TYR A 190 ARG 0.000 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 0.678 Fit side-chains REVERT: A 70 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7673 (tm-30) REVERT: A 119 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8171 (mp0) REVERT: A 155 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8321 (mm-30) REVERT: A 200 TYR cc_start: 0.9380 (t80) cc_final: 0.9145 (t80) REVERT: A 211 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7885 (tp30) REVERT: B 70 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7697 (tm-30) REVERT: B 119 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8271 (mp0) REVERT: B 155 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8329 (mm-30) REVERT: B 200 TYR cc_start: 0.9379 (t80) cc_final: 0.9127 (t80) REVERT: B 211 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7772 (tp30) REVERT: C 70 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7659 (tm-30) REVERT: C 119 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8242 (mp0) REVERT: C 155 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8294 (mm-30) REVERT: C 200 TYR cc_start: 0.9378 (t80) cc_final: 0.9175 (t80) REVERT: C 211 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7790 (tp30) REVERT: D 70 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7663 (tm-30) REVERT: D 119 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8251 (mp0) REVERT: D 155 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8327 (mm-30) REVERT: D 200 TYR cc_start: 0.9378 (t80) cc_final: 0.9172 (t80) REVERT: D 211 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7765 (tp30) outliers start: 24 outliers final: 17 residues processed: 113 average time/residue: 1.2896 time to fit residues: 152.6225 Evaluate side-chains 119 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 0.0040 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 0.0470 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 overall best weight: 0.4090 ------------------------------------------------------------------------------- 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: 0.8157 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6412 Z= 0.164 Angle : 0.515 8.332 8724 Z= 0.265 Chirality : 0.038 0.122 904 Planarity : 0.004 0.036 1140 Dihedral : 6.918 83.110 844 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.32 % Allowed : 15.51 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.43 (0.29), residues: 784 helix: 1.14 (0.22), residues: 508 sheet: 2.39 (0.60), residues: 64 loop : 0.24 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 147 HIS 0.002 0.001 HIS D 187 PHE 0.004 0.001 PHE A 101 TYR 0.006 0.001 TYR C 200 ARG 0.000 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 0.693 Fit side-chains REVERT: A 70 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7712 (tm-30) REVERT: A 119 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8176 (mp0) REVERT: A 155 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8297 (mm-30) REVERT: A 200 TYR cc_start: 0.9371 (t80) cc_final: 0.9147 (t80) REVERT: A 211 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7885 (tp30) REVERT: B 70 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7707 (tm-30) REVERT: B 119 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8233 (mp0) REVERT: B 155 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8313 (mm-30) REVERT: B 200 TYR cc_start: 0.9367 (t80) cc_final: 0.9121 (t80) REVERT: B 211 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7765 (tp30) REVERT: C 70 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7652 (tm-30) REVERT: C 119 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8217 (mp0) REVERT: C 155 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8288 (mm-30) REVERT: C 200 TYR cc_start: 0.9367 (t80) cc_final: 0.9121 (t80) REVERT: C 211 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7758 (tp30) REVERT: D 70 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7640 (tm-30) REVERT: D 119 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8219 (mp0) REVERT: D 155 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8310 (mm-30) REVERT: D 200 TYR cc_start: 0.9365 (t80) cc_final: 0.9115 (t80) REVERT: D 211 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7762 (tp30) outliers start: 21 outliers final: 10 residues processed: 120 average time/residue: 1.2393 time to fit residues: 155.8657 Evaluate side-chains 122 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 55 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.8190 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6412 Z= 0.248 Angle : 0.568 10.666 8724 Z= 0.287 Chirality : 0.040 0.121 904 Planarity : 0.004 0.035 1140 Dihedral : 6.918 82.311 844 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.37 % Allowed : 16.61 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.38 (0.29), residues: 784 helix: 1.14 (0.23), residues: 508 sheet: 2.16 (0.58), residues: 64 loop : 0.19 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 147 HIS 0.003 0.001 HIS D 187 PHE 0.005 0.001 PHE A 101 TYR 0.009 0.001 TYR B 190 ARG 0.001 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 0.752 Fit side-chains REVERT: A 70 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7756 (tm-30) REVERT: A 119 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8159 (mp0) REVERT: A 155 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8306 (mm-30) REVERT: A 200 TYR cc_start: 0.9391 (t80) cc_final: 0.9174 (t80) REVERT: A 211 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7902 (tp30) REVERT: B 70 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7762 (tm-30) REVERT: B 119 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8237 (mp0) REVERT: B 155 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8334 (mm-30) REVERT: B 200 TYR cc_start: 0.9394 (t80) cc_final: 0.9164 (t80) REVERT: B 211 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7827 (OUTLIER) REVERT: C 70 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7752 (tm-30) REVERT: C 119 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8233 (mp0) REVERT: C 155 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8296 (mm-30) REVERT: C 200 TYR cc_start: 0.9393 (t80) cc_final: 0.9163 (t80) REVERT: C 211 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7828 (OUTLIER) REVERT: D 70 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7784 (tm-30) REVERT: D 119 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8278 (mp0) REVERT: D 155 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8333 (mm-30) REVERT: D 200 TYR cc_start: 0.9395 (t80) cc_final: 0.9163 (t80) REVERT: D 211 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7828 (OUTLIER) outliers start: 15 outliers final: 15 residues processed: 111 average time/residue: 1.2848 time to fit residues: 149.3946 Evaluate side-chains 110 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.085421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.074823 restraints weight = 12476.969| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.37 r_work: 0.2895 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6412 Z= 0.230 Angle : 0.538 8.549 8724 Z= 0.278 Chirality : 0.039 0.120 904 Planarity : 0.004 0.035 1140 Dihedral : 6.897 82.001 844 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.53 % Allowed : 16.14 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.34 (0.29), residues: 784 helix: 1.11 (0.22), residues: 508 sheet: 2.10 (0.58), residues: 64 loop : 0.20 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 147 HIS 0.003 0.001 HIS D 187 PHE 0.005 0.001 PHE C 101 TYR 0.008 0.001 TYR B 190 ARG 0.001 0.000 ARG D 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2946.83 seconds wall clock time: 53 minutes 33.97 seconds (3213.97 seconds total)