Starting phenix.real_space_refine on Sun Aug 4 03:33:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ty6_41711/08_2024/8ty6_41711.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ty6_41711/08_2024/8ty6_41711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ty6_41711/08_2024/8ty6_41711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ty6_41711/08_2024/8ty6_41711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ty6_41711/08_2024/8ty6_41711.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ty6_41711/08_2024/8ty6_41711.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 6096 2.51 5 N 1692 2.21 5 O 1806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9678 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1613 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1613 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1613 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1613 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1613 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1613 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 5.44, per 1000 atoms: 0.56 Number of scatterers: 9678 At special positions: 0 Unit cell: (106.92, 117.72, 73.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 1806 8.00 N 1692 7.00 C 6096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS F 45 " distance=2.03 Simple disulfide: pdb=" SG CYS A 45 " - pdb=" SG CYS B 14 " distance=2.03 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS C 14 " distance=2.03 Simple disulfide: pdb=" SG CYS C 45 " - pdb=" SG CYS D 14 " distance=2.03 Simple disulfide: pdb=" SG CYS D 45 " - pdb=" SG CYS E 14 " distance=2.03 Simple disulfide: pdb=" SG CYS E 45 " - pdb=" SG CYS F 14 " distance=2.03 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: 3.89 Conformation dependent library (CDL) restraints added in 1.8 seconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 6 sheets defined 72.5% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 177 Processing helix chain 'A' and resid 183 through 193 Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.602A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'B' and resid 16 through 31 removed outlier: 3.601A pdb=" N ALA B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 44 removed outlier: 3.508A pdb=" N MET B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 110 through 119 Processing helix chain 'B' and resid 125 through 145 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 160 through 177 Processing helix chain 'B' and resid 183 through 194 Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'C' and resid 16 through 31 removed outlier: 3.562A pdb=" N LEU C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 106 Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 177 removed outlier: 3.518A pdb=" N GLN C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 193 Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.550A pdb=" N ILE C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'D' and resid 16 through 31 Processing helix chain 'D' and resid 35 through 44 removed outlier: 3.634A pdb=" N MET D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 119 Processing helix chain 'D' and resid 125 through 145 Processing helix chain 'D' and resid 160 through 177 Processing helix chain 'D' and resid 183 through 193 Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.756A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 119 Processing helix chain 'E' and resid 125 through 145 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 177 Processing helix chain 'E' and resid 183 through 193 Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.828A pdb=" N ILE E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'F' and resid 16 through 31 Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 118 Processing helix chain 'F' and resid 125 through 145 Processing helix chain 'F' and resid 149 through 153 removed outlier: 3.707A pdb=" N ILE F 153 " --> pdb=" O ILE F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 177 Processing helix chain 'F' and resid 183 through 193 Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.581A pdb=" N ILE F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY F 206 " --> pdb=" O LEU F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 removed outlier: 3.563A pdb=" N GLN F 219 " --> pdb=" O MET F 215 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA4, first strand: chain 'D' and resid 3 through 4 Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 4 630 hydrogen bonds defined for protein. 1857 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: 2.67 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3252 1.34 - 1.46: 1919 1.46 - 1.58: 4561 1.58 - 1.70: 0 1.70 - 1.81: 144 Bond restraints: 9876 Sorted by residual: bond pdb=" N ALA B 31 " pdb=" CA ALA B 31 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.62e-01 bond pdb=" C VAL B 181 " pdb=" O VAL B 181 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 7.01e-01 bond pdb=" N ALA F 31 " pdb=" CA ALA F 31 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 6.68e-01 bond pdb=" CA ILE B 37 " pdb=" CB ILE B 37 " ideal model delta sigma weight residual 1.539 1.543 -0.004 5.40e-03 3.43e+04 5.76e-01 bond pdb=" CA ILE C 37 " pdb=" CB ILE C 37 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 4.70e-01 ... (remaining 9871 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.98: 471 106.98 - 113.73: 5584 113.73 - 120.48: 3667 120.48 - 127.23: 3551 127.23 - 133.98: 155 Bond angle restraints: 13428 Sorted by residual: angle pdb=" C ALA B 31 " pdb=" CA ALA B 31 " pdb=" CB ALA B 31 " ideal model delta sigma weight residual 110.42 115.84 -5.42 1.99e+00 2.53e-01 7.43e+00 angle pdb=" C ALA F 31 " pdb=" CA ALA F 31 " pdb=" CB ALA F 31 " ideal model delta sigma weight residual 110.42 115.73 -5.31 1.99e+00 2.53e-01 7.11e+00 angle pdb=" N ALA B 31 " pdb=" CA ALA B 31 " pdb=" C ALA B 31 " ideal model delta sigma weight residual 110.80 106.71 4.09 2.13e+00 2.20e-01 3.69e+00 angle pdb=" N ALA F 31 " pdb=" CA ALA F 31 " pdb=" C ALA F 31 " ideal model delta sigma weight residual 110.80 106.88 3.92 2.13e+00 2.20e-01 3.38e+00 angle pdb=" N GLU C 175 " pdb=" CA GLU C 175 " pdb=" C GLU C 175 " ideal model delta sigma weight residual 110.97 112.93 -1.96 1.09e+00 8.42e-01 3.24e+00 ... (remaining 13423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 5652 16.28 - 32.55: 310 32.55 - 48.83: 97 48.83 - 65.11: 23 65.11 - 81.39: 2 Dihedral angle restraints: 6084 sinusoidal: 2436 harmonic: 3648 Sorted by residual: dihedral pdb=" CA LEU A 202 " pdb=" CB LEU A 202 " pdb=" CG LEU A 202 " pdb=" CD1 LEU A 202 " ideal model delta sinusoidal sigma weight residual -60.00 -0.07 -59.93 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LEU C 202 " pdb=" CB LEU C 202 " pdb=" CG LEU C 202 " pdb=" CD1 LEU C 202 " ideal model delta sinusoidal sigma weight residual 60.00 0.48 59.52 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG A 100 " pdb=" CB ARG A 100 " pdb=" CG ARG A 100 " pdb=" CD ARG A 100 " ideal model delta sinusoidal sigma weight residual -180.00 -120.57 -59.43 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 6081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1057 0.030 - 0.059: 325 0.059 - 0.089: 98 0.089 - 0.118: 50 0.118 - 0.148: 6 Chirality restraints: 1536 Sorted by residual: chirality pdb=" CA ILE D 124 " pdb=" N ILE D 124 " pdb=" C ILE D 124 " pdb=" CB ILE D 124 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ILE E 124 " pdb=" N ILE E 124 " pdb=" C ILE E 124 " pdb=" CB ILE E 124 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1533 not shown) Planarity restraints: 1746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 48 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO B 49 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 49 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 49 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 33 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.33e+00 pdb=" N PRO F 34 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO F 34 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO F 34 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 48 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO A 49 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 49 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 49 " -0.016 5.00e-02 4.00e+02 ... (remaining 1743 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 151 2.70 - 3.25: 9675 3.25 - 3.80: 15358 3.80 - 4.35: 18843 4.35 - 4.90: 32496 Nonbonded interactions: 76523 Sorted by model distance: nonbonded pdb=" OG1 THR C 48 " pdb=" OD1 ASP C 51 " model vdw 2.144 3.040 nonbonded pdb=" OG1 THR B 48 " pdb=" OD1 ASP B 51 " model vdw 2.161 3.040 nonbonded pdb=" OG1 THR A 48 " pdb=" OD1 ASP A 51 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR D 48 " pdb=" OD1 ASP D 51 " model vdw 2.178 3.040 nonbonded pdb=" OG1 THR F 48 " pdb=" OD1 ASP F 51 " model vdw 2.193 3.040 ... (remaining 76518 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.510 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.540 Find NCS groups from input model: 0.330 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: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.002 0.030 9876 Z= 0.146 Angle : 0.444 5.425 13428 Z= 0.230 Chirality : 0.036 0.148 1536 Planarity : 0.004 0.030 1746 Dihedral : 11.547 81.386 3690 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.71 % Allowed : 5.72 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.36 (0.25), residues: 1236 helix: 2.02 (0.18), residues: 894 sheet: -1.53 (0.69), residues: 54 loop : 0.97 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 80 HIS 0.002 0.000 HIS F 62 PHE 0.008 0.001 PHE A 168 TYR 0.009 0.001 TYR D 169 ARG 0.002 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 305 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8247 (mt) cc_final: 0.7990 (mt) REVERT: A 118 MET cc_start: 0.8981 (mtp) cc_final: 0.8777 (mtp) REVERT: A 120 HIS cc_start: 0.7826 (t-90) cc_final: 0.7157 (t-90) REVERT: A 175 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: A 195 ASN cc_start: 0.7819 (m-40) cc_final: 0.7562 (m110) REVERT: A 213 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7543 (mt-10) REVERT: B 18 ARG cc_start: 0.6755 (ttp-170) cc_final: 0.6189 (ttt180) REVERT: B 69 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8473 (tt) REVERT: B 170 LYS cc_start: 0.8577 (tttt) cc_final: 0.8253 (tppt) REVERT: B 175 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6098 (mp0) REVERT: B 214 MET cc_start: 0.8251 (mtt) cc_final: 0.7924 (mtt) REVERT: C 23 TRP cc_start: 0.8888 (t-100) cc_final: 0.8633 (t-100) REVERT: C 30 LYS cc_start: 0.7334 (mmtt) cc_final: 0.7090 (mttt) REVERT: C 149 SER cc_start: 0.8929 (t) cc_final: 0.8727 (t) REVERT: D 25 LYS cc_start: 0.7964 (mptt) cc_final: 0.7604 (mttt) REVERT: D 70 LYS cc_start: 0.8152 (ttmm) cc_final: 0.7938 (ttpp) REVERT: D 218 CYS cc_start: 0.7734 (m) cc_final: 0.7288 (m) REVERT: E 10 MET cc_start: 0.7149 (mmt) cc_final: 0.6777 (mmt) REVERT: E 68 MET cc_start: 0.8752 (mtm) cc_final: 0.8439 (mtp) REVERT: E 175 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.6643 (mp0) REVERT: E 214 MET cc_start: 0.8596 (mtt) cc_final: 0.8210 (mtm) REVERT: F 4 GLN cc_start: 0.8331 (tt0) cc_final: 0.8061 (pm20) REVERT: F 69 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7959 (mt) REVERT: F 171 THR cc_start: 0.8315 (m) cc_final: 0.6444 (m) REVERT: F 175 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.5530 (mp0) REVERT: F 189 LEU cc_start: 0.8423 (tp) cc_final: 0.8096 (tp) REVERT: F 202 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8776 (mp) outliers start: 28 outliers final: 6 residues processed: 330 average time/residue: 0.2589 time to fit residues: 112.0811 Evaluate side-chains 245 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 232 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 202 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 60 optimal weight: 0.0870 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 HIS B 21 ASN B 67 GLN B 139 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN E 120 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9876 Z= 0.178 Angle : 0.511 4.755 13428 Z= 0.266 Chirality : 0.039 0.144 1536 Planarity : 0.005 0.041 1746 Dihedral : 6.336 59.258 1362 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.65 % Allowed : 11.82 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.25), residues: 1236 helix: 2.11 (0.18), residues: 894 sheet: -1.36 (0.67), residues: 54 loop : 1.11 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 80 HIS 0.005 0.001 HIS E 120 PHE 0.009 0.001 PHE D 161 TYR 0.009 0.001 TYR D 169 ARG 0.007 0.001 ARG D 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 256 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8191 (mmt) cc_final: 0.7968 (mmt) REVERT: A 83 LEU cc_start: 0.8329 (mt) cc_final: 0.8055 (mt) REVERT: A 175 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6288 (mp0) REVERT: A 195 ASN cc_start: 0.7802 (m-40) cc_final: 0.7216 (m110) REVERT: A 210 THR cc_start: 0.8262 (p) cc_final: 0.7788 (p) REVERT: A 213 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7589 (mt-10) REVERT: B 18 ARG cc_start: 0.6564 (ttp-170) cc_final: 0.5856 (ttt180) REVERT: B 69 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8440 (tt) REVERT: B 118 MET cc_start: 0.8470 (mtp) cc_final: 0.8126 (mtp) REVERT: B 170 LYS cc_start: 0.8453 (tttt) cc_final: 0.8155 (tppt) REVERT: B 175 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6117 (mp0) REVERT: B 213 GLU cc_start: 0.7386 (tp30) cc_final: 0.6775 (tp30) REVERT: C 23 TRP cc_start: 0.8929 (t-100) cc_final: 0.8723 (t-100) REVERT: C 30 LYS cc_start: 0.7330 (mmtt) cc_final: 0.6900 (mttt) REVERT: C 54 THR cc_start: 0.7825 (m) cc_final: 0.7126 (p) REVERT: C 171 THR cc_start: 0.8623 (m) cc_final: 0.8254 (p) REVERT: C 195 ASN cc_start: 0.7505 (t0) cc_final: 0.7211 (t0) REVERT: D 25 LYS cc_start: 0.7733 (mptt) cc_final: 0.7367 (mttt) REVERT: E 68 MET cc_start: 0.8682 (mtm) cc_final: 0.8364 (mtp) REVERT: E 79 GLU cc_start: 0.8859 (tp30) cc_final: 0.8165 (tp30) REVERT: E 82 ARG cc_start: 0.7502 (mtp-110) cc_final: 0.7231 (ttp80) REVERT: E 175 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6216 (mp0) REVERT: E 195 ASN cc_start: 0.8294 (t0) cc_final: 0.8087 (t0) REVERT: E 197 ASP cc_start: 0.8311 (m-30) cc_final: 0.7945 (p0) REVERT: F 4 GLN cc_start: 0.8344 (tt0) cc_final: 0.8045 (pm20) REVERT: F 69 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7890 (mt) REVERT: F 175 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.5707 (mp0) REVERT: F 189 LEU cc_start: 0.8431 (tp) cc_final: 0.8061 (tp) outliers start: 17 outliers final: 6 residues processed: 268 average time/residue: 0.2691 time to fit residues: 95.6543 Evaluate side-chains 236 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 224 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 175 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 0.0980 chunk 95 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 0.0470 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN D 67 GLN D 139 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9876 Z= 0.214 Angle : 0.514 8.657 13428 Z= 0.259 Chirality : 0.039 0.140 1536 Planarity : 0.005 0.048 1746 Dihedral : 5.621 58.700 1353 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.52 % Allowed : 12.69 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.44 (0.24), residues: 1236 helix: 2.03 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.69 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 80 HIS 0.002 0.000 HIS E 12 PHE 0.009 0.002 PHE F 40 TYR 0.011 0.001 TYR D 130 ARG 0.008 0.001 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 236 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8337 (mt) cc_final: 0.8050 (mt) REVERT: A 175 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6254 (mp0) REVERT: A 195 ASN cc_start: 0.7653 (m-40) cc_final: 0.7289 (m110) REVERT: A 213 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7490 (mt-10) REVERT: B 18 ARG cc_start: 0.6658 (ttp-170) cc_final: 0.5905 (ttt180) REVERT: B 69 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8467 (tt) REVERT: B 170 LYS cc_start: 0.8449 (tttt) cc_final: 0.8165 (tppt) REVERT: B 175 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.5981 (mp0) REVERT: C 23 TRP cc_start: 0.8965 (t-100) cc_final: 0.8725 (t-100) REVERT: C 30 LYS cc_start: 0.7298 (mmtt) cc_final: 0.6884 (mttt) REVERT: C 54 THR cc_start: 0.7948 (m) cc_final: 0.7133 (p) REVERT: D 25 LYS cc_start: 0.7814 (mptt) cc_final: 0.7408 (mttt) REVERT: E 68 MET cc_start: 0.8723 (mtm) cc_final: 0.8421 (mtp) REVERT: E 79 GLU cc_start: 0.8847 (tp30) cc_final: 0.7945 (tp30) REVERT: E 82 ARG cc_start: 0.7609 (mtp-110) cc_final: 0.7124 (ttp80) REVERT: E 175 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6361 (mp0) REVERT: F 4 GLN cc_start: 0.8418 (tt0) cc_final: 0.8011 (pm20) REVERT: F 69 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7948 (mt) REVERT: F 175 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.5720 (mp0) REVERT: F 189 LEU cc_start: 0.8455 (tp) cc_final: 0.8114 (tp) outliers start: 26 outliers final: 9 residues processed: 251 average time/residue: 0.2448 time to fit residues: 82.1624 Evaluate side-chains 235 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 220 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 175 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 0.2980 chunk 32 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 HIS D 139 ASN E 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9876 Z= 0.169 Angle : 0.490 8.936 13428 Z= 0.245 Chirality : 0.038 0.152 1536 Planarity : 0.005 0.048 1746 Dihedral : 5.613 58.691 1353 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.52 % Allowed : 14.05 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.51 (0.24), residues: 1236 helix: 2.08 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.73 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 80 HIS 0.001 0.000 HIS B 12 PHE 0.009 0.001 PHE F 40 TYR 0.010 0.001 TYR E 145 ARG 0.009 0.001 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 225 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8336 (mt) cc_final: 0.8051 (mt) REVERT: A 143 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.8030 (mtm-85) REVERT: A 175 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6298 (mp0) REVERT: B 18 ARG cc_start: 0.6646 (ttp-170) cc_final: 0.5869 (ttt180) REVERT: B 69 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8429 (tt) REVERT: B 136 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7996 (tp) REVERT: B 170 LYS cc_start: 0.8438 (tttt) cc_final: 0.8156 (tppt) REVERT: B 175 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6019 (mp0) REVERT: B 213 GLU cc_start: 0.7287 (tp30) cc_final: 0.6880 (tp30) REVERT: B 214 MET cc_start: 0.7630 (mtm) cc_final: 0.7393 (mtt) REVERT: C 23 TRP cc_start: 0.8963 (t-100) cc_final: 0.8748 (t-100) REVERT: C 30 LYS cc_start: 0.7272 (mmtt) cc_final: 0.6884 (mttt) REVERT: C 54 THR cc_start: 0.7900 (m) cc_final: 0.7086 (p) REVERT: D 25 LYS cc_start: 0.7797 (mptt) cc_final: 0.7363 (mttt) REVERT: E 68 MET cc_start: 0.8696 (mtm) cc_final: 0.8344 (mtp) REVERT: E 79 GLU cc_start: 0.8832 (tp30) cc_final: 0.7864 (tp30) REVERT: E 82 ARG cc_start: 0.7457 (mtp-110) cc_final: 0.7108 (ttp80) REVERT: E 175 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6484 (mp0) REVERT: F 4 GLN cc_start: 0.8354 (tt0) cc_final: 0.7970 (pm20) REVERT: F 69 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7930 (mt) REVERT: F 175 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.5861 (mp0) REVERT: F 189 LEU cc_start: 0.8516 (tp) cc_final: 0.8166 (tp) outliers start: 26 outliers final: 13 residues processed: 242 average time/residue: 0.2456 time to fit residues: 78.8515 Evaluate side-chains 230 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 210 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 175 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN D 139 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9876 Z= 0.194 Angle : 0.499 12.426 13428 Z= 0.249 Chirality : 0.039 0.139 1536 Planarity : 0.005 0.051 1746 Dihedral : 5.607 58.661 1353 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.52 % Allowed : 14.63 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.24), residues: 1236 helix: 2.07 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.76 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 80 HIS 0.013 0.001 HIS E 12 PHE 0.010 0.001 PHE F 40 TYR 0.010 0.001 TYR E 145 ARG 0.011 0.001 ARG D 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 220 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8333 (mt) cc_final: 0.8050 (mt) REVERT: A 175 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: B 18 ARG cc_start: 0.6594 (ttp-170) cc_final: 0.5775 (ttt180) REVERT: B 69 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8438 (tt) REVERT: B 136 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8012 (tp) REVERT: B 170 LYS cc_start: 0.8467 (tttt) cc_final: 0.8183 (tppt) REVERT: B 175 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6027 (mp0) REVERT: B 214 MET cc_start: 0.7583 (mtm) cc_final: 0.7350 (mtt) REVERT: C 23 TRP cc_start: 0.8971 (t-100) cc_final: 0.8735 (t-100) REVERT: C 30 LYS cc_start: 0.7272 (mmtt) cc_final: 0.6878 (mttt) REVERT: C 54 THR cc_start: 0.7931 (m) cc_final: 0.7113 (p) REVERT: D 25 LYS cc_start: 0.7864 (mptt) cc_final: 0.7423 (mttt) REVERT: D 74 ASN cc_start: 0.8240 (m110) cc_final: 0.7896 (m110) REVERT: D 212 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7791 (tm-30) REVERT: E 68 MET cc_start: 0.8717 (mtm) cc_final: 0.8373 (mtp) REVERT: E 79 GLU cc_start: 0.8836 (tp30) cc_final: 0.8553 (tp30) REVERT: E 175 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: F 4 GLN cc_start: 0.8391 (tt0) cc_final: 0.7965 (pm20) REVERT: F 25 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8292 (ttpt) REVERT: F 69 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8004 (mt) REVERT: F 175 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.5851 (mp0) REVERT: F 189 LEU cc_start: 0.8510 (tp) cc_final: 0.8161 (tp) outliers start: 26 outliers final: 13 residues processed: 238 average time/residue: 0.2433 time to fit residues: 77.1783 Evaluate side-chains 235 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 214 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 199 LYS Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 175 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 24 optimal weight: 0.0270 chunk 71 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 0.0970 chunk 117 optimal weight: 0.5980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN D 67 GLN D 139 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9876 Z= 0.153 Angle : 0.487 11.812 13428 Z= 0.243 Chirality : 0.038 0.132 1536 Planarity : 0.005 0.050 1746 Dihedral : 5.606 58.799 1353 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.13 % Allowed : 15.02 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.54 (0.24), residues: 1236 helix: 2.10 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.74 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 117 HIS 0.007 0.001 HIS E 12 PHE 0.012 0.001 PHE F 161 TYR 0.018 0.001 TYR D 130 ARG 0.014 0.001 ARG D 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 226 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8335 (mt) cc_final: 0.8064 (mt) REVERT: A 143 ARG cc_start: 0.8406 (ttm-80) cc_final: 0.7929 (mtm-85) REVERT: A 175 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6235 (mp0) REVERT: B 18 ARG cc_start: 0.6602 (ttp-170) cc_final: 0.5806 (ttt180) REVERT: B 136 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7925 (tp) REVERT: B 170 LYS cc_start: 0.8405 (tttt) cc_final: 0.8148 (tppt) REVERT: B 213 GLU cc_start: 0.7279 (tp30) cc_final: 0.6888 (tp30) REVERT: B 214 MET cc_start: 0.7544 (mtm) cc_final: 0.7318 (mtt) REVERT: C 23 TRP cc_start: 0.8953 (t-100) cc_final: 0.8686 (t-100) REVERT: C 30 LYS cc_start: 0.7168 (mmtt) cc_final: 0.6836 (mttt) REVERT: C 54 THR cc_start: 0.7847 (m) cc_final: 0.7092 (p) REVERT: D 25 LYS cc_start: 0.7852 (mptt) cc_final: 0.7376 (mttt) REVERT: D 163 ASP cc_start: 0.8182 (m-30) cc_final: 0.7892 (m-30) REVERT: D 212 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7741 (tm-30) REVERT: E 68 MET cc_start: 0.8686 (mtm) cc_final: 0.8373 (mtp) REVERT: E 79 GLU cc_start: 0.8831 (tp30) cc_final: 0.8551 (tp30) REVERT: E 175 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: F 4 GLN cc_start: 0.8396 (tt0) cc_final: 0.8017 (pm20) REVERT: F 13 GLN cc_start: 0.8187 (mt0) cc_final: 0.7252 (pt0) REVERT: F 175 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.5885 (mp0) REVERT: F 189 LEU cc_start: 0.8492 (tp) cc_final: 0.8137 (tp) outliers start: 22 outliers final: 12 residues processed: 243 average time/residue: 0.2404 time to fit residues: 78.9033 Evaluate side-chains 233 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 217 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 175 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 121 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN D 139 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9876 Z= 0.174 Angle : 0.506 12.564 13428 Z= 0.250 Chirality : 0.039 0.168 1536 Planarity : 0.005 0.052 1746 Dihedral : 5.011 59.744 1346 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.94 % Allowed : 15.70 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.24), residues: 1236 helix: 2.07 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.77 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 80 HIS 0.001 0.000 HIS F 84 PHE 0.009 0.001 PHE F 40 TYR 0.008 0.001 TYR B 169 ARG 0.012 0.001 ARG D 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 226 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8348 (mt) cc_final: 0.8068 (mt) REVERT: A 175 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6189 (mp0) REVERT: B 18 ARG cc_start: 0.6606 (ttp-170) cc_final: 0.5639 (ttt180) REVERT: B 170 LYS cc_start: 0.8405 (tttt) cc_final: 0.8138 (tppt) REVERT: B 213 GLU cc_start: 0.7472 (tp30) cc_final: 0.7055 (tp30) REVERT: C 23 TRP cc_start: 0.8958 (t-100) cc_final: 0.8716 (t-100) REVERT: C 30 LYS cc_start: 0.7193 (mmtt) cc_final: 0.6877 (mttt) REVERT: D 25 LYS cc_start: 0.7881 (mptt) cc_final: 0.7398 (mttt) REVERT: D 74 ASN cc_start: 0.8212 (m110) cc_final: 0.7877 (m110) REVERT: D 163 ASP cc_start: 0.8196 (m-30) cc_final: 0.7925 (m-30) REVERT: D 212 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7751 (tm-30) REVERT: E 68 MET cc_start: 0.8697 (mtm) cc_final: 0.8385 (mtp) REVERT: E 175 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: F 4 GLN cc_start: 0.8407 (tt0) cc_final: 0.8020 (pm20) REVERT: F 13 GLN cc_start: 0.8198 (mt0) cc_final: 0.7272 (pt0) REVERT: F 82 ARG cc_start: 0.8417 (mtm110) cc_final: 0.8071 (ttp80) REVERT: F 175 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6056 (mp0) REVERT: F 189 LEU cc_start: 0.8488 (tp) cc_final: 0.8126 (tp) outliers start: 20 outliers final: 11 residues processed: 241 average time/residue: 0.2374 time to fit residues: 76.8210 Evaluate side-chains 235 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 221 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 175 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 0.0770 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 139 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9876 Z= 0.209 Angle : 0.520 12.517 13428 Z= 0.259 Chirality : 0.040 0.154 1536 Planarity : 0.005 0.057 1746 Dihedral : 5.031 58.761 1346 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.74 % Allowed : 16.96 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.44 (0.24), residues: 1236 helix: 2.01 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.75 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 80 HIS 0.001 0.000 HIS A 84 PHE 0.010 0.001 PHE F 40 TYR 0.009 0.001 TYR D 169 ARG 0.013 0.001 ARG D 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 231 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8350 (mt) cc_final: 0.8074 (mt) REVERT: A 175 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6186 (mp0) REVERT: B 18 ARG cc_start: 0.6636 (ttp-170) cc_final: 0.5640 (ttt180) REVERT: B 170 LYS cc_start: 0.8434 (tttt) cc_final: 0.8153 (tppt) REVERT: B 214 MET cc_start: 0.7590 (mtm) cc_final: 0.7370 (mtp) REVERT: C 23 TRP cc_start: 0.8967 (t-100) cc_final: 0.8708 (t-100) REVERT: C 30 LYS cc_start: 0.7242 (mmtt) cc_final: 0.6999 (mttt) REVERT: D 25 LYS cc_start: 0.7905 (mptt) cc_final: 0.7410 (mttt) REVERT: D 163 ASP cc_start: 0.8229 (m-30) cc_final: 0.7934 (m-30) REVERT: D 212 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7728 (tm-30) REVERT: E 15 ILE cc_start: 0.8907 (tt) cc_final: 0.8665 (tt) REVERT: E 68 MET cc_start: 0.8724 (mtm) cc_final: 0.8405 (mtp) REVERT: E 79 GLU cc_start: 0.8824 (tp30) cc_final: 0.8544 (tp30) REVERT: E 175 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6794 (mp0) REVERT: F 4 GLN cc_start: 0.8425 (tt0) cc_final: 0.8017 (pm20) REVERT: F 13 GLN cc_start: 0.8195 (mt0) cc_final: 0.7384 (pt0) REVERT: F 175 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: F 189 LEU cc_start: 0.8501 (tp) cc_final: 0.8132 (tp) outliers start: 18 outliers final: 11 residues processed: 242 average time/residue: 0.2457 time to fit residues: 79.1334 Evaluate side-chains 232 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 218 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 175 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN E 9 GLN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9876 Z= 0.286 Angle : 0.569 12.071 13428 Z= 0.286 Chirality : 0.041 0.155 1536 Planarity : 0.005 0.055 1746 Dihedral : 5.140 58.345 1346 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.94 % Allowed : 17.05 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.21 (0.24), residues: 1236 helix: 1.83 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.70 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 80 HIS 0.002 0.000 HIS A 84 PHE 0.011 0.002 PHE A 168 TYR 0.014 0.002 TYR E 145 ARG 0.014 0.001 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 220 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8339 (mt) cc_final: 0.8046 (mt) REVERT: A 175 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6272 (mp0) REVERT: B 18 ARG cc_start: 0.6463 (ttp-170) cc_final: 0.5528 (ttt180) REVERT: B 170 LYS cc_start: 0.8474 (tttt) cc_final: 0.8185 (tppt) REVERT: B 218 CYS cc_start: 0.6810 (m) cc_final: 0.6602 (m) REVERT: C 23 TRP cc_start: 0.8991 (t-100) cc_final: 0.8719 (t-100) REVERT: C 30 LYS cc_start: 0.7310 (mmtt) cc_final: 0.7070 (mttt) REVERT: D 25 LYS cc_start: 0.7894 (mptt) cc_final: 0.7417 (mttt) REVERT: D 212 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7737 (tm-30) REVERT: E 9 GLN cc_start: 0.6592 (OUTLIER) cc_final: 0.6369 (pm20) REVERT: E 68 MET cc_start: 0.8759 (mtm) cc_final: 0.8435 (mtp) REVERT: E 79 GLU cc_start: 0.8814 (tp30) cc_final: 0.8520 (tp30) REVERT: E 96 MET cc_start: 0.7267 (tmm) cc_final: 0.6869 (pmm) REVERT: E 175 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: F 4 GLN cc_start: 0.8480 (tt0) cc_final: 0.8005 (pm20) REVERT: F 175 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6409 (mp0) REVERT: F 189 LEU cc_start: 0.8497 (tp) cc_final: 0.8124 (tp) outliers start: 20 outliers final: 12 residues processed: 234 average time/residue: 0.2536 time to fit residues: 78.7990 Evaluate side-chains 229 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 213 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 175 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.5980 chunk 56 optimal weight: 0.0970 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 77 optimal weight: 0.0170 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9876 Z= 0.169 Angle : 0.535 13.207 13428 Z= 0.268 Chirality : 0.039 0.159 1536 Planarity : 0.005 0.060 1746 Dihedral : 5.077 58.588 1346 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.26 % Allowed : 17.15 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.24), residues: 1236 helix: 1.87 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.71 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 80 HIS 0.002 0.000 HIS B 12 PHE 0.009 0.001 PHE F 40 TYR 0.009 0.001 TYR E 169 ARG 0.014 0.001 ARG D 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 227 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8362 (mt) cc_final: 0.8070 (mt) REVERT: A 143 ARG cc_start: 0.8400 (ttm-80) cc_final: 0.8015 (mtm-85) REVERT: A 175 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6225 (mp0) REVERT: A 212 GLU cc_start: 0.7267 (pt0) cc_final: 0.6898 (pm20) REVERT: B 18 ARG cc_start: 0.6631 (ttp-170) cc_final: 0.5640 (ttt180) REVERT: B 170 LYS cc_start: 0.8415 (tttt) cc_final: 0.8153 (tppt) REVERT: B 214 MET cc_start: 0.7584 (mtm) cc_final: 0.7274 (mtt) REVERT: B 218 CYS cc_start: 0.6510 (m) cc_final: 0.6206 (m) REVERT: C 30 LYS cc_start: 0.7134 (mmtt) cc_final: 0.6872 (mttt) REVERT: C 193 ASN cc_start: 0.6636 (t0) cc_final: 0.6284 (t0) REVERT: D 25 LYS cc_start: 0.7867 (mptt) cc_final: 0.7381 (mttt) REVERT: D 74 ASN cc_start: 0.8189 (m110) cc_final: 0.7823 (m110) REVERT: D 163 ASP cc_start: 0.8145 (m-30) cc_final: 0.7912 (m-30) REVERT: D 212 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7687 (tm-30) REVERT: E 25 LYS cc_start: 0.8300 (mmtp) cc_final: 0.8077 (mmtp) REVERT: E 68 MET cc_start: 0.8693 (mtm) cc_final: 0.8391 (mtp) REVERT: E 79 GLU cc_start: 0.8765 (tp30) cc_final: 0.8495 (tp30) REVERT: E 96 MET cc_start: 0.7308 (tmm) cc_final: 0.6813 (pmm) REVERT: E 118 MET cc_start: 0.8400 (mmm) cc_final: 0.8113 (mmm) REVERT: E 175 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: E 197 ASP cc_start: 0.8268 (m-30) cc_final: 0.7863 (p0) REVERT: F 4 GLN cc_start: 0.8414 (tt0) cc_final: 0.8036 (pm20) REVERT: F 13 GLN cc_start: 0.8174 (mt0) cc_final: 0.7222 (pt0) REVERT: F 66 MET cc_start: 0.8691 (mmt) cc_final: 0.8400 (mmm) REVERT: F 175 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6338 (mp0) REVERT: F 189 LEU cc_start: 0.8532 (tp) cc_final: 0.8164 (tp) outliers start: 13 outliers final: 10 residues processed: 237 average time/residue: 0.2593 time to fit residues: 81.6085 Evaluate side-chains 237 residues out of total 1086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 224 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 175 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 0.0370 chunk 14 optimal weight: 0.0010 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 overall best weight: 0.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.149229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122848 restraints weight = 14693.779| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.54 r_work: 0.3361 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9876 Z= 0.162 Angle : 0.528 13.753 13428 Z= 0.262 Chirality : 0.039 0.154 1536 Planarity : 0.005 0.062 1746 Dihedral : 5.001 57.853 1346 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.16 % Allowed : 17.44 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.34 (0.24), residues: 1236 helix: 1.94 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.70 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 23 HIS 0.002 0.000 HIS B 12 PHE 0.009 0.001 PHE F 32 TYR 0.008 0.001 TYR E 169 ARG 0.016 0.001 ARG D 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2446.85 seconds wall clock time: 44 minutes 9.25 seconds (2649.25 seconds total)