Starting phenix.real_space_refine on Fri Mar 14 07:03:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xqh_33396/03_2025/7xqh_33396.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xqh_33396/03_2025/7xqh_33396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xqh_33396/03_2025/7xqh_33396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xqh_33396/03_2025/7xqh_33396.map" model { file = "/net/cci-nas-00/data/ceres_data/7xqh_33396/03_2025/7xqh_33396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xqh_33396/03_2025/7xqh_33396.cif" } resolution = 3.8 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= 0.001 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 48 5.16 5 C 6516 2.51 5 N 1548 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9774 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1629 Classifications: {'peptide': 200} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 193} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 3.46, per 1000 atoms: 0.35 Number of scatterers: 9774 At special positions: 0 Unit cell: (102.608, 106, 102.608, 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 48 16.00 O 1662 8.00 N 1548 7.00 C 6516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.19 Conformation dependent library (CDL) restraints added in 1.7 seconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 72.0% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.801A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 45' Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.972A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 107 removed outlier: 3.535A pdb=" N VAL A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 149 through 177 removed outlier: 4.059A pdb=" N ARG A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 235 removed outlier: 3.848A pdb=" N LYS A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 228 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 27 through 32 Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.800A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TRP B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.972A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 107 removed outlier: 3.535A pdb=" N VAL B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 149 through 177 removed outlier: 4.058A pdb=" N ARG B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 235 removed outlier: 3.848A pdb=" N LYS B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 228 " --> pdb=" O ASN B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 15 Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.801A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 45' Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.972A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 107 removed outlier: 3.535A pdb=" N VAL C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 149 through 177 removed outlier: 4.059A pdb=" N ARG C 153 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 235 removed outlier: 3.848A pdb=" N LYS C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 228 " --> pdb=" O ASN C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 15 Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 27 through 32 Processing helix chain 'D' and resid 33 through 40 Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.801A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 45' Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.972A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 107 removed outlier: 3.535A pdb=" N VAL D 87 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 149 through 177 removed outlier: 4.059A pdb=" N ARG D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 235 removed outlier: 3.848A pdb=" N LYS D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 228 " --> pdb=" O ASN D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 15 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 27 through 32 Processing helix chain 'E' and resid 33 through 40 Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.801A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 45' Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.972A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 107 removed outlier: 3.535A pdb=" N VAL E 87 " --> pdb=" O ILE E 83 " (cutoff:3.500A) Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 149 through 177 removed outlier: 4.059A pdb=" N ARG E 153 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 235 removed outlier: 3.848A pdb=" N LYS E 206 " --> pdb=" O ARG E 202 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU E 228 " --> pdb=" O ASN E 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 15 Processing helix chain 'F' and resid 20 through 25 Processing helix chain 'F' and resid 27 through 32 Processing helix chain 'F' and resid 33 through 40 Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.801A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.972A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 107 removed outlier: 3.535A pdb=" N VAL F 87 " --> pdb=" O ILE F 83 " (cutoff:3.500A) Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 149 through 177 removed outlier: 4.059A pdb=" N ARG F 153 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 235 removed outlier: 3.848A pdb=" N LYS F 206 " --> pdb=" O ARG F 202 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU F 227 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU F 228 " --> pdb=" O ASN F 224 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) 612 hydrogen bonds defined for protein. 1818 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: 2.93 Time building geometry restraints manager: 2.64 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: 2898 1.34 - 1.46: 2154 1.46 - 1.57: 4920 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 10032 Sorted by residual: bond pdb=" CA VAL B 87 " pdb=" C VAL B 87 " ideal model delta sigma weight residual 1.520 1.538 -0.018 8.80e-03 1.29e+04 4.35e+00 bond pdb=" CA VAL E 87 " pdb=" C VAL E 87 " ideal model delta sigma weight residual 1.520 1.538 -0.018 8.80e-03 1.29e+04 4.28e+00 bond pdb=" CA VAL F 87 " pdb=" C VAL F 87 " ideal model delta sigma weight residual 1.520 1.538 -0.018 8.80e-03 1.29e+04 4.25e+00 bond pdb=" CA VAL C 87 " pdb=" C VAL C 87 " ideal model delta sigma weight residual 1.520 1.538 -0.018 8.80e-03 1.29e+04 4.25e+00 bond pdb=" CA VAL A 87 " pdb=" C VAL A 87 " ideal model delta sigma weight residual 1.520 1.538 -0.018 8.80e-03 1.29e+04 4.20e+00 ... (remaining 10027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 12981 1.59 - 3.17: 481 3.17 - 4.76: 80 4.76 - 6.34: 36 6.34 - 7.93: 12 Bond angle restraints: 13590 Sorted by residual: angle pdb=" C SER D 86 " pdb=" N VAL D 87 " pdb=" CA VAL D 87 " ideal model delta sigma weight residual 120.24 124.52 -4.28 6.30e-01 2.52e+00 4.63e+01 angle pdb=" C SER B 86 " pdb=" N VAL B 87 " pdb=" CA VAL B 87 " ideal model delta sigma weight residual 120.24 124.52 -4.28 6.30e-01 2.52e+00 4.62e+01 angle pdb=" C SER A 86 " pdb=" N VAL A 87 " pdb=" CA VAL A 87 " ideal model delta sigma weight residual 120.24 124.51 -4.27 6.30e-01 2.52e+00 4.60e+01 angle pdb=" C SER C 86 " pdb=" N VAL C 87 " pdb=" CA VAL C 87 " ideal model delta sigma weight residual 120.24 124.51 -4.27 6.30e-01 2.52e+00 4.60e+01 angle pdb=" C SER F 86 " pdb=" N VAL F 87 " pdb=" CA VAL F 87 " ideal model delta sigma weight residual 120.24 124.50 -4.26 6.30e-01 2.52e+00 4.58e+01 ... (remaining 13585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.78: 4992 13.78 - 27.56: 534 27.56 - 41.33: 222 41.33 - 55.11: 90 55.11 - 68.89: 36 Dihedral angle restraints: 5874 sinusoidal: 2364 harmonic: 3510 Sorted by residual: dihedral pdb=" CA TYR E 177 " pdb=" C TYR E 177 " pdb=" N GLY E 178 " pdb=" CA GLY E 178 " ideal model delta harmonic sigma weight residual -180.00 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA TYR A 177 " pdb=" C TYR A 177 " pdb=" N GLY A 178 " pdb=" CA GLY A 178 " ideal model delta harmonic sigma weight residual 180.00 -163.34 -16.66 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA TYR B 177 " pdb=" C TYR B 177 " pdb=" N GLY B 178 " pdb=" CA GLY B 178 " ideal model delta harmonic sigma weight residual 180.00 -163.35 -16.65 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 5871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1119 0.044 - 0.088: 334 0.088 - 0.132: 83 0.132 - 0.176: 0 0.176 - 0.220: 6 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA HIS A 194 " pdb=" N HIS A 194 " pdb=" C HIS A 194 " pdb=" CB HIS A 194 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA HIS D 194 " pdb=" N HIS D 194 " pdb=" C HIS D 194 " pdb=" CB HIS D 194 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA HIS E 194 " pdb=" N HIS E 194 " pdb=" C HIS E 194 " pdb=" CB HIS E 194 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1539 not shown) Planarity restraints: 1644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 87 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.48e+00 pdb=" N PRO B 88 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 87 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO E 88 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO E 88 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 88 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 87 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO C 88 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 88 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 88 " 0.027 5.00e-02 4.00e+02 ... (remaining 1641 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3398 2.85 - 3.36: 8833 3.36 - 3.87: 15659 3.87 - 4.39: 15479 4.39 - 4.90: 27451 Nonbonded interactions: 70820 Sorted by model distance: nonbonded pdb=" O LEU C 35 " pdb=" OG1 THR C 39 " model vdw 2.337 3.040 nonbonded pdb=" O LEU B 35 " pdb=" OG1 THR B 39 " model vdw 2.337 3.040 nonbonded pdb=" O LEU E 35 " pdb=" OG1 THR E 39 " model vdw 2.338 3.040 nonbonded pdb=" O LEU A 35 " pdb=" OG1 THR A 39 " model vdw 2.338 3.040 nonbonded pdb=" O LEU D 35 " pdb=" OG1 THR D 39 " model vdw 2.338 3.040 ... (remaining 70815 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.030 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: 0.080 Set scattering table: 0.090 Process input model: 23.590 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10032 Z= 0.298 Angle : 0.781 7.929 13590 Z= 0.475 Chirality : 0.042 0.220 1542 Planarity : 0.006 0.047 1644 Dihedral : 15.527 68.889 3552 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.57 % Favored : 95.92 % Rotamer: Outliers : 2.23 % Allowed : 15.08 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -2.01 (0.21), residues: 1176 helix: -1.31 (0.15), residues: 774 sheet: 2.72 (0.64), residues: 66 loop : -1.88 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 78 HIS 0.001 0.000 HIS D 95 PHE 0.011 0.001 PHE D 52 TYR 0.010 0.002 TYR F 92 ARG 0.003 0.001 ARG F 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8384 (p0) cc_final: 0.8140 (p0) REVERT: A 100 MET cc_start: 0.8239 (ttt) cc_final: 0.7884 (ttt) REVERT: A 104 GLU cc_start: 0.9259 (tt0) cc_final: 0.9014 (pt0) REVERT: A 190 ASP cc_start: 0.8872 (m-30) cc_final: 0.8635 (t0) REVERT: B 212 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8340 (t80) REVERT: C 47 ASP cc_start: 0.8435 (p0) cc_final: 0.8195 (p0) REVERT: C 100 MET cc_start: 0.8139 (ttt) cc_final: 0.7810 (ttt) REVERT: C 104 GLU cc_start: 0.9281 (tt0) cc_final: 0.9011 (pt0) REVERT: C 190 ASP cc_start: 0.8807 (m-30) cc_final: 0.8514 (t0) REVERT: D 47 ASP cc_start: 0.8393 (p0) cc_final: 0.8178 (p0) REVERT: D 100 MET cc_start: 0.8246 (ttt) cc_final: 0.7944 (ttt) REVERT: D 104 GLU cc_start: 0.9301 (tt0) cc_final: 0.9029 (pt0) REVERT: D 190 ASP cc_start: 0.8852 (m-30) cc_final: 0.8558 (t0) REVERT: E 100 MET cc_start: 0.8083 (ttt) cc_final: 0.7604 (tmm) REVERT: E 104 GLU cc_start: 0.9378 (tt0) cc_final: 0.8962 (pt0) REVERT: E 212 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8288 (t80) REVERT: F 47 ASP cc_start: 0.8452 (p0) cc_final: 0.8201 (p0) REVERT: F 100 MET cc_start: 0.8186 (ttt) cc_final: 0.7883 (ttt) REVERT: F 104 GLU cc_start: 0.9277 (tt0) cc_final: 0.9015 (pt0) REVERT: F 190 ASP cc_start: 0.8832 (m-30) cc_final: 0.8526 (t0) outliers start: 24 outliers final: 22 residues processed: 239 average time/residue: 0.2036 time to fit residues: 70.4408 Evaluate side-chains 184 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 3 ASP Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 229 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 30.0000 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 224 ASN B 81 GLN B 224 ASN C 81 GLN C 224 ASN D 81 GLN D 224 ASN E 81 GLN E 224 ASN F 81 GLN F 224 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.095385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.072392 restraints weight = 30218.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.074730 restraints weight = 14026.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.076023 restraints weight = 8731.152| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10032 Z= 0.214 Angle : 0.630 9.289 13590 Z= 0.317 Chirality : 0.040 0.186 1542 Planarity : 0.003 0.021 1644 Dihedral : 7.480 59.679 1338 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.06 % Favored : 96.43 % Rotamer: Outliers : 8.85 % Allowed : 15.55 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.50 (0.24), residues: 1176 helix: 0.90 (0.17), residues: 780 sheet: 3.93 (0.69), residues: 60 loop : -1.68 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 4 HIS 0.002 0.001 HIS D 194 PHE 0.008 0.001 PHE E 179 TYR 0.009 0.001 TYR B 177 ARG 0.002 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 147 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8252 (p0) cc_final: 0.8025 (p0) REVERT: A 100 MET cc_start: 0.8403 (ttt) cc_final: 0.8054 (ttt) REVERT: A 104 GLU cc_start: 0.9319 (tt0) cc_final: 0.9043 (pt0) REVERT: A 223 LEU cc_start: 0.9421 (tp) cc_final: 0.9099 (tt) REVERT: C 47 ASP cc_start: 0.8303 (p0) cc_final: 0.8066 (p0) REVERT: C 100 MET cc_start: 0.8382 (ttt) cc_final: 0.8057 (ttt) REVERT: C 104 GLU cc_start: 0.9320 (tt0) cc_final: 0.9058 (pt0) REVERT: D 47 ASP cc_start: 0.8266 (p0) cc_final: 0.8065 (p0) REVERT: D 100 MET cc_start: 0.8388 (ttt) cc_final: 0.8084 (ttt) REVERT: D 104 GLU cc_start: 0.9319 (tt0) cc_final: 0.9045 (pt0) REVERT: E 47 ASP cc_start: 0.8173 (p0) cc_final: 0.7877 (p0) REVERT: E 100 MET cc_start: 0.8286 (ttt) cc_final: 0.7941 (ttp) REVERT: E 104 GLU cc_start: 0.9440 (tt0) cc_final: 0.9215 (pt0) REVERT: E 213 MET cc_start: 0.8899 (mmp) cc_final: 0.8505 (mmp) REVERT: F 47 ASP cc_start: 0.8313 (p0) cc_final: 0.8085 (p0) REVERT: F 100 MET cc_start: 0.8398 (ttt) cc_final: 0.8064 (ttt) REVERT: F 104 GLU cc_start: 0.9310 (tt0) cc_final: 0.9055 (pt0) outliers start: 95 outliers final: 64 residues processed: 210 average time/residue: 0.1848 time to fit residues: 56.3659 Evaluate side-chains 204 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 140 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 229 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 61 optimal weight: 8.9990 chunk 1 optimal weight: 0.0870 chunk 108 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 22 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 4 optimal weight: 0.0010 chunk 92 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.8766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN D 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.095054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.072199 restraints weight = 30944.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.074533 restraints weight = 13996.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.076100 restraints weight = 8565.816| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10032 Z= 0.170 Angle : 0.646 10.553 13590 Z= 0.314 Chirality : 0.040 0.212 1542 Planarity : 0.003 0.025 1644 Dihedral : 6.705 59.923 1320 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.89 % Favored : 96.60 % Rotamer: Outliers : 5.96 % Allowed : 18.34 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.26 (0.25), residues: 1176 helix: 1.41 (0.18), residues: 816 sheet: 3.81 (0.73), residues: 60 loop : -1.38 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 4 HIS 0.004 0.001 HIS B 74 PHE 0.006 0.001 PHE B 233 TYR 0.013 0.001 TYR A 17 ARG 0.001 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 163 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.6780 (m-80) REVERT: A 92 TYR cc_start: 0.8664 (t80) cc_final: 0.8120 (t80) REVERT: A 100 MET cc_start: 0.8441 (ttt) cc_final: 0.8011 (ttt) REVERT: A 104 GLU cc_start: 0.9307 (tt0) cc_final: 0.9037 (pt0) REVERT: A 223 LEU cc_start: 0.9390 (tp) cc_final: 0.9074 (tt) REVERT: B 91 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8878 (tt) REVERT: C 223 LEU cc_start: 0.9471 (tp) cc_final: 0.9196 (tt) REVERT: D 100 MET cc_start: 0.8405 (ttt) cc_final: 0.8002 (ttt) REVERT: D 104 GLU cc_start: 0.9327 (tt0) cc_final: 0.9056 (pt0) REVERT: D 223 LEU cc_start: 0.9416 (tp) cc_final: 0.9113 (tt) REVERT: E 100 MET cc_start: 0.8384 (ttt) cc_final: 0.8014 (ttp) REVERT: E 104 GLU cc_start: 0.9441 (tt0) cc_final: 0.9209 (pt0) REVERT: E 223 LEU cc_start: 0.9537 (tp) cc_final: 0.9278 (tt) REVERT: F 100 MET cc_start: 0.8398 (ttt) cc_final: 0.8055 (ttt) REVERT: F 104 GLU cc_start: 0.9326 (tt0) cc_final: 0.9063 (pt0) REVERT: F 223 LEU cc_start: 0.9463 (tp) cc_final: 0.9192 (tt) outliers start: 64 outliers final: 45 residues processed: 196 average time/residue: 0.2022 time to fit residues: 57.2858 Evaluate side-chains 182 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 212 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 118 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 0.0070 chunk 95 optimal weight: 0.1980 chunk 79 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN D 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.094511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.071455 restraints weight = 32301.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.073771 restraints weight = 14730.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.075191 restraints weight = 9141.121| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10032 Z= 0.161 Angle : 0.613 10.411 13590 Z= 0.298 Chirality : 0.039 0.180 1542 Planarity : 0.003 0.024 1644 Dihedral : 5.797 59.985 1302 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.81 % Favored : 96.68 % Rotamer: Outliers : 4.93 % Allowed : 20.48 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.79 (0.26), residues: 1176 helix: 1.85 (0.19), residues: 816 sheet: 3.52 (0.76), residues: 60 loop : -1.20 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 4 HIS 0.003 0.001 HIS B 74 PHE 0.006 0.001 PHE E 169 TYR 0.013 0.001 TYR C 66 ARG 0.002 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 139 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8282 (p0) cc_final: 0.8067 (p0) REVERT: A 92 TYR cc_start: 0.8653 (t80) cc_final: 0.8080 (t80) REVERT: A 223 LEU cc_start: 0.9360 (tp) cc_final: 0.9144 (tt) REVERT: B 91 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8878 (tt) REVERT: B 212 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8213 (t80) REVERT: D 92 TYR cc_start: 0.8576 (t80) cc_final: 0.7957 (t80) REVERT: E 100 MET cc_start: 0.8372 (ttt) cc_final: 0.8113 (ttt) REVERT: E 104 GLU cc_start: 0.9473 (tt0) cc_final: 0.9248 (pt0) REVERT: E 223 LEU cc_start: 0.9523 (tp) cc_final: 0.9231 (tt) outliers start: 53 outliers final: 47 residues processed: 168 average time/residue: 0.1674 time to fit residues: 42.3494 Evaluate side-chains 173 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 124 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 212 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 119 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 48 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 65 optimal weight: 0.0970 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN D 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.094104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.070975 restraints weight = 32237.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.073239 restraints weight = 14995.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.074544 restraints weight = 9379.519| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10032 Z= 0.164 Angle : 0.606 11.437 13590 Z= 0.293 Chirality : 0.038 0.152 1542 Planarity : 0.003 0.025 1644 Dihedral : 5.694 59.998 1302 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.72 % Favored : 96.77 % Rotamer: Outliers : 6.05 % Allowed : 20.48 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.88 (0.26), residues: 1176 helix: 1.86 (0.19), residues: 840 sheet: 2.92 (0.78), residues: 60 loop : -1.09 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 78 HIS 0.002 0.001 HIS A 74 PHE 0.007 0.001 PHE F 52 TYR 0.008 0.001 TYR C 66 ARG 0.006 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 126 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8292 (p0) cc_final: 0.7431 (p0) REVERT: A 92 TYR cc_start: 0.8682 (t80) cc_final: 0.8138 (t80) REVERT: A 202 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7548 (mtm180) REVERT: A 223 LEU cc_start: 0.9332 (tp) cc_final: 0.9065 (tt) REVERT: B 91 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8859 (tt) REVERT: B 212 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8242 (t80) REVERT: B 223 LEU cc_start: 0.9450 (tp) cc_final: 0.9180 (tt) REVERT: E 100 MET cc_start: 0.8327 (ttt) cc_final: 0.8047 (ttt) REVERT: E 104 GLU cc_start: 0.9506 (tt0) cc_final: 0.9259 (pt0) outliers start: 65 outliers final: 50 residues processed: 170 average time/residue: 0.1760 time to fit residues: 44.6561 Evaluate side-chains 178 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 125 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 212 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 92 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 13 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.095153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.072306 restraints weight = 32159.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.074574 restraints weight = 14950.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.075989 restraints weight = 9287.054| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10032 Z= 0.135 Angle : 0.598 11.998 13590 Z= 0.280 Chirality : 0.037 0.150 1542 Planarity : 0.003 0.027 1644 Dihedral : 5.538 59.904 1302 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.04 % Favored : 97.45 % Rotamer: Outliers : 4.84 % Allowed : 21.51 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.98 (0.26), residues: 1176 helix: 2.06 (0.19), residues: 834 sheet: 2.69 (0.79), residues: 60 loop : -1.37 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP F 78 HIS 0.003 0.001 HIS D 74 PHE 0.006 0.001 PHE E 169 TYR 0.011 0.001 TYR D 66 ARG 0.004 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 149 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8636 (t80) cc_final: 0.8256 (t80) REVERT: A 223 LEU cc_start: 0.9324 (tp) cc_final: 0.9071 (tt) REVERT: B 91 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8858 (tt) REVERT: B 212 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8215 (t80) REVERT: C 92 TYR cc_start: 0.8606 (t80) cc_final: 0.8290 (t80) REVERT: D 92 TYR cc_start: 0.8594 (t80) cc_final: 0.8145 (t80) REVERT: E 49 GLN cc_start: 0.9116 (tp40) cc_final: 0.8883 (mm110) REVERT: E 100 MET cc_start: 0.8339 (ttt) cc_final: 0.8131 (ttt) REVERT: E 104 GLU cc_start: 0.9467 (tt0) cc_final: 0.9162 (pt0) REVERT: F 92 TYR cc_start: 0.8628 (t80) cc_final: 0.8309 (t80) outliers start: 52 outliers final: 42 residues processed: 185 average time/residue: 0.1565 time to fit residues: 44.7590 Evaluate side-chains 184 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 212 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 14 optimal weight: 0.0970 chunk 54 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 106 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.094501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.071296 restraints weight = 33074.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.073595 restraints weight = 15423.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.074990 restraints weight = 9597.578| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10032 Z= 0.163 Angle : 0.607 12.510 13590 Z= 0.287 Chirality : 0.038 0.150 1542 Planarity : 0.003 0.027 1644 Dihedral : 5.533 59.888 1302 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.04 % Favored : 97.45 % Rotamer: Outliers : 5.12 % Allowed : 22.63 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.15 (0.26), residues: 1176 helix: 2.21 (0.19), residues: 834 sheet: 2.56 (0.79), residues: 60 loop : -1.34 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP F 78 HIS 0.002 0.001 HIS A 74 PHE 0.008 0.001 PHE C 52 TYR 0.009 0.001 TYR E 66 ARG 0.002 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 140 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.9332 (tp) cc_final: 0.9080 (tt) REVERT: B 91 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8874 (tt) REVERT: B 155 TYR cc_start: 0.8209 (t80) cc_final: 0.7899 (t80) REVERT: B 212 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8224 (t80) REVERT: E 100 MET cc_start: 0.8353 (ttt) cc_final: 0.8067 (ttt) REVERT: E 104 GLU cc_start: 0.9499 (tt0) cc_final: 0.9233 (pt0) outliers start: 55 outliers final: 46 residues processed: 180 average time/residue: 0.1528 time to fit residues: 42.0983 Evaluate side-chains 186 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 10 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.093388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.070457 restraints weight = 31175.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.072703 restraints weight = 14545.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.074151 restraints weight = 9012.786| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10032 Z= 0.187 Angle : 0.615 12.183 13590 Z= 0.291 Chirality : 0.038 0.152 1542 Planarity : 0.003 0.027 1644 Dihedral : 5.588 59.922 1302 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.98 % Favored : 96.51 % Rotamer: Outliers : 5.21 % Allowed : 23.56 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.37 (0.26), residues: 1176 helix: 2.48 (0.18), residues: 810 sheet: 2.37 (0.80), residues: 60 loop : -1.22 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.001 0.001 HIS A 74 PHE 0.007 0.001 PHE F 209 TYR 0.025 0.001 TYR B 92 ARG 0.005 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 135 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8184 (p0) cc_final: 0.7610 (p0) REVERT: A 202 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7636 (mtm180) REVERT: A 223 LEU cc_start: 0.9342 (tp) cc_final: 0.9088 (tt) REVERT: B 91 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8868 (tt) REVERT: B 212 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8196 (t80) REVERT: E 100 MET cc_start: 0.8414 (ttt) cc_final: 0.8170 (ttt) REVERT: E 104 GLU cc_start: 0.9501 (tt0) cc_final: 0.9153 (pt0) REVERT: E 212 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8235 (t80) outliers start: 56 outliers final: 47 residues processed: 176 average time/residue: 0.1670 time to fit residues: 44.3914 Evaluate side-chains 185 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 95 HIS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 41 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.094518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.071638 restraints weight = 30790.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.073932 restraints weight = 14404.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.075232 restraints weight = 8947.235| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10032 Z= 0.141 Angle : 0.606 12.196 13590 Z= 0.284 Chirality : 0.037 0.151 1542 Planarity : 0.003 0.027 1644 Dihedral : 5.501 59.792 1302 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.36 % Favored : 98.13 % Rotamer: Outliers : 4.56 % Allowed : 24.58 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.26), residues: 1176 helix: 2.62 (0.18), residues: 804 sheet: 2.35 (0.79), residues: 60 loop : -1.39 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 78 HIS 0.002 0.001 HIS A 74 PHE 0.005 0.001 PHE F 52 TYR 0.021 0.001 TYR B 92 ARG 0.005 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 138 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.9330 (tp) cc_final: 0.9078 (tt) REVERT: B 91 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8858 (tt) REVERT: B 212 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8202 (t80) REVERT: E 100 MET cc_start: 0.8353 (ttt) cc_final: 0.8066 (ttt) REVERT: E 104 GLU cc_start: 0.9533 (tt0) cc_final: 0.9213 (pt0) REVERT: E 212 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8203 (t80) outliers start: 49 outliers final: 43 residues processed: 173 average time/residue: 0.1543 time to fit residues: 41.6173 Evaluate side-chains 180 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 95 HIS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 212 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 20 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN D 224 ASN F 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.094483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.071817 restraints weight = 30940.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.074100 restraints weight = 14404.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.075457 restraints weight = 8937.870| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10032 Z= 0.139 Angle : 0.599 12.300 13590 Z= 0.278 Chirality : 0.038 0.151 1542 Planarity : 0.003 0.028 1644 Dihedral : 5.479 59.832 1302 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.87 % Favored : 97.62 % Rotamer: Outliers : 4.84 % Allowed : 24.30 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.42 (0.26), residues: 1176 helix: 2.62 (0.18), residues: 804 sheet: 2.33 (0.80), residues: 60 loop : -1.43 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 78 HIS 0.002 0.001 HIS F 74 PHE 0.006 0.001 PHE D 70 TYR 0.022 0.001 TYR B 92 ARG 0.005 0.000 ARG B 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 135 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.9328 (tp) cc_final: 0.9076 (tt) REVERT: B 91 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8861 (tt) REVERT: B 212 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8218 (t80) REVERT: E 92 TYR cc_start: 0.8343 (t80) cc_final: 0.8111 (t80) REVERT: E 100 MET cc_start: 0.8391 (ttt) cc_final: 0.8190 (ttt) REVERT: E 104 GLU cc_start: 0.9529 (tt0) cc_final: 0.9152 (pt0) REVERT: E 212 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8228 (t80) outliers start: 52 outliers final: 48 residues processed: 172 average time/residue: 0.1536 time to fit residues: 41.2145 Evaluate side-chains 185 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 95 HIS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 61 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 115 optimal weight: 0.0000 chunk 84 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 ASN F 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.094461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.071975 restraints weight = 30585.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.074224 restraints weight = 14261.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.075530 restraints weight = 8848.339| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10032 Z= 0.141 Angle : 0.602 12.143 13590 Z= 0.281 Chirality : 0.037 0.151 1542 Planarity : 0.003 0.027 1644 Dihedral : 5.473 59.922 1302 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.53 % Favored : 97.96 % Rotamer: Outliers : 4.84 % Allowed : 24.39 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.46 (0.26), residues: 1176 helix: 2.68 (0.18), residues: 804 sheet: 2.20 (0.78), residues: 60 loop : -1.49 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 78 HIS 0.002 0.001 HIS F 74 PHE 0.007 0.001 PHE D 70 TYR 0.022 0.001 TYR B 92 ARG 0.005 0.000 ARG B 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2640.79 seconds wall clock time: 47 minutes 26.31 seconds (2846.31 seconds total)