Starting phenix.real_space_refine on Sun Jul 27 20:34:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xqh_33396/07_2025/7xqh_33396.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xqh_33396/07_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_33396/07_2025/7xqh_33396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xqh_33396/07_2025/7xqh_33396.map" model { file = "/net/cci-nas-00/data/ceres_data/7xqh_33396/07_2025/7xqh_33396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xqh_33396/07_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-5711/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: 3.18, per 1000 atoms: 0.33 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: 2.06 Conformation dependent library (CDL) restraints added in 991.9 milliseconds 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: 1.12 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: 2.70 Time building geometry restraints manager: 2.47 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: 0.08 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: 0.790 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 20.720 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.080 ------------------------------------------------------------------------------- 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 10050 Z= 0.235 Angle : 0.782 7.929 13626 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 Details of bonding type rmsd hydrogen bonds : bond 0.13365 ( 612) hydrogen bonds : angle 5.37252 ( 1818) SS BOND : bond 0.00166 ( 18) SS BOND : angle 0.85593 ( 36) covalent geometry : bond 0.00479 (10032) covalent geometry : angle 0.78132 (13590) *********************** 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 : 1.237 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: 0.1881 time to fit residues: 65.2427 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 : 1.095 ------------------------------------------------------------------------------- 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 10050 Z= 0.146 Angle : 0.643 9.289 13626 Z= 0.323 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 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 612) hydrogen bonds : angle 3.74652 ( 1818) SS BOND : bond 0.00611 ( 18) SS BOND : angle 2.57082 ( 36) covalent geometry : bond 0.00340 (10032) covalent geometry : angle 0.63021 (13590) *********************** 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 : 1.081 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: 0.1847 time to fit residues: 56.4129 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 : 1.146 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.6766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 224 ASN D 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.095558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.072589 restraints weight = 31005.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.074947 restraints weight = 14037.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.076317 restraints weight = 8602.172| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10050 Z= 0.119 Angle : 0.659 10.620 13626 Z= 0.319 Chirality : 0.039 0.208 1542 Planarity : 0.003 0.025 1644 Dihedral : 6.693 59.969 1320 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.06 % Favored : 96.43 % Rotamer: Outliers : 5.87 % Allowed : 18.44 % 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: 1.24 (0.25), residues: 1176 helix: 1.39 (0.18), residues: 816 sheet: 3.72 (0.72), residues: 60 loop : -1.38 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 4 HIS 0.003 0.001 HIS B 74 PHE 0.007 0.001 PHE B 233 TYR 0.014 0.001 TYR A 17 ARG 0.001 0.000 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.03468 ( 612) hydrogen bonds : angle 3.64855 ( 1818) SS BOND : bond 0.00742 ( 18) SS BOND : angle 2.56373 ( 36) covalent geometry : bond 0.00270 (10032) covalent geometry : angle 0.64643 (13590) *********************** 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 233 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 170 time to evaluate : 1.174 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: 0.7448 (OUTLIER) cc_final: 0.6800 (m-80) REVERT: A 92 TYR cc_start: 0.8645 (t80) cc_final: 0.8099 (t80) REVERT: A 100 MET cc_start: 0.8418 (ttt) cc_final: 0.8007 (ttt) REVERT: A 104 GLU cc_start: 0.9336 (tt0) cc_final: 0.9054 (pt0) REVERT: A 223 LEU cc_start: 0.9387 (tp) cc_final: 0.9071 (tt) REVERT: B 91 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8875 (tt) REVERT: C 223 LEU cc_start: 0.9471 (tp) cc_final: 0.9211 (tt) REVERT: D 92 TYR cc_start: 0.8554 (t80) cc_final: 0.7933 (t80) REVERT: D 100 MET cc_start: 0.8381 (ttt) cc_final: 0.7999 (ttt) REVERT: D 104 GLU cc_start: 0.9361 (tt0) cc_final: 0.9073 (pt0) REVERT: D 223 LEU cc_start: 0.9409 (tp) cc_final: 0.9104 (tt) REVERT: E 100 MET cc_start: 0.8362 (ttt) cc_final: 0.8002 (ttp) REVERT: E 104 GLU cc_start: 0.9478 (tt0) cc_final: 0.9224 (pt0) REVERT: E 223 LEU cc_start: 0.9532 (tp) cc_final: 0.9286 (tt) REVERT: F 100 MET cc_start: 0.8371 (ttt) cc_final: 0.8038 (ttt) REVERT: F 104 GLU cc_start: 0.9358 (tt0) cc_final: 0.9094 (pt0) REVERT: F 223 LEU cc_start: 0.9472 (tp) cc_final: 0.9207 (tt) outliers start: 63 outliers final: 44 residues processed: 204 average time/residue: 0.1832 time to fit residues: 54.2618 Evaluate side-chains 184 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN C 49 GLN D 49 GLN D 224 ASN F 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.094113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.070950 restraints weight = 32422.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.073233 restraints weight = 15037.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.074614 restraints weight = 9346.653| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10050 Z= 0.141 Angle : 0.632 10.480 13626 Z= 0.311 Chirality : 0.039 0.191 1542 Planarity : 0.003 0.024 1644 Dihedral : 5.862 59.967 1302 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.81 % Favored : 96.68 % Rotamer: Outliers : 5.68 % Allowed : 20.67 % 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: 1.81 (0.26), residues: 1176 helix: 1.86 (0.19), residues: 816 sheet: 3.57 (0.76), residues: 60 loop : -1.22 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 4 HIS 0.003 0.001 HIS A 74 PHE 0.007 0.001 PHE F 209 TYR 0.013 0.001 TYR C 66 ARG 0.002 0.000 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 612) hydrogen bonds : angle 3.61175 ( 1818) SS BOND : bond 0.00619 ( 18) SS BOND : angle 2.15303 ( 36) covalent geometry : bond 0.00323 (10032) covalent geometry : angle 0.62307 (13590) *********************** 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 190 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 129 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.9376 (tp) cc_final: 0.9162 (tt) REVERT: B 91 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8883 (tt) REVERT: B 212 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8238 (t80) REVERT: E 100 MET cc_start: 0.8366 (ttt) cc_final: 0.8091 (ttt) REVERT: E 104 GLU cc_start: 0.9472 (tt0) cc_final: 0.9242 (pt0) outliers start: 61 outliers final: 53 residues processed: 164 average time/residue: 0.1795 time to fit residues: 43.2258 Evaluate side-chains 174 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 119 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 89 THR 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 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 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 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 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 106 LEU 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 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 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: 6.9990 chunk 84 optimal weight: 4.9990 chunk 104 optimal weight: 0.0670 chunk 70 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN D 224 ASN F 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.094290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.071276 restraints weight = 32043.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.073531 restraints weight = 14946.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.074994 restraints weight = 9311.080| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10050 Z= 0.127 Angle : 0.617 11.249 13626 Z= 0.300 Chirality : 0.038 0.150 1542 Planarity : 0.003 0.025 1644 Dihedral : 5.719 59.796 1302 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.06 % Favored : 96.43 % Rotamer: Outliers : 6.42 % Allowed : 20.39 % Favored : 73.18 % 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: 1.97 (0.26), residues: 1176 helix: 1.99 (0.19), residues: 822 sheet: 2.97 (0.77), residues: 60 loop : -1.08 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 78 HIS 0.003 0.001 HIS B 74 PHE 0.007 0.001 PHE C 52 TYR 0.008 0.001 TYR B 177 ARG 0.005 0.000 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 612) hydrogen bonds : angle 3.59434 ( 1818) SS BOND : bond 0.00538 ( 18) SS BOND : angle 1.78710 ( 36) covalent geometry : bond 0.00288 (10032) covalent geometry : angle 0.61060 (13590) *********************** 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 194 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 125 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.9343 (tp) cc_final: 0.9070 (tt) REVERT: B 91 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8867 (tt) REVERT: B 212 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8232 (t80) REVERT: C 202 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7539 (mtm180) REVERT: E 100 MET cc_start: 0.8369 (ttt) cc_final: 0.8068 (ttt) REVERT: E 104 GLU cc_start: 0.9468 (tt0) cc_final: 0.9230 (pt0) outliers start: 69 outliers final: 53 residues processed: 169 average time/residue: 0.1841 time to fit residues: 46.1113 Evaluate side-chains 179 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 123 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 212 PHE Chi-restraints excluded: chain A residue 219 VAL 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 106 LEU 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 91 LEU Chi-restraints excluded: chain C residue 202 ARG 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 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 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 91 LEU Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 92 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3706 r_free = 0.3706 target = 0.093851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.070498 restraints weight = 32435.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.072811 restraints weight = 15065.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.074177 restraints weight = 9390.854| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10050 Z= 0.129 Angle : 0.607 11.577 13626 Z= 0.293 Chirality : 0.038 0.149 1542 Planarity : 0.003 0.026 1644 Dihedral : 5.652 59.809 1302 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.72 % Favored : 96.77 % Rotamer: Outliers : 6.15 % Allowed : 20.39 % 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: 2.01 (0.26), residues: 1176 helix: 2.00 (0.19), residues: 840 sheet: 2.64 (0.78), residues: 60 loop : -1.12 (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 C 74 PHE 0.008 0.001 PHE C 52 TYR 0.013 0.001 TYR D 66 ARG 0.005 0.000 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 612) hydrogen bonds : angle 3.56391 ( 1818) SS BOND : bond 0.00518 ( 18) SS BOND : angle 1.67102 ( 36) covalent geometry : bond 0.00290 (10032) covalent geometry : angle 0.60206 (13590) *********************** 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 193 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 127 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 223 LEU cc_start: 0.9328 (tp) cc_final: 0.9059 (tt) REVERT: B 91 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8856 (tt) REVERT: B 212 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8203 (t80) REVERT: C 202 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7496 (mtm180) REVERT: E 100 MET cc_start: 0.8321 (ttt) cc_final: 0.8041 (ttt) REVERT: E 104 GLU cc_start: 0.9499 (tt0) cc_final: 0.9230 (pt0) outliers start: 66 outliers final: 56 residues processed: 170 average time/residue: 0.1606 time to fit residues: 41.3743 Evaluate side-chains 181 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 122 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 91 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 219 VAL 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 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 224 ASN 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 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 202 ARG 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 91 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 17 TYR Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 67 ASP 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 91 LEU Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 226 ILE 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: 4.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 0.4980 chunk 96 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.095805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.072551 restraints weight = 32541.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.074926 restraints weight = 15020.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.076226 restraints weight = 9298.403| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10050 Z= 0.101 Angle : 0.608 12.258 13626 Z= 0.286 Chirality : 0.037 0.158 1542 Planarity : 0.003 0.027 1644 Dihedral : 5.543 59.754 1302 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.62 % Favored : 97.87 % Rotamer: Outliers : 4.75 % Allowed : 22.07 % Favored : 73.18 % 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: 2.10 (0.26), residues: 1176 helix: 2.16 (0.19), residues: 834 sheet: 2.59 (0.80), residues: 60 loop : -1.35 (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 B 74 PHE 0.006 0.001 PHE E 169 TYR 0.012 0.001 TYR B 17 ARG 0.002 0.000 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.02911 ( 612) hydrogen bonds : angle 3.53708 ( 1818) SS BOND : bond 0.00536 ( 18) SS BOND : angle 1.51279 ( 36) covalent geometry : bond 0.00217 (10032) covalent geometry : angle 0.60383 (13590) *********************** 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 196 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8661 (t80) cc_final: 0.8099 (t80) REVERT: A 223 LEU cc_start: 0.9327 (tp) cc_final: 0.9068 (tt) REVERT: B 91 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8843 (tt) REVERT: B 212 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8174 (t80) REVERT: B 223 LEU cc_start: 0.9419 (tp) cc_final: 0.9127 (tt) REVERT: C 92 TYR cc_start: 0.8657 (t80) cc_final: 0.8079 (t80) REVERT: D 92 TYR cc_start: 0.8602 (t80) cc_final: 0.8021 (t80) REVERT: E 100 MET cc_start: 0.8344 (ttt) cc_final: 0.8084 (ttt) REVERT: E 104 GLU cc_start: 0.9528 (tt0) cc_final: 0.9260 (pt0) REVERT: E 212 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8205 (t80) REVERT: F 92 TYR cc_start: 0.8651 (t80) cc_final: 0.8066 (t80) outliers start: 51 outliers final: 39 residues processed: 176 average time/residue: 0.1540 time to fit residues: 42.7339 Evaluate side-chains 174 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 10 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 14 optimal weight: 0.0010 chunk 33 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.094245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.071132 restraints weight = 31000.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.073396 restraints weight = 14386.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.074883 restraints weight = 8944.062| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10050 Z= 0.114 Angle : 0.605 12.356 13626 Z= 0.285 Chirality : 0.038 0.147 1542 Planarity : 0.003 0.027 1644 Dihedral : 5.532 59.907 1302 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.96 % Favored : 97.53 % Rotamer: Outliers : 4.75 % Allowed : 23.18 % Favored : 72.07 % 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: 2.38 (0.26), residues: 1176 helix: 2.55 (0.19), residues: 804 sheet: 2.50 (0.81), residues: 60 loop : -1.39 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 78 HIS 0.002 0.001 HIS B 74 PHE 0.008 0.001 PHE C 52 TYR 0.014 0.001 TYR B 92 ARG 0.005 0.000 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.03039 ( 612) hydrogen bonds : angle 3.49697 ( 1818) SS BOND : bond 0.00506 ( 18) SS BOND : angle 1.49048 ( 36) covalent geometry : bond 0.00255 (10032) covalent geometry : angle 0.60140 (13590) *********************** 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 178 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 1.117 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 92 TYR cc_start: 0.8701 (t80) cc_final: 0.8201 (t80) REVERT: A 223 LEU cc_start: 0.9318 (tp) cc_final: 0.9049 (tt) REVERT: B 91 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8867 (tt) REVERT: B 92 TYR cc_start: 0.8340 (t80) cc_final: 0.7851 (t80) REVERT: B 212 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8189 (t80) REVERT: E 100 MET cc_start: 0.8393 (ttt) cc_final: 0.8093 (ttt) REVERT: E 104 GLU cc_start: 0.9482 (tt0) cc_final: 0.9190 (pt0) REVERT: E 212 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8211 (t80) outliers start: 51 outliers final: 42 residues processed: 162 average time/residue: 0.1580 time to fit residues: 40.0154 Evaluate side-chains 169 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 124 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 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 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 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: 20.0000 chunk 49 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 28 optimal weight: 0.0870 chunk 62 optimal weight: 0.7980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 = 0.3711 r_free = 0.3711 target = 0.094842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.072048 restraints weight = 30610.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.074350 restraints weight = 14224.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.075789 restraints weight = 8844.954| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10050 Z= 0.101 Angle : 0.607 12.155 13626 Z= 0.282 Chirality : 0.037 0.154 1542 Planarity : 0.003 0.028 1644 Dihedral : 5.466 59.981 1302 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.62 % Favored : 97.87 % Rotamer: Outliers : 4.38 % Allowed : 23.65 % Favored : 71.97 % 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: 2.43 (0.26), residues: 1176 helix: 2.63 (0.18), residues: 804 sheet: 2.48 (0.81), residues: 60 loop : -1.49 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 78 HIS 0.002 0.001 HIS D 74 PHE 0.006 0.001 PHE E 169 TYR 0.012 0.001 TYR B 92 ARG 0.004 0.000 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.02804 ( 612) hydrogen bonds : angle 3.46972 ( 1818) SS BOND : bond 0.00498 ( 18) SS BOND : angle 1.39606 ( 36) covalent geometry : bond 0.00220 (10032) covalent geometry : angle 0.60319 (13590) *********************** 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 184 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8667 (t80) cc_final: 0.8319 (t80) REVERT: A 212 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8483 (t80) REVERT: A 223 LEU cc_start: 0.9325 (tp) cc_final: 0.9067 (tt) REVERT: B 91 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8873 (tt) REVERT: B 92 TYR cc_start: 0.8350 (t80) cc_final: 0.7877 (t80) REVERT: B 212 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8197 (t80) REVERT: C 92 TYR cc_start: 0.8665 (t80) cc_final: 0.8351 (t80) REVERT: D 92 TYR cc_start: 0.8621 (t80) cc_final: 0.8327 (t80) REVERT: E 100 MET cc_start: 0.8369 (ttt) cc_final: 0.8098 (ttt) REVERT: E 104 GLU cc_start: 0.9505 (tt0) cc_final: 0.9235 (pt0) REVERT: E 212 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8181 (t80) REVERT: F 92 TYR cc_start: 0.8684 (t80) cc_final: 0.8367 (t80) outliers start: 47 outliers final: 41 residues processed: 167 average time/residue: 0.1519 time to fit residues: 39.7672 Evaluate side-chains 180 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 135 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 7 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 20 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.094093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.071535 restraints weight = 30685.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.073807 restraints weight = 14279.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.075246 restraints weight = 8847.290| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10050 Z= 0.107 Angle : 0.597 12.198 13626 Z= 0.277 Chirality : 0.038 0.149 1542 Planarity : 0.003 0.028 1644 Dihedral : 5.473 59.993 1302 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.96 % Favored : 97.53 % Rotamer: Outliers : 4.28 % Allowed : 23.93 % Favored : 71.79 % 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: 2.41 (0.26), residues: 1176 helix: 2.63 (0.18), residues: 804 sheet: 2.27 (0.79), residues: 60 loop : -1.49 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 78 HIS 0.002 0.001 HIS F 74 PHE 0.006 0.001 PHE C 52 TYR 0.013 0.001 TYR B 92 ARG 0.005 0.000 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.02847 ( 612) hydrogen bonds : angle 3.41691 ( 1818) SS BOND : bond 0.00495 ( 18) SS BOND : angle 1.40859 ( 36) covalent geometry : bond 0.00238 (10032) covalent geometry : angle 0.59363 (13590) ********************** 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 180 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 1.169 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: 0.8502 (t80) cc_final: 0.8020 (t80) REVERT: A 223 LEU cc_start: 0.9328 (tp) cc_final: 0.9069 (tt) REVERT: B 91 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8869 (tt) REVERT: B 92 TYR cc_start: 0.8405 (t80) cc_final: 0.7923 (t80) REVERT: B 212 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8212 (t80) REVERT: C 92 TYR cc_start: 0.8506 (t80) cc_final: 0.8033 (t80) REVERT: E 100 MET cc_start: 0.8411 (ttt) cc_final: 0.8114 (ttt) REVERT: E 104 GLU cc_start: 0.9492 (tt0) cc_final: 0.9189 (pt0) REVERT: E 212 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8215 (t80) REVERT: F 92 TYR cc_start: 0.8532 (t80) cc_final: 0.8061 (t80) outliers start: 46 outliers final: 41 residues processed: 165 average time/residue: 0.1436 time to fit residues: 37.1944 Evaluate side-chains 177 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 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 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 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 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: 6.9990 chunk 101 optimal weight: 20.0000 chunk 115 optimal weight: 0.7980 chunk 84 optimal weight: 0.1980 chunk 73 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 119 optimal weight: 0.0470 chunk 59 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 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 = 0.095436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.073067 restraints weight = 30584.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.075370 restraints weight = 14169.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.076830 restraints weight = 8748.885| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10050 Z= 0.099 Angle : 0.604 12.301 13626 Z= 0.279 Chirality : 0.037 0.153 1542 Planarity : 0.003 0.028 1644 Dihedral : 5.416 59.725 1302 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.45 % Favored : 98.04 % Rotamer: Outliers : 4.10 % Allowed : 24.77 % Favored : 71.14 % 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: 2.40 (0.26), residues: 1176 helix: 2.67 (0.18), residues: 804 sheet: 2.09 (0.76), residues: 60 loop : -1.60 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 78 HIS 0.003 0.001 HIS D 74 PHE 0.008 0.001 PHE D 70 TYR 0.011 0.001 TYR B 92 ARG 0.004 0.000 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.02641 ( 612) hydrogen bonds : angle 3.43970 ( 1818) SS BOND : bond 0.00496 ( 18) SS BOND : angle 1.31973 ( 36) covalent geometry : bond 0.00212 (10032) covalent geometry : angle 0.60079 (13590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2827.60 seconds wall clock time: 50 minutes 1.33 seconds (3001.33 seconds total)