Starting phenix.real_space_refine on Sun Dec 29 03:08:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xqh_33396/12_2024/7xqh_33396.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xqh_33396/12_2024/7xqh_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_33396/12_2024/7xqh_33396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xqh_33396/12_2024/7xqh_33396.map" model { file = "/net/cci-nas-00/data/ceres_data/7xqh_33396/12_2024/7xqh_33396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xqh_33396/12_2024/7xqh_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-5532/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: 3.88, per 1000 atoms: 0.40 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=3, 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 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: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 72.0% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 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: 2.66 Time building geometry restraints manager: 2.81 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: 4972 13.78 - 27.56: 514 27.56 - 41.33: 217 41.33 - 55.11: 90 55.11 - 68.89: 36 Dihedral angle restraints: 5829 sinusoidal: 2319 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 5826 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: 2.03 - 2.60: 68 2.60 - 3.18: 7753 3.18 - 3.75: 14912 3.75 - 4.33: 18426 4.33 - 4.90: 29706 Nonbonded interactions: 70865 Sorted by model distance: nonbonded pdb=" SG CYS B 61 " pdb=" SG CYS B 192 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS D 61 " pdb=" SG CYS D 192 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS F 61 " pdb=" SG CYS F 192 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 61 " pdb=" SG CYS C 192 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS E 61 " pdb=" SG CYS E 192 " model vdw 2.031 3.760 ... (remaining 70860 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.680 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 21.660 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.020 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10032 Z= 0.303 Angle : 0.781 7.929 13590 Z= 0.475 Chirality : 0.042 0.220 1542 Planarity : 0.006 0.047 1644 Dihedral : 15.527 68.889 3552 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.57 % Favored : 95.92 % Rotamer: Outliers : 2.23 % Allowed : 15.08 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.21), residues: 1176 helix: -1.31 (0.15), residues: 774 sheet: 2.72 (0.64), residues: 66 loop : -1.88 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 78 HIS 0.001 0.000 HIS D 95 PHE 0.011 0.001 PHE D 52 TYR 0.010 0.002 TYR F 92 ARG 0.003 0.001 ARG F 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 1.199 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: 0.1886 time to fit residues: 64.9819 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 : 1.139 ------------------------------------------------------------------------------- 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: 1.9990 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10032 Z= 0.201 Angle : 0.603 9.193 13590 Z= 0.305 Chirality : 0.038 0.201 1542 Planarity : 0.003 0.021 1644 Dihedral : 7.168 59.657 1338 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.15 % Favored : 96.34 % Rotamer: Outliers : 7.54 % Allowed : 16.57 % Favored : 75.88 % 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: 0.64 (0.24), residues: 1176 helix: 0.97 (0.17), residues: 780 sheet: 3.98 (0.68), residues: 60 loop : -1.51 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 4 HIS 0.003 0.001 HIS B 194 PHE 0.010 0.001 PHE A 52 TYR 0.010 0.001 TYR E 177 ARG 0.004 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 160 time to evaluate : 1.102 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: 0.8412 (p0) cc_final: 0.8159 (p0) REVERT: A 100 MET cc_start: 0.8349 (ttt) cc_final: 0.8017 (ttt) REVERT: A 104 GLU cc_start: 0.9359 (tt0) cc_final: 0.9070 (pt0) REVERT: A 190 ASP cc_start: 0.8863 (m-30) cc_final: 0.8658 (t0) REVERT: A 223 LEU cc_start: 0.9398 (tp) cc_final: 0.9070 (tt) REVERT: B 104 GLU cc_start: 0.8781 (pt0) cc_final: 0.8272 (mm-30) REVERT: C 47 ASP cc_start: 0.8457 (p0) cc_final: 0.8194 (p0) REVERT: C 100 MET cc_start: 0.8326 (ttt) cc_final: 0.7996 (ttt) REVERT: C 104 GLU cc_start: 0.9327 (tt0) cc_final: 0.9060 (pt0) REVERT: C 190 ASP cc_start: 0.8833 (m-30) cc_final: 0.8583 (t0) REVERT: D 47 ASP cc_start: 0.8413 (p0) cc_final: 0.8166 (p0) REVERT: D 100 MET cc_start: 0.8367 (ttt) cc_final: 0.8069 (ttt) REVERT: D 104 GLU cc_start: 0.9369 (tt0) cc_final: 0.9070 (pt0) REVERT: D 187 CYS cc_start: 0.8546 (t) cc_final: 0.7674 (t) REVERT: D 190 ASP cc_start: 0.8943 (m-30) cc_final: 0.8722 (t0) REVERT: E 47 ASP cc_start: 0.8364 (p0) cc_final: 0.8057 (p0) REVERT: E 100 MET cc_start: 0.8250 (ttt) cc_final: 0.7918 (ttp) REVERT: E 104 GLU cc_start: 0.9453 (tt0) cc_final: 0.9207 (pt0) REVERT: E 213 MET cc_start: 0.8929 (mmp) cc_final: 0.8520 (mmp) REVERT: F 47 ASP cc_start: 0.8456 (p0) cc_final: 0.8199 (p0) REVERT: F 100 MET cc_start: 0.8326 (ttt) cc_final: 0.7994 (ttt) REVERT: F 104 GLU cc_start: 0.9324 (tt0) cc_final: 0.9058 (pt0) REVERT: F 190 ASP cc_start: 0.8865 (m-30) cc_final: 0.8614 (t0) outliers start: 81 outliers final: 50 residues processed: 214 average time/residue: 0.1928 time to fit residues: 59.5631 Evaluate side-chains 188 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 138 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 B residue 32 PHE 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 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 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 212 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 37 LEU 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 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 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 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 212 PHE Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 224 ASN C 224 ASN D 224 ASN F 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10032 Z= 0.199 Angle : 0.609 10.120 13590 Z= 0.299 Chirality : 0.038 0.211 1542 Planarity : 0.003 0.024 1644 Dihedral : 5.807 59.875 1304 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.49 % Favored : 96.00 % Rotamer: Outliers : 6.98 % Allowed : 18.25 % Favored : 74.77 % 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: 1.32 (0.25), residues: 1176 helix: 1.44 (0.18), residues: 816 sheet: 3.85 (0.66), residues: 60 loop : -1.33 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 4 HIS 0.003 0.001 HIS B 74 PHE 0.008 0.001 PHE F 209 TYR 0.012 0.001 TYR B 177 ARG 0.002 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 150 time to evaluate : 1.179 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: 0.8362 (p0) cc_final: 0.8149 (p0) REVERT: B 104 GLU cc_start: 0.8781 (pt0) cc_final: 0.8356 (mm-30) REVERT: B 212 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8183 (t80) REVERT: C 47 ASP cc_start: 0.8452 (p0) cc_final: 0.8239 (p0) REVERT: C 190 ASP cc_start: 0.8953 (m-30) cc_final: 0.8664 (t0) REVERT: D 47 ASP cc_start: 0.8369 (p0) cc_final: 0.8140 (p0) REVERT: D 190 ASP cc_start: 0.9023 (m-30) cc_final: 0.8771 (t0) REVERT: E 47 ASP cc_start: 0.8401 (p0) cc_final: 0.8138 (p0) REVERT: E 100 MET cc_start: 0.8326 (ttt) cc_final: 0.8087 (ttt) REVERT: E 104 GLU cc_start: 0.9480 (tt0) cc_final: 0.9260 (pt0) REVERT: E 213 MET cc_start: 0.8960 (mmp) cc_final: 0.8478 (mmp) REVERT: E 223 LEU cc_start: 0.9488 (tp) cc_final: 0.9240 (tt) REVERT: F 47 ASP cc_start: 0.8433 (p0) cc_final: 0.8221 (p0) REVERT: F 190 ASP cc_start: 0.8959 (m-30) cc_final: 0.8662 (t0) outliers start: 75 outliers final: 58 residues processed: 198 average time/residue: 0.1980 time to fit residues: 56.0913 Evaluate side-chains 188 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 129 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 96 VAL Chi-restraints excluded: chain A residue 106 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 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 65 CYS 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 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 65 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 96 VAL Chi-restraints excluded: chain D residue 106 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 65 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 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 65 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 96 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 115 optimal weight: 0.0770 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- 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 C 224 ASN D 224 ASN F 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10032 Z= 0.154 Angle : 0.571 10.549 13590 Z= 0.276 Chirality : 0.037 0.150 1542 Planarity : 0.002 0.024 1644 Dihedral : 5.532 59.889 1302 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.47 % Favored : 97.02 % Rotamer: Outliers : 5.49 % Allowed : 20.39 % Favored : 74.12 % 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: 1.84 (0.25), residues: 1176 helix: 1.92 (0.19), residues: 816 sheet: 3.63 (0.66), residues: 60 loop : -1.32 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 4 HIS 0.003 0.001 HIS B 74 PHE 0.006 0.001 PHE F 209 TYR 0.011 0.001 TYR C 66 ARG 0.002 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 139 time to evaluate : 1.166 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: 0.8412 (p0) cc_final: 0.8189 (p0) REVERT: A 92 TYR cc_start: 0.8643 (t80) cc_final: 0.8087 (t80) REVERT: B 91 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8860 (tt) REVERT: B 104 GLU cc_start: 0.8844 (pt0) cc_final: 0.8458 (tp30) REVERT: B 212 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8231 (t80) REVERT: C 190 ASP cc_start: 0.8949 (m-30) cc_final: 0.8730 (t0) REVERT: D 47 ASP cc_start: 0.8320 (p0) cc_final: 0.8087 (p0) REVERT: E 100 MET cc_start: 0.8334 (ttt) cc_final: 0.8067 (ttt) REVERT: E 104 GLU cc_start: 0.9470 (tt0) cc_final: 0.9219 (pt0) REVERT: F 190 ASP cc_start: 0.8951 (m-30) cc_final: 0.8718 (t0) outliers start: 59 outliers final: 46 residues processed: 180 average time/residue: 0.2018 time to fit residues: 52.1472 Evaluate side-chains 186 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain 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 65 CYS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 65 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 212 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 65 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 37 LEU Chi-restraints excluded: chain F residue 65 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 104 optimal weight: 0.0370 chunk 29 optimal weight: 7.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10032 Z= 0.239 Angle : 0.616 11.517 13590 Z= 0.299 Chirality : 0.038 0.145 1542 Planarity : 0.003 0.028 1644 Dihedral : 5.564 59.643 1302 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.83 % Favored : 95.66 % Rotamer: Outliers : 6.89 % Allowed : 20.58 % Favored : 72.53 % 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: 2.17 (0.25), residues: 1176 helix: 2.27 (0.18), residues: 792 sheet: 3.56 (0.67), residues: 60 loop : -1.22 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.003 0.001 HIS A 74 PHE 0.010 0.001 PHE F 209 TYR 0.009 0.001 TYR C 92 ARG 0.002 0.000 ARG C 202 *********************** 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: 74 poor density : 120 time to evaluate : 1.083 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: 0.8421 (p0) cc_final: 0.8213 (p0) REVERT: B 212 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8252 (t80) REVERT: B 223 LEU cc_start: 0.9442 (tp) cc_final: 0.9168 (tt) REVERT: C 47 ASP cc_start: 0.8333 (p0) cc_final: 0.7607 (p0) REVERT: C 202 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7520 (mtm180) REVERT: D 47 ASP cc_start: 0.8360 (p0) cc_final: 0.8099 (p0) REVERT: E 100 MET cc_start: 0.8351 (ttt) cc_final: 0.8098 (ttt) REVERT: E 104 GLU cc_start: 0.9493 (tt0) cc_final: 0.9233 (pt0) REVERT: F 190 ASP cc_start: 0.8945 (m-30) cc_final: 0.8743 (t0) outliers start: 74 outliers final: 57 residues processed: 171 average time/residue: 0.1721 time to fit residues: 44.4373 Evaluate side-chains 173 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 114 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 96 VAL 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 219 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 96 VAL 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 65 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 96 VAL 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 65 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 106 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 65 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 96 VAL Chi-restraints excluded: chain F residue 106 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 39 optimal weight: 10.0000 chunk 104 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 28 optimal weight: 0.0980 chunk 116 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN C 224 ASN D 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10032 Z= 0.130 Angle : 0.583 11.332 13590 Z= 0.277 Chirality : 0.037 0.152 1542 Planarity : 0.003 0.030 1644 Dihedral : 5.414 59.441 1302 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.87 % Favored : 97.62 % Rotamer: Outliers : 4.75 % Allowed : 23.74 % Favored : 71.51 % 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: 2.04 (0.26), residues: 1176 helix: 2.11 (0.19), residues: 828 sheet: 3.56 (0.67), residues: 60 loop : -1.51 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 78 HIS 0.003 0.001 HIS A 74 PHE 0.006 0.001 PHE E 169 TYR 0.005 0.001 TYR D 177 ARG 0.003 0.000 ARG E 189 *********************** 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 206 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 155 time to evaluate : 1.125 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: 0.8415 (p0) cc_final: 0.8213 (p0) REVERT: A 92 TYR cc_start: 0.8612 (t80) cc_final: 0.7952 (t80) REVERT: B 91 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8851 (tt) REVERT: B 187 CYS cc_start: 0.7979 (t) cc_final: 0.7030 (t) REVERT: B 192 CYS cc_start: 0.8021 (m) cc_final: 0.7585 (m) REVERT: B 212 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8168 (t80) REVERT: C 92 TYR cc_start: 0.8619 (t80) cc_final: 0.8053 (t80) REVERT: C 103 GLU cc_start: 0.9495 (mm-30) cc_final: 0.9077 (mm-30) REVERT: D 92 TYR cc_start: 0.8574 (t80) cc_final: 0.7971 (t80) REVERT: E 100 MET cc_start: 0.8301 (ttt) cc_final: 0.8013 (ttt) REVERT: E 104 GLU cc_start: 0.9488 (tt0) cc_final: 0.9217 (pt0) REVERT: E 212 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8212 (t80) REVERT: F 92 TYR cc_start: 0.8662 (t80) cc_final: 0.8084 (t80) outliers start: 51 outliers final: 37 residues processed: 184 average time/residue: 0.1641 time to fit residues: 46.2022 Evaluate side-chains 175 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 212 PHE Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 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 65 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 65 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 65 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 17 TYR Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 212 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 84 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10032 Z= 0.138 Angle : 0.586 12.192 13590 Z= 0.276 Chirality : 0.036 0.151 1542 Planarity : 0.003 0.029 1644 Dihedral : 5.409 59.788 1302 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.87 % Favored : 97.62 % Rotamer: Outliers : 4.00 % Allowed : 24.77 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.26), residues: 1176 helix: 2.20 (0.19), residues: 828 sheet: 3.56 (0.67), residues: 60 loop : -1.72 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 78 HIS 0.003 0.001 HIS F 194 PHE 0.006 0.001 PHE E 169 TYR 0.013 0.001 TYR B 17 ARG 0.002 0.000 ARG F 189 *********************** 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 187 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 1.149 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: 0.8396 (p0) cc_final: 0.8184 (p0) REVERT: A 92 TYR cc_start: 0.8578 (t80) cc_final: 0.8234 (t80) REVERT: A 223 LEU cc_start: 0.9378 (tp) cc_final: 0.9095 (tt) REVERT: B 91 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8871 (tt) REVERT: B 187 CYS cc_start: 0.7947 (t) cc_final: 0.7037 (t) REVERT: B 192 CYS cc_start: 0.8086 (m) cc_final: 0.7644 (m) REVERT: B 212 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8176 (t80) REVERT: C 92 TYR cc_start: 0.8637 (t80) cc_final: 0.8314 (t80) REVERT: D 92 TYR cc_start: 0.8585 (t80) cc_final: 0.8240 (t80) REVERT: D 223 LEU cc_start: 0.9391 (tp) cc_final: 0.9110 (tt) REVERT: E 100 MET cc_start: 0.8297 (ttt) cc_final: 0.8038 (ttt) REVERT: E 104 GLU cc_start: 0.9508 (tt0) cc_final: 0.9243 (pt0) REVERT: E 212 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8177 (t80) REVERT: F 92 TYR cc_start: 0.8639 (t80) cc_final: 0.8306 (t80) outliers start: 43 outliers final: 35 residues processed: 171 average time/residue: 0.1510 time to fit residues: 40.8538 Evaluate side-chains 178 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 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 65 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 65 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL 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 65 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 17 TYR Chi-restraints excluded: chain F residue 32 PHE 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 71 optimal weight: 20.0000 chunk 46 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10032 Z= 0.140 Angle : 0.589 12.448 13590 Z= 0.275 Chirality : 0.036 0.151 1542 Planarity : 0.003 0.026 1644 Dihedral : 5.366 59.969 1302 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.79 % Favored : 97.70 % Rotamer: Outliers : 3.63 % Allowed : 26.35 % Favored : 70.02 % 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: 2.27 (0.26), residues: 1176 helix: 2.55 (0.19), residues: 798 sheet: 3.52 (0.67), residues: 60 loop : -1.86 (0.33), residues: 318 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 0.006 0.001 PHE E 169 TYR 0.012 0.001 TYR B 92 ARG 0.004 0.000 ARG B 189 *********************** 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 181 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 1.142 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: 0.8401 (p0) cc_final: 0.8194 (p0) REVERT: A 223 LEU cc_start: 0.9389 (tp) cc_final: 0.9051 (tt) REVERT: B 91 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8882 (tt) REVERT: B 92 TYR cc_start: 0.8270 (t80) cc_final: 0.7802 (t80) REVERT: B 187 CYS cc_start: 0.7962 (t) cc_final: 0.7091 (t) REVERT: B 192 CYS cc_start: 0.7979 (m) cc_final: 0.7544 (m) REVERT: B 212 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8216 (t80) REVERT: E 100 MET cc_start: 0.8314 (ttt) cc_final: 0.8033 (ttt) REVERT: E 104 GLU cc_start: 0.9496 (tt0) cc_final: 0.9192 (pt0) REVERT: E 212 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8173 (t80) outliers start: 39 outliers final: 33 residues processed: 166 average time/residue: 0.1739 time to fit residues: 45.3933 Evaluate side-chains 176 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 65 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 65 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL 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 65 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 17 TYR Chi-restraints excluded: chain F residue 32 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10032 Z= 0.174 Angle : 0.602 11.898 13590 Z= 0.284 Chirality : 0.036 0.145 1542 Planarity : 0.003 0.027 1644 Dihedral : 5.367 59.900 1302 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.51 % Allowed : 2.38 % Favored : 97.11 % Rotamer: Outliers : 4.38 % Allowed : 25.70 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.26), residues: 1176 helix: 2.61 (0.18), residues: 804 sheet: 3.49 (0.67), residues: 60 loop : -1.85 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 78 HIS 0.002 0.001 HIS D 74 PHE 0.006 0.001 PHE A 52 TYR 0.014 0.001 TYR B 92 ARG 0.002 0.000 ARG D 189 *********************** 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 182 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 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: A 47 ASP cc_start: 0.8415 (p0) cc_final: 0.8209 (p0) REVERT: B 29 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8803 (tt) REVERT: B 91 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8866 (tt) REVERT: B 187 CYS cc_start: 0.7875 (t) cc_final: 0.7040 (t) REVERT: B 192 CYS cc_start: 0.8046 (m) cc_final: 0.7606 (m) REVERT: B 212 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8234 (t80) REVERT: C 92 TYR cc_start: 0.8498 (t80) cc_final: 0.8170 (t80) REVERT: E 100 MET cc_start: 0.8302 (ttt) cc_final: 0.8037 (ttt) REVERT: E 104 GLU cc_start: 0.9520 (tt0) cc_final: 0.9224 (pt0) REVERT: E 212 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8191 (t80) REVERT: F 92 TYR cc_start: 0.8504 (t80) cc_final: 0.8121 (t80) outliers start: 47 outliers final: 38 residues processed: 167 average time/residue: 0.1469 time to fit residues: 38.9636 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 : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE 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 65 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 65 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 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 54 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN C 224 ASN D 224 ASN F 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10032 Z= 0.258 Angle : 0.639 11.685 13590 Z= 0.308 Chirality : 0.038 0.143 1542 Planarity : 0.003 0.031 1644 Dihedral : 5.480 59.120 1302 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.10 % Favored : 94.56 % Rotamer: Outliers : 4.84 % Allowed : 25.70 % Favored : 69.46 % 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: 2.31 (0.26), residues: 1176 helix: 2.59 (0.18), residues: 804 sheet: 3.34 (0.66), residues: 60 loop : -1.92 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 4 HIS 0.003 0.001 HIS A 194 PHE 0.010 0.001 PHE F 209 TYR 0.020 0.001 TYR B 92 ARG 0.003 0.000 ARG C 189 ********************** 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 174 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 122 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8835 (tt) REVERT: A 47 ASP cc_start: 0.8436 (p0) cc_final: 0.8230 (p0) REVERT: A 92 TYR cc_start: 0.8634 (t80) cc_final: 0.8243 (t80) REVERT: B 29 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8836 (tt) REVERT: B 47 ASP cc_start: 0.8217 (p0) cc_final: 0.8013 (p0) REVERT: B 212 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8285 (t80) REVERT: C 92 TYR cc_start: 0.8569 (t80) cc_final: 0.8212 (t80) REVERT: D 29 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8835 (tt) REVERT: E 100 MET cc_start: 0.8309 (ttt) cc_final: 0.7796 (ttp) REVERT: E 104 GLU cc_start: 0.9524 (tt0) cc_final: 0.9207 (pt0) REVERT: E 212 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8219 (t80) REVERT: F 92 TYR cc_start: 0.8584 (t80) cc_final: 0.8224 (t80) outliers start: 52 outliers final: 40 residues processed: 162 average time/residue: 0.1485 time to fit residues: 38.2358 Evaluate side-chains 165 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 65 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 65 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 17 TYR Chi-restraints excluded: chain F residue 32 PHE 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 87 optimal weight: 0.4980 chunk 14 optimal weight: 0.0070 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.093048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.070336 restraints weight = 30516.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.072375 restraints weight = 14288.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.073796 restraints weight = 9142.670| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10032 Z= 0.137 Angle : 0.600 12.148 13590 Z= 0.279 Chirality : 0.037 0.152 1542 Planarity : 0.003 0.027 1644 Dihedral : 5.336 58.955 1302 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.04 % Favored : 97.70 % Rotamer: Outliers : 3.82 % Allowed : 26.54 % Favored : 69.65 % 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: 2.47 (0.26), residues: 1176 helix: 2.72 (0.18), residues: 798 sheet: 3.46 (0.66), residues: 60 loop : -1.80 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 78 HIS 0.003 0.001 HIS A 74 PHE 0.006 0.001 PHE E 169 TYR 0.016 0.001 TYR D 92 ARG 0.003 0.000 ARG F 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1824.81 seconds wall clock time: 34 minutes 27.61 seconds (2067.61 seconds total)