Starting phenix.real_space_refine on Tue Jan 14 00:00:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wy0_37914/01_2025/8wy0_37914.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wy0_37914/01_2025/8wy0_37914.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/8wy0_37914/01_2025/8wy0_37914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wy0_37914/01_2025/8wy0_37914.map" model { file = "/net/cci-nas-00/data/ceres_data/8wy0_37914/01_2025/8wy0_37914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wy0_37914/01_2025/8wy0_37914.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= 0.002 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 37 5.16 5 C 3021 2.51 5 N 738 2.21 5 O 860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4656 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 234 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "b" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 243 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "d" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "e" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "f" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 933 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "g" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 890 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "m" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "n" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 302 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.20, per 1000 atoms: 0.69 Number of scatterers: 4656 At special positions: 0 Unit cell: (70.0245, 90.4932, 106.653, 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 37 16.00 O 860 8.00 N 738 7.00 C 3021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.18 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " 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: 1.04 Conformation dependent library (CDL) restraints added in 522.0 milliseconds 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1094 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 9 sheets defined 39.7% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'a' and resid 27 through 52 removed outlier: 3.961A pdb=" N TYR a 33 " --> pdb=" O PRO a 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 56 Processing helix chain 'd' and resid 102 through 126 removed outlier: 3.620A pdb=" N GLY d 106 " --> pdb=" O ALA d 102 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE d 108 " --> pdb=" O VAL d 104 " (cutoff:3.500A) Processing helix chain 'e' and resid 127 through 152 removed outlier: 3.754A pdb=" N THR e 132 " --> pdb=" O MET e 128 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE e 133 " --> pdb=" O SER e 129 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER e 152 " --> pdb=" O VAL e 148 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 108 removed outlier: 3.773A pdb=" N ASP f 107 " --> pdb=" O LYS f 104 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 154 removed outlier: 3.552A pdb=" N VAL f 130 " --> pdb=" O ASP f 126 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU f 147 " --> pdb=" O GLY f 143 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL f 148 " --> pdb=" O LEU f 144 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS f 153 " --> pdb=" O TYR f 149 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN f 154 " --> pdb=" O TYR f 150 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 80 removed outlier: 3.513A pdb=" N LYS g 79 " --> pdb=" O SER g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 135 Processing helix chain 'm' and resid 260 through 291 removed outlier: 3.528A pdb=" N LEU m 266 " --> pdb=" O ASN m 262 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU m 269 " --> pdb=" O SER m 265 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA m 280 " --> pdb=" O ALA m 276 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA m 291 " --> pdb=" O ALA m 287 " (cutoff:3.500A) Processing helix chain 'n' and resid 272 through 307 removed outlier: 3.927A pdb=" N TYR n 283 " --> pdb=" O THR n 279 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET n 284 " --> pdb=" O SER n 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 26 through 28 removed outlier: 7.349A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU d 60 " --> pdb=" O VAL d 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 42 through 46 removed outlier: 6.817A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR d 71 " --> pdb=" O VAL d 86 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL d 86 " --> pdb=" O TYR d 71 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR d 85 " --> pdb=" O TYR e 111 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N TYR e 113 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN d 87 " --> pdb=" O TYR e 113 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ARG e 115 " --> pdb=" O GLN d 87 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N HIS d 89 " --> pdb=" O ARG e 115 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE e 110 " --> pdb=" O CYS e 98 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N CYS e 98 " --> pdb=" O PHE e 110 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL e 97 " --> pdb=" O GLN e 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 97 Processing sheet with id=AA4, first strand: chain 'e' and resid 37 through 41 removed outlier: 3.506A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR e 44 " --> pdb=" O SER e 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 37 through 41 removed outlier: 3.985A pdb=" N LYS f 37 " --> pdb=" O THR f 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 113 through 114 removed outlier: 5.541A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'f' and resid 122 through 124 removed outlier: 3.632A pdb=" N ILE g 108 " --> pdb=" O MET f 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'g' and resid 31 through 33 removed outlier: 3.910A pdb=" N GLY g 75 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU g 44 " --> pdb=" O ASN g 73 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ASN g 73 " --> pdb=" O LEU g 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'g' and resid 55 through 57 removed outlier: 3.705A pdb=" N GLN g 86 " --> pdb=" O PHE g 56 " (cutoff:3.500A) 214 hydrogen bonds defined for protein. 615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1440 1.34 - 1.46: 1109 1.46 - 1.59: 2143 1.59 - 1.71: 0 1.71 - 1.83: 51 Bond restraints: 4743 Sorted by residual: bond pdb=" CA THR f 34 " pdb=" CB THR f 34 " ideal model delta sigma weight residual 1.528 1.553 -0.025 1.68e-02 3.54e+03 2.19e+00 bond pdb=" CA LEU g 110 " pdb=" CB LEU g 110 " ideal model delta sigma weight residual 1.528 1.564 -0.035 2.61e-02 1.47e+03 1.83e+00 bond pdb=" CA ASN e 121 " pdb=" CB ASN e 121 " ideal model delta sigma weight residual 1.533 1.548 -0.015 1.37e-02 5.33e+03 1.18e+00 bond pdb=" C3 CLR b 201 " pdb=" O1 CLR b 201 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" CB ASN d 36 " pdb=" CG ASN d 36 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.04e+00 ... (remaining 4738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 6234 1.75 - 3.51: 151 3.51 - 5.26: 33 5.26 - 7.01: 10 7.01 - 8.77: 2 Bond angle restraints: 6430 Sorted by residual: angle pdb=" CA LYS d 80 " pdb=" CB LYS d 80 " pdb=" CG LYS d 80 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CA TYR d 79 " pdb=" CB TYR d 79 " pdb=" CG TYR d 79 " ideal model delta sigma weight residual 113.90 119.74 -5.84 1.80e+00 3.09e-01 1.05e+01 angle pdb=" N PRO g 96 " pdb=" CA PRO g 96 " pdb=" C PRO g 96 " ideal model delta sigma weight residual 110.40 115.33 -4.93 1.61e+00 3.86e-01 9.38e+00 angle pdb=" CB LYS f 85 " pdb=" CG LYS f 85 " pdb=" CD LYS f 85 " ideal model delta sigma weight residual 111.30 118.18 -6.88 2.30e+00 1.89e-01 8.96e+00 angle pdb=" CB MET g 103 " pdb=" CG MET g 103 " pdb=" SD MET g 103 " ideal model delta sigma weight residual 112.70 120.71 -8.01 3.00e+00 1.11e-01 7.12e+00 ... (remaining 6425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 2413 17.75 - 35.50: 374 35.50 - 53.25: 95 53.25 - 70.99: 10 70.99 - 88.74: 5 Dihedral angle restraints: 2897 sinusoidal: 1190 harmonic: 1707 Sorted by residual: dihedral pdb=" CB CYS e 119 " pdb=" SG CYS e 119 " pdb=" SG CYS e 122 " pdb=" CB CYS e 122 " ideal model delta sinusoidal sigma weight residual 93.00 145.92 -52.92 1 1.00e+01 1.00e-02 3.81e+01 dihedral pdb=" CA ASN g 106 " pdb=" C ASN g 106 " pdb=" N CYS g 107 " pdb=" CA CYS g 107 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CB CYS d 37 " pdb=" SG CYS d 37 " pdb=" SG CYS d 73 " pdb=" CB CYS d 73 " ideal model delta sinusoidal sigma weight residual 93.00 53.21 39.79 1 1.00e+01 1.00e-02 2.22e+01 ... (remaining 2894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 603 0.047 - 0.095: 123 0.095 - 0.142: 32 0.142 - 0.189: 0 0.189 - 0.237: 1 Chirality restraints: 759 Sorted by residual: chirality pdb=" CB ILE f 133 " pdb=" CA ILE f 133 " pdb=" CG1 ILE f 133 " pdb=" CG2 ILE f 133 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA GLU f 91 " pdb=" N GLU f 91 " pdb=" C GLU f 91 " pdb=" CB GLU f 91 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA ILE d 24 " pdb=" N ILE d 24 " pdb=" C ILE d 24 " pdb=" CB ILE d 24 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 756 not shown) Planarity restraints: 786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN e 121 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C ASN e 121 " 0.046 2.00e-02 2.50e+03 pdb=" O ASN e 121 " -0.018 2.00e-02 2.50e+03 pdb=" N CYS e 122 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU g 97 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C LEU g 97 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU g 97 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN g 98 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS g 95 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO g 96 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO g 96 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO g 96 " -0.021 5.00e-02 4.00e+02 ... (remaining 783 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 152 2.69 - 3.25: 4671 3.25 - 3.80: 7081 3.80 - 4.35: 8584 4.35 - 4.90: 14176 Nonbonded interactions: 34664 Sorted by model distance: nonbonded pdb=" O ILE d 24 " pdb=" OH TYR e 95 " model vdw 2.142 3.040 nonbonded pdb=" OG SER f 88 " pdb=" OE1 GLU f 91 " model vdw 2.155 3.040 nonbonded pdb=" O ASN e 121 " pdb=" ND2 ASN e 121 " model vdw 2.166 3.120 nonbonded pdb=" OD1 ASP e 126 " pdb=" OG SER e 129 " model vdw 2.186 3.040 nonbonded pdb=" O GLN e 92 " pdb=" OH TYR e 96 " model vdw 2.204 3.040 ... (remaining 34659 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' and resid 27 through 54) selection = (chain 'b' and resid 27 through 54) } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 153)) selection = (chain 'f' and resid 33 through 153) } 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.350 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 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 : 0.003 0.035 4743 Z= 0.201 Angle : 0.710 8.769 6430 Z= 0.363 Chirality : 0.041 0.237 759 Planarity : 0.004 0.038 786 Dihedral : 17.421 88.742 1776 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 1.16 % Allowed : 36.87 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.34), residues: 569 helix: 1.39 (0.35), residues: 215 sheet: -2.08 (0.55), residues: 84 loop : -2.88 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP f 59 HIS 0.004 0.001 HIS g 29 PHE 0.012 0.001 PHE n 296 TYR 0.025 0.002 TYR f 99 ARG 0.005 0.001 ARG e 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 190 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 47 THR cc_start: 0.8423 (m) cc_final: 0.8167 (p) REVERT: b 52 ARG cc_start: 0.6619 (tpt170) cc_final: 0.6358 (ttm170) REVERT: d 27 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8242 (mt-10) REVERT: d 43 TRP cc_start: 0.7895 (t60) cc_final: 0.7634 (t60) REVERT: e 72 ASP cc_start: 0.7079 (m-30) cc_final: 0.6803 (m-30) REVERT: e 74 ASN cc_start: 0.8062 (m-40) cc_final: 0.7771 (m110) REVERT: f 37 LYS cc_start: 0.7000 (ttpp) cc_final: 0.6564 (tptp) REVERT: f 60 GLN cc_start: 0.7220 (pm20) cc_final: 0.6861 (mt0) REVERT: f 117 ARG cc_start: 0.8050 (ttm170) cc_final: 0.7824 (ttp-110) REVERT: f 123 MET cc_start: 0.6624 (ttt) cc_final: 0.6176 (ttm) REVERT: g 71 LYS cc_start: 0.6165 (mtmt) cc_final: 0.5918 (mttt) REVERT: m 288 LYS cc_start: 0.7961 (tptt) cc_final: 0.7590 (tmtt) REVERT: n 275 GLN cc_start: 0.8373 (tm-30) cc_final: 0.7928 (tm-30) outliers start: 6 outliers final: 3 residues processed: 193 average time/residue: 0.1746 time to fit residues: 41.9035 Evaluate side-chains 177 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 174 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 110 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 0.0670 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS f 61 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.157455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.129359 restraints weight = 7516.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.133412 restraints weight = 4148.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.136093 restraints weight = 2820.692| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4743 Z= 0.210 Angle : 0.672 7.502 6430 Z= 0.338 Chirality : 0.042 0.170 759 Planarity : 0.004 0.039 786 Dihedral : 5.382 49.213 701 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 7.34 % Allowed : 29.15 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.35), residues: 569 helix: 2.09 (0.35), residues: 218 sheet: -2.12 (0.52), residues: 93 loop : -2.73 (0.33), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP f 59 HIS 0.005 0.001 HIS f 81 PHE 0.015 0.002 PHE n 296 TYR 0.028 0.002 TYR f 99 ARG 0.003 0.001 ARG e 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 22 PHE cc_start: 0.6685 (m-80) cc_final: 0.6270 (m-80) REVERT: e 72 ASP cc_start: 0.7234 (m-30) cc_final: 0.6991 (m-30) REVERT: e 74 ASN cc_start: 0.7504 (m-40) cc_final: 0.7227 (m110) REVERT: f 79 GLU cc_start: 0.4066 (OUTLIER) cc_final: 0.3034 (mm-30) REVERT: f 106 GLU cc_start: 0.8953 (pm20) cc_final: 0.8584 (pm20) REVERT: m 288 LYS cc_start: 0.8753 (tptt) cc_final: 0.8520 (tmtt) outliers start: 38 outliers final: 24 residues processed: 190 average time/residue: 0.1705 time to fit residues: 40.2029 Evaluate side-chains 186 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 51 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.154810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127646 restraints weight = 7538.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.131364 restraints weight = 4178.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.133942 restraints weight = 2860.071| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4743 Z= 0.268 Angle : 0.695 7.947 6430 Z= 0.351 Chirality : 0.043 0.135 759 Planarity : 0.004 0.036 786 Dihedral : 5.442 45.101 699 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 8.30 % Allowed : 32.43 % Favored : 59.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.35), residues: 569 helix: 2.16 (0.34), residues: 219 sheet: -2.18 (0.53), residues: 93 loop : -2.79 (0.33), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP d 43 HIS 0.004 0.002 HIS f 81 PHE 0.013 0.002 PHE n 296 TYR 0.023 0.002 TYR e 150 ARG 0.004 0.001 ARG e 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 22 PHE cc_start: 0.6816 (m-80) cc_final: 0.6418 (m-80) REVERT: d 90 TYR cc_start: 0.7877 (m-80) cc_final: 0.7568 (m-80) REVERT: d 98 GLU cc_start: 0.7912 (tt0) cc_final: 0.7665 (tm-30) REVERT: e 72 ASP cc_start: 0.7445 (m-30) cc_final: 0.7148 (m-30) REVERT: f 106 GLU cc_start: 0.8912 (pm20) cc_final: 0.8703 (pm20) REVERT: m 288 LYS cc_start: 0.8753 (tptt) cc_final: 0.8504 (tmtt) outliers start: 43 outliers final: 33 residues processed: 196 average time/residue: 0.1689 time to fit residues: 41.2661 Evaluate side-chains 200 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 19 optimal weight: 0.0470 chunk 50 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.161469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.134481 restraints weight = 7375.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.138415 restraints weight = 3999.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.141073 restraints weight = 2682.154| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4743 Z= 0.181 Angle : 0.641 8.433 6430 Z= 0.321 Chirality : 0.041 0.133 759 Planarity : 0.003 0.033 786 Dihedral : 4.709 29.113 697 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 6.76 % Allowed : 32.63 % Favored : 60.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.36), residues: 569 helix: 2.39 (0.34), residues: 218 sheet: -1.84 (0.54), residues: 82 loop : -2.70 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP g 55 HIS 0.004 0.001 HIS f 81 PHE 0.011 0.001 PHE n 296 TYR 0.021 0.001 TYR e 150 ARG 0.004 0.001 ARG f 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 52 ARG cc_start: 0.7611 (tpt170) cc_final: 0.7361 (ttm170) REVERT: d 22 PHE cc_start: 0.6563 (m-80) cc_final: 0.6263 (m-80) REVERT: d 90 TYR cc_start: 0.7756 (m-80) cc_final: 0.7495 (m-80) REVERT: e 72 ASP cc_start: 0.7311 (m-30) cc_final: 0.6993 (m-30) REVERT: f 117 ARG cc_start: 0.8250 (ttp-110) cc_final: 0.8030 (ttm-80) REVERT: m 289 LEU cc_start: 0.8982 (tp) cc_final: 0.8530 (tp) outliers start: 35 outliers final: 24 residues processed: 183 average time/residue: 0.1599 time to fit residues: 36.9953 Evaluate side-chains 182 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain m residue 266 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.158691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.131211 restraints weight = 7486.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.135206 restraints weight = 4099.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137685 restraints weight = 2758.562| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4743 Z= 0.221 Angle : 0.698 7.856 6430 Z= 0.342 Chirality : 0.042 0.153 759 Planarity : 0.003 0.033 786 Dihedral : 4.861 27.080 697 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 7.53 % Allowed : 32.05 % Favored : 60.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.35), residues: 569 helix: 2.45 (0.34), residues: 217 sheet: -1.93 (0.54), residues: 91 loop : -2.73 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP e 59 HIS 0.005 0.001 HIS f 81 PHE 0.010 0.001 PHE n 296 TYR 0.028 0.002 TYR b 33 ARG 0.003 0.001 ARG e 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 90 TYR cc_start: 0.7877 (m-80) cc_final: 0.7545 (m-80) REVERT: e 65 ASN cc_start: 0.8824 (t0) cc_final: 0.8592 (t0) REVERT: e 72 ASP cc_start: 0.7467 (m-30) cc_final: 0.7108 (m-30) REVERT: f 117 ARG cc_start: 0.8137 (ttp-110) cc_final: 0.7930 (ttm-80) REVERT: m 289 LEU cc_start: 0.9012 (tp) cc_final: 0.8556 (tp) outliers start: 39 outliers final: 34 residues processed: 188 average time/residue: 0.1601 time to fit residues: 38.1756 Evaluate side-chains 193 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 41 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.156235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.127899 restraints weight = 7674.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.131798 restraints weight = 4336.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.134420 restraints weight = 3017.894| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4743 Z= 0.268 Angle : 0.733 8.270 6430 Z= 0.359 Chirality : 0.043 0.136 759 Planarity : 0.004 0.035 786 Dihedral : 4.970 23.280 697 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 9.27 % Allowed : 31.85 % Favored : 58.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.35), residues: 569 helix: 2.21 (0.34), residues: 218 sheet: -2.00 (0.53), residues: 87 loop : -2.66 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP g 55 HIS 0.005 0.001 HIS f 81 PHE 0.029 0.002 PHE g 56 TYR 0.016 0.002 TYR e 150 ARG 0.004 0.001 ARG e 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: a 32 CYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7920 (t) REVERT: d 90 TYR cc_start: 0.7901 (m-80) cc_final: 0.7565 (m-80) REVERT: e 72 ASP cc_start: 0.7612 (m-30) cc_final: 0.7249 (m-30) REVERT: e 91 GLU cc_start: 0.8352 (tp30) cc_final: 0.8139 (tp30) REVERT: e 109 ASN cc_start: 0.7893 (m-40) cc_final: 0.7625 (p0) REVERT: f 106 GLU cc_start: 0.9064 (pm20) cc_final: 0.8703 (pm20) REVERT: m 289 LEU cc_start: 0.9022 (tp) cc_final: 0.8814 (tt) outliers start: 48 outliers final: 40 residues processed: 189 average time/residue: 0.1613 time to fit residues: 38.7324 Evaluate side-chains 204 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 41 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 92 GLN Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 16 optimal weight: 4.9990 chunk 38 optimal weight: 0.0570 chunk 19 optimal weight: 0.0980 chunk 44 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.160526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.132024 restraints weight = 7553.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.136290 restraints weight = 4088.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.139189 restraints weight = 2762.806| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4743 Z= 0.188 Angle : 0.723 8.401 6430 Z= 0.351 Chirality : 0.043 0.167 759 Planarity : 0.003 0.031 786 Dihedral : 4.809 29.526 697 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 6.18 % Allowed : 36.49 % Favored : 57.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.36), residues: 569 helix: 2.37 (0.34), residues: 216 sheet: -2.06 (0.50), residues: 97 loop : -2.43 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP d 43 HIS 0.004 0.001 HIS f 81 PHE 0.022 0.002 PHE g 56 TYR 0.027 0.001 TYR f 99 ARG 0.003 0.000 ARG e 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: a 32 CYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7484 (t) REVERT: d 22 PHE cc_start: 0.6517 (m-80) cc_final: 0.5960 (m-80) REVERT: d 90 TYR cc_start: 0.7843 (m-80) cc_final: 0.7512 (m-80) REVERT: e 72 ASP cc_start: 0.7488 (m-30) cc_final: 0.7148 (m-30) REVERT: e 109 ASN cc_start: 0.7890 (m-40) cc_final: 0.7539 (p0) REVERT: f 106 GLU cc_start: 0.9035 (pm20) cc_final: 0.8728 (pm20) REVERT: g 85 TYR cc_start: 0.8302 (m-80) cc_final: 0.7898 (m-80) outliers start: 32 outliers final: 26 residues processed: 184 average time/residue: 0.1555 time to fit residues: 36.3662 Evaluate side-chains 188 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 92 GLN Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.160074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.131597 restraints weight = 7490.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.135938 restraints weight = 4025.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.138828 restraints weight = 2693.883| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4743 Z= 0.198 Angle : 0.744 9.090 6430 Z= 0.356 Chirality : 0.043 0.139 759 Planarity : 0.003 0.032 786 Dihedral : 4.869 27.066 697 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 6.56 % Allowed : 37.07 % Favored : 56.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.36), residues: 569 helix: 2.47 (0.34), residues: 215 sheet: -1.89 (0.50), residues: 102 loop : -2.44 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP d 43 HIS 0.005 0.001 HIS f 81 PHE 0.020 0.002 PHE g 56 TYR 0.017 0.001 TYR n 283 ARG 0.015 0.001 ARG b 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 32 CYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7555 (t) REVERT: b 52 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7039 (ttm170) REVERT: d 90 TYR cc_start: 0.7830 (m-80) cc_final: 0.7487 (m-80) REVERT: e 72 ASP cc_start: 0.7471 (m-30) cc_final: 0.7134 (m-30) REVERT: e 109 ASN cc_start: 0.7860 (m-40) cc_final: 0.7560 (p0) REVERT: f 106 GLU cc_start: 0.8998 (pm20) cc_final: 0.8702 (pm20) REVERT: g 85 TYR cc_start: 0.8348 (m-80) cc_final: 0.7914 (m-80) outliers start: 34 outliers final: 30 residues processed: 185 average time/residue: 0.1542 time to fit residues: 36.0975 Evaluate side-chains 195 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 32 CYS Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 86 GLU Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 92 GLN Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain m residue 284 LEU Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 0.0980 chunk 6 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.153027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.124269 restraints weight = 7658.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.128387 restraints weight = 4168.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.131243 restraints weight = 2851.855| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4743 Z= 0.323 Angle : 0.837 8.813 6430 Z= 0.407 Chirality : 0.045 0.146 759 Planarity : 0.004 0.036 786 Dihedral : 5.397 27.921 697 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 7.92 % Allowed : 35.91 % Favored : 56.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.35), residues: 569 helix: 2.06 (0.34), residues: 215 sheet: -1.93 (0.51), residues: 92 loop : -2.61 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP d 43 HIS 0.005 0.002 HIS f 81 PHE 0.020 0.002 PHE n 296 TYR 0.030 0.002 TYR n 283 ARG 0.011 0.001 ARG b 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 52 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7051 (ttm170) REVERT: d 22 PHE cc_start: 0.6221 (m-80) cc_final: 0.5600 (m-80) REVERT: d 90 TYR cc_start: 0.7918 (m-80) cc_final: 0.7554 (m-80) REVERT: e 72 ASP cc_start: 0.7558 (m-30) cc_final: 0.7236 (m-30) REVERT: e 109 ASN cc_start: 0.8151 (m-40) cc_final: 0.7865 (p0) REVERT: f 106 GLU cc_start: 0.8998 (pm20) cc_final: 0.8718 (pm20) outliers start: 41 outliers final: 35 residues processed: 190 average time/residue: 0.1617 time to fit residues: 38.7651 Evaluate side-chains 202 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 32 CYS Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 86 GLU Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 92 GLN Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain m residue 284 LEU Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.158367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.130100 restraints weight = 7454.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.134369 restraints weight = 3979.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.137227 restraints weight = 2681.752| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4743 Z= 0.220 Angle : 0.808 10.063 6430 Z= 0.390 Chirality : 0.043 0.153 759 Planarity : 0.003 0.032 786 Dihedral : 5.128 25.581 697 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 6.76 % Allowed : 37.64 % Favored : 55.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.35), residues: 569 helix: 2.26 (0.34), residues: 215 sheet: -1.91 (0.51), residues: 97 loop : -2.50 (0.35), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP d 43 HIS 0.004 0.001 HIS f 81 PHE 0.019 0.001 PHE g 56 TYR 0.022 0.001 TYR n 283 ARG 0.010 0.001 ARG b 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 32 CYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7858 (t) REVERT: d 90 TYR cc_start: 0.7814 (m-80) cc_final: 0.7489 (m-80) REVERT: e 109 ASN cc_start: 0.8159 (m-40) cc_final: 0.7800 (p0) REVERT: e 117 ARG cc_start: 0.7694 (ttt-90) cc_final: 0.7451 (ttt-90) REVERT: f 106 GLU cc_start: 0.8888 (pm20) cc_final: 0.8616 (pm20) REVERT: f 111 TYR cc_start: 0.7489 (m-80) cc_final: 0.6947 (m-80) REVERT: m 269 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8278 (tp) outliers start: 35 outliers final: 28 residues processed: 181 average time/residue: 0.1603 time to fit residues: 36.8035 Evaluate side-chains 194 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 32 CYS Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 86 GLU Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain m residue 284 LEU Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 53 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 30 optimal weight: 0.0070 chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 24 optimal weight: 0.0980 chunk 47 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.160948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.132973 restraints weight = 7567.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.137014 restraints weight = 4226.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.139753 restraints weight = 2918.204| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4743 Z= 0.205 Angle : 0.794 9.573 6430 Z= 0.383 Chirality : 0.042 0.146 759 Planarity : 0.003 0.031 786 Dihedral : 4.936 24.818 697 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 5.98 % Allowed : 38.80 % Favored : 55.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.35), residues: 569 helix: 2.32 (0.34), residues: 215 sheet: -1.69 (0.52), residues: 97 loop : -2.52 (0.34), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP d 43 HIS 0.005 0.002 HIS f 81 PHE 0.018 0.002 PHE g 56 TYR 0.018 0.001 TYR n 295 ARG 0.014 0.001 ARG b 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1782.71 seconds wall clock time: 32 minutes 42.42 seconds (1962.42 seconds total)