Starting phenix.real_space_refine on Fri Aug 22 15:04:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wy0_37914/08_2025/8wy0_37914.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wy0_37914/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wy0_37914/08_2025/8wy0_37914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wy0_37914/08_2025/8wy0_37914.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wy0_37914/08_2025/8wy0_37914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wy0_37914/08_2025/8wy0_37914.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.19, per 1000 atoms: 0.26 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: 0.36 Conformation dependent library (CDL) restraints added in 172.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.08 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: 0.60 Time building geometry restraints manager: 0.49 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: 0.520 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.670 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.480 ------------------------------------------------------------------------------- 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 : 0.004 0.152 4752 Z= 0.182 Angle : 0.776 21.458 6448 Z= 0.392 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 : 14.40 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG e 101 TYR 0.025 0.002 TYR f 99 PHE 0.012 0.001 PHE n 296 TRP 0.012 0.001 TRP f 59 HIS 0.004 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 4743) covalent geometry : angle 0.70961 ( 6430) SS BOND : bond 0.05061 ( 9) SS BOND : angle 5.97840 ( 18) hydrogen bonds : bond 0.20116 ( 214) hydrogen bonds : angle 6.16074 ( 615) *********************** 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 : 0.166 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: 0.0629 time to fit residues: 15.3190 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 : 0.109 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.157460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.129419 restraints weight = 7633.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133418 restraints weight = 4169.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136124 restraints weight = 2845.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.137912 restraints weight = 2194.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.139017 restraints weight = 1835.743| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4752 Z= 0.143 Angle : 0.678 7.744 6448 Z= 0.341 Chirality : 0.043 0.170 759 Planarity : 0.004 0.039 786 Dihedral : 5.380 49.230 701 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 7.53 % Allowed : 28.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.35), residues: 569 helix: 2.11 (0.35), residues: 218 sheet: -2.13 (0.52), residues: 93 loop : -2.73 (0.33), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG e 117 TYR 0.029 0.002 TYR f 99 PHE 0.014 0.002 PHE n 296 TRP 0.018 0.002 TRP f 59 HIS 0.005 0.001 HIS f 81 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4743) covalent geometry : angle 0.67208 ( 6430) SS BOND : bond 0.00576 ( 9) SS BOND : angle 1.76355 ( 18) hydrogen bonds : bond 0.04523 ( 214) hydrogen bonds : angle 4.16178 ( 615) *********************** 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 217 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 22 PHE cc_start: 0.6707 (m-80) cc_final: 0.6074 (m-80) REVERT: e 72 ASP cc_start: 0.7266 (m-30) cc_final: 0.7020 (m-30) REVERT: e 74 ASN cc_start: 0.7486 (m-40) cc_final: 0.7208 (m110) REVERT: e 80 ASP cc_start: 0.6983 (m-30) cc_final: 0.6575 (m-30) REVERT: f 79 GLU cc_start: 0.4093 (OUTLIER) cc_final: 0.3061 (mm-30) REVERT: f 92 GLN cc_start: 0.7638 (mt0) cc_final: 0.7419 (mt0) REVERT: f 106 GLU cc_start: 0.8946 (pm20) cc_final: 0.8574 (pm20) REVERT: m 288 LYS cc_start: 0.8740 (tptt) cc_final: 0.8513 (tmtt) outliers start: 39 outliers final: 25 residues processed: 193 average time/residue: 0.0659 time to fit residues: 15.9295 Evaluate side-chains 190 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 g residue 128 VAL 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 7 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.150918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.122442 restraints weight = 7694.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.126473 restraints weight = 4156.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.129206 restraints weight = 2820.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.130849 restraints weight = 2188.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.132216 restraints weight = 1855.102| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4752 Z= 0.231 Angle : 0.758 7.798 6448 Z= 0.380 Chirality : 0.045 0.175 759 Planarity : 0.004 0.037 786 Dihedral : 5.610 44.151 699 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 8.69 % Allowed : 32.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.35), residues: 569 helix: 2.00 (0.34), residues: 218 sheet: -2.25 (0.53), residues: 93 loop : -2.79 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG d 68 TYR 0.022 0.002 TYR e 150 PHE 0.014 0.002 PHE n 296 TRP 0.015 0.002 TRP d 43 HIS 0.005 0.002 HIS f 81 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 4743) covalent geometry : angle 0.75026 ( 6430) SS BOND : bond 0.01088 ( 9) SS BOND : angle 2.15364 ( 18) hydrogen bonds : bond 0.05075 ( 214) hydrogen bonds : angle 4.30647 ( 615) *********************** 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 223 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 22 PHE cc_start: 0.6892 (m-80) cc_final: 0.6361 (m-80) REVERT: d 90 TYR cc_start: 0.8021 (m-80) cc_final: 0.7709 (m-80) REVERT: d 98 GLU cc_start: 0.7999 (tt0) cc_final: 0.7699 (tm-30) REVERT: e 72 ASP cc_start: 0.7687 (m-30) cc_final: 0.7325 (m-30) REVERT: e 74 ASN cc_start: 0.7663 (m-40) cc_final: 0.7406 (m110) REVERT: e 79 GLU cc_start: 0.7022 (tp30) cc_final: 0.6761 (tp30) REVERT: e 80 ASP cc_start: 0.7093 (m-30) cc_final: 0.6563 (m-30) REVERT: f 106 GLU cc_start: 0.8855 (pm20) cc_final: 0.8637 (pm20) REVERT: f 117 ARG cc_start: 0.8199 (ttm110) cc_final: 0.7969 (ttp-170) REVERT: g 28 ASN cc_start: 0.8217 (t0) cc_final: 0.7979 (t0) REVERT: g 120 PHE cc_start: 0.7649 (t80) cc_final: 0.7304 (m-80) REVERT: m 288 LYS cc_start: 0.8754 (tptt) cc_final: 0.8500 (tmtt) outliers start: 45 outliers final: 34 residues processed: 196 average time/residue: 0.0659 time to fit residues: 16.4879 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 : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 47 THR 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 b residue 49 LEU 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 84 LEU 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 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 298 ILE 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 37 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.0770 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- 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 = 0.154466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.125881 restraints weight = 7638.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129975 restraints weight = 4120.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.132759 restraints weight = 2796.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.134653 restraints weight = 2156.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.135901 restraints weight = 1792.693| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4752 Z= 0.157 Angle : 0.671 9.011 6448 Z= 0.336 Chirality : 0.042 0.129 759 Planarity : 0.003 0.038 786 Dihedral : 4.972 22.617 697 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 8.88 % Allowed : 31.47 % Favored : 59.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.35), residues: 569 helix: 2.19 (0.34), residues: 218 sheet: -2.09 (0.54), residues: 84 loop : -2.74 (0.33), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG e 117 TYR 0.016 0.002 TYR g 85 PHE 0.012 0.001 PHE n 296 TRP 0.018 0.002 TRP d 43 HIS 0.004 0.001 HIS f 81 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 4743) covalent geometry : angle 0.66687 ( 6430) SS BOND : bond 0.00803 ( 9) SS BOND : angle 1.50184 ( 18) hydrogen bonds : bond 0.04380 ( 214) hydrogen bonds : angle 3.96491 ( 615) *********************** 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 217 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 22 PHE cc_start: 0.6557 (m-80) cc_final: 0.6257 (m-80) REVERT: d 90 TYR cc_start: 0.7919 (m-80) cc_final: 0.7625 (m-80) REVERT: e 72 ASP cc_start: 0.7488 (m-30) cc_final: 0.7158 (m-30) REVERT: e 74 ASN cc_start: 0.7588 (m-40) cc_final: 0.7346 (m-40) REVERT: e 79 GLU cc_start: 0.7032 (tp30) cc_final: 0.6768 (tp30) REVERT: e 80 ASP cc_start: 0.7140 (m-30) cc_final: 0.6513 (m-30) REVERT: e 91 GLU cc_start: 0.8401 (tp30) cc_final: 0.8171 (tp30) REVERT: f 81 HIS cc_start: 0.6474 (OUTLIER) cc_final: 0.6232 (t70) REVERT: f 85 LYS cc_start: 0.8087 (tppt) cc_final: 0.7874 (mmmt) REVERT: f 104 LYS cc_start: 0.8924 (mmtm) cc_final: 0.8480 (mmmt) REVERT: m 288 LYS cc_start: 0.8730 (tptt) cc_final: 0.8516 (tmtt) outliers start: 46 outliers final: 35 residues processed: 192 average time/residue: 0.0582 time to fit residues: 14.3141 Evaluate side-chains 198 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 44 VAL Chi-restraints excluded: chain b residue 47 THR 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 40 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 81 HIS 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 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 g residue 131 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 n residue 293 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.156326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.128020 restraints weight = 7506.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.132163 restraints weight = 4064.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.134787 restraints weight = 2755.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.136761 restraints weight = 2136.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.137966 restraints weight = 1775.081| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4752 Z= 0.142 Angle : 0.694 9.059 6448 Z= 0.343 Chirality : 0.043 0.142 759 Planarity : 0.003 0.036 786 Dihedral : 4.906 23.926 697 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 8.49 % Allowed : 32.05 % Favored : 59.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.35), residues: 569 helix: 2.35 (0.33), residues: 216 sheet: -1.96 (0.55), residues: 82 loop : -2.67 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 117 TYR 0.017 0.001 TYR g 85 PHE 0.010 0.001 PHE b 40 TRP 0.014 0.002 TRP g 55 HIS 0.005 0.001 HIS f 81 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4743) covalent geometry : angle 0.68766 ( 6430) SS BOND : bond 0.00714 ( 9) SS BOND : angle 1.84386 ( 18) hydrogen bonds : bond 0.04011 ( 214) hydrogen bonds : angle 3.87970 ( 615) *********************** 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 213 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 90 TYR cc_start: 0.7892 (m-80) cc_final: 0.7579 (m-80) REVERT: e 72 ASP cc_start: 0.7479 (m-30) cc_final: 0.7140 (m-30) REVERT: e 74 ASN cc_start: 0.7533 (m-40) cc_final: 0.7331 (m-40) REVERT: e 79 GLU cc_start: 0.6878 (tp30) cc_final: 0.6604 (tp30) REVERT: e 80 ASP cc_start: 0.7180 (m-30) cc_final: 0.6397 (m-30) REVERT: e 109 ASN cc_start: 0.7852 (m-40) cc_final: 0.7593 (p0) REVERT: m 288 LYS cc_start: 0.8757 (tptt) cc_final: 0.8551 (tmtt) REVERT: m 289 LEU cc_start: 0.8960 (tp) cc_final: 0.8520 (tp) outliers start: 44 outliers final: 36 residues processed: 191 average time/residue: 0.0614 time to fit residues: 15.1013 Evaluate side-chains 195 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 44 VAL 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 84 LEU 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 110 LEU Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 268 VAL 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 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.158391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129814 restraints weight = 7709.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.134024 restraints weight = 4151.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.136695 restraints weight = 2792.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.138789 restraints weight = 2162.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.140068 restraints weight = 1785.951| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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 : 0.003 0.034 4752 Z= 0.132 Angle : 0.712 8.858 6448 Z= 0.346 Chirality : 0.043 0.142 759 Planarity : 0.003 0.033 786 Dihedral : 4.762 26.013 697 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 7.34 % Allowed : 33.01 % Favored : 59.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.36), residues: 569 helix: 2.46 (0.34), residues: 215 sheet: -1.80 (0.55), residues: 82 loop : -2.58 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 117 TYR 0.016 0.001 TYR g 85 PHE 0.019 0.001 PHE e 110 TRP 0.014 0.001 TRP g 55 HIS 0.005 0.001 HIS f 81 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4743) covalent geometry : angle 0.70782 ( 6430) SS BOND : bond 0.00557 ( 9) SS BOND : angle 1.57109 ( 18) hydrogen bonds : bond 0.03837 ( 214) hydrogen bonds : angle 3.86314 ( 615) *********************** 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 208 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 32 CYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7553 (t) REVERT: b 55 PHE cc_start: 0.7031 (OUTLIER) cc_final: 0.6811 (t80) REVERT: d 22 PHE cc_start: 0.6602 (m-80) cc_final: 0.5979 (m-80) REVERT: d 90 TYR cc_start: 0.7852 (m-80) cc_final: 0.7514 (m-80) REVERT: e 72 ASP cc_start: 0.7407 (m-30) cc_final: 0.7072 (m-30) REVERT: e 74 ASN cc_start: 0.7521 (m-40) cc_final: 0.7315 (m-40) REVERT: e 109 ASN cc_start: 0.7865 (m-40) cc_final: 0.7516 (p0) REVERT: e 119 CYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6579 (p) REVERT: m 289 LEU cc_start: 0.8967 (tp) cc_final: 0.8485 (tp) outliers start: 38 outliers final: 30 residues processed: 188 average time/residue: 0.0614 time to fit residues: 14.8887 Evaluate side-chains 195 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 36 ASP Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 55 PHE Chi-restraints excluded: chain d residue 52 LEU 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 119 CYS 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 48 THR Chi-restraints excluded: chain f residue 84 LEU 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 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 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 n residue 300 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.158173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.129675 restraints weight = 7552.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.133907 restraints weight = 4090.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.136739 restraints weight = 2752.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.138482 restraints weight = 2112.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.139805 restraints weight = 1770.791| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4752 Z= 0.139 Angle : 0.726 8.762 6448 Z= 0.353 Chirality : 0.043 0.141 759 Planarity : 0.003 0.032 786 Dihedral : 4.920 29.599 697 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 8.11 % Allowed : 32.24 % Favored : 59.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.35), residues: 569 helix: 2.48 (0.34), residues: 215 sheet: -1.72 (0.55), residues: 82 loop : -2.60 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 117 TYR 0.021 0.001 TYR n 283 PHE 0.016 0.001 PHE e 110 TRP 0.011 0.001 TRP g 55 HIS 0.005 0.001 HIS f 81 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4743) covalent geometry : angle 0.71737 ( 6430) SS BOND : bond 0.00614 ( 9) SS BOND : angle 2.20100 ( 18) hydrogen bonds : bond 0.03811 ( 214) hydrogen bonds : angle 3.83540 ( 615) *********************** 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 209 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 32 CYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7823 (t) REVERT: d 90 TYR cc_start: 0.7849 (m-80) cc_final: 0.7496 (m-80) REVERT: e 72 ASP cc_start: 0.7397 (m-30) cc_final: 0.7060 (m-30) REVERT: e 109 ASN cc_start: 0.7904 (m-40) cc_final: 0.7618 (p0) REVERT: m 289 LEU cc_start: 0.9014 (tp) cc_final: 0.8554 (tp) outliers start: 42 outliers final: 36 residues processed: 186 average time/residue: 0.0583 time to fit residues: 13.9803 Evaluate side-chains 199 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 42 TYR 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 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 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 43 THR Chi-restraints excluded: chain f residue 47 LEU 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 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 145 LEU 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 266 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 33 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 41 optimal weight: 0.0980 chunk 9 optimal weight: 5.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.160663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132445 restraints weight = 7625.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.136715 restraints weight = 4121.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.139623 restraints weight = 2768.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.141599 restraints weight = 2120.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.142810 restraints weight = 1751.799| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4752 Z= 0.128 Angle : 0.725 8.562 6448 Z= 0.350 Chirality : 0.042 0.136 759 Planarity : 0.003 0.031 786 Dihedral : 4.771 27.788 697 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 7.53 % Allowed : 33.98 % Favored : 58.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.35), residues: 569 helix: 2.54 (0.34), residues: 215 sheet: -1.52 (0.55), residues: 82 loop : -2.58 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 117 TYR 0.019 0.001 TYR n 283 PHE 0.008 0.001 PHE n 296 TRP 0.011 0.001 TRP g 55 HIS 0.005 0.001 HIS f 81 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4743) covalent geometry : angle 0.71619 ( 6430) SS BOND : bond 0.00648 ( 9) SS BOND : angle 2.21711 ( 18) hydrogen bonds : bond 0.03558 ( 214) hydrogen bonds : angle 3.73494 ( 615) *********************** 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 209 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 32 CYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7572 (t) REVERT: e 72 ASP cc_start: 0.7426 (m-30) cc_final: 0.7088 (m-30) REVERT: e 109 ASN cc_start: 0.7958 (m-40) cc_final: 0.7693 (p0) REVERT: f 111 TYR cc_start: 0.7478 (m-80) cc_final: 0.6868 (m-80) REVERT: g 85 TYR cc_start: 0.8296 (m-80) cc_final: 0.7987 (m-80) outliers start: 39 outliers final: 31 residues processed: 187 average time/residue: 0.0614 time to fit residues: 14.8015 Evaluate side-chains 197 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 32 CYS 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 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 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 84 LEU 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 145 LEU 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 110 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 n residue 300 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS ** e 92 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 = 0.4046 r_free = 0.4046 target = 0.156869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.128147 restraints weight = 7577.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.132285 restraints weight = 4110.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.135133 restraints weight = 2795.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.137078 restraints weight = 2156.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.138243 restraints weight = 1797.876| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4752 Z= 0.165 Angle : 0.785 8.616 6448 Z= 0.377 Chirality : 0.044 0.154 759 Planarity : 0.003 0.032 786 Dihedral : 5.010 27.030 697 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 6.76 % Allowed : 36.29 % Favored : 56.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.35), residues: 569 helix: 2.40 (0.34), residues: 216 sheet: -1.80 (0.55), residues: 87 loop : -2.59 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 117 TYR 0.024 0.002 TYR n 283 PHE 0.011 0.001 PHE n 296 TRP 0.015 0.002 TRP d 43 HIS 0.004 0.001 HIS f 81 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 4743) covalent geometry : angle 0.77679 ( 6430) SS BOND : bond 0.00718 ( 9) SS BOND : angle 2.28942 ( 18) hydrogen bonds : bond 0.04038 ( 214) hydrogen bonds : angle 3.84900 ( 615) *********************** 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 209 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 32 CYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7933 (t) REVERT: d 43 TRP cc_start: 0.7590 (t60) cc_final: 0.7316 (t60) REVERT: d 90 TYR cc_start: 0.7869 (m-80) cc_final: 0.7353 (m-80) REVERT: e 72 ASP cc_start: 0.7628 (m-30) cc_final: 0.7262 (m-30) REVERT: e 109 ASN cc_start: 0.8124 (m-40) cc_final: 0.7771 (p0) REVERT: f 111 TYR cc_start: 0.7508 (m-80) cc_final: 0.6907 (m-80) outliers start: 35 outliers final: 32 residues processed: 190 average time/residue: 0.0577 time to fit residues: 14.0998 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 : 0.136 ------------------------------------------------------------------------------- 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 32 CYS 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 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 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 84 LEU 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 145 LEU 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 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 m residue 284 LEU Chi-restraints excluded: chain n residue 293 VAL 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 37 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 41 optimal weight: 0.0770 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.159244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.131177 restraints weight = 7569.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.135149 restraints weight = 4258.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.137815 restraints weight = 2953.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.139591 restraints weight = 2307.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.140639 restraints weight = 1957.326| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4752 Z= 0.141 Angle : 0.769 10.172 6448 Z= 0.374 Chirality : 0.043 0.163 759 Planarity : 0.003 0.032 786 Dihedral : 4.841 25.414 697 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 6.18 % Allowed : 36.68 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.35), residues: 569 helix: 2.47 (0.34), residues: 216 sheet: -1.42 (0.55), residues: 82 loop : -2.64 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG d 72 TYR 0.018 0.001 TYR n 283 PHE 0.011 0.001 PHE n 296 TRP 0.018 0.002 TRP g 55 HIS 0.005 0.001 HIS f 81 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4743) covalent geometry : angle 0.75856 ( 6430) SS BOND : bond 0.00645 ( 9) SS BOND : angle 2.45808 ( 18) hydrogen bonds : bond 0.03761 ( 214) hydrogen bonds : angle 3.78026 ( 615) ********************** 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 197 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 32 CYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7857 (t) REVERT: d 43 TRP cc_start: 0.7638 (t60) cc_final: 0.7353 (t60) REVERT: e 72 ASP cc_start: 0.7459 (m-30) cc_final: 0.7135 (m-30) REVERT: e 109 ASN cc_start: 0.8029 (m-40) cc_final: 0.7763 (p0) REVERT: f 111 TYR cc_start: 0.7472 (m-80) cc_final: 0.6950 (m-80) REVERT: g 85 TYR cc_start: 0.8318 (m-80) cc_final: 0.7963 (m-80) REVERT: m 269 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8442 (tt) outliers start: 32 outliers final: 30 residues processed: 181 average time/residue: 0.0575 time to fit residues: 13.4657 Evaluate side-chains 196 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 32 CYS 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 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 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 84 LEU 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 145 LEU 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 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 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 1 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 35 optimal weight: 0.0060 chunk 30 optimal weight: 7.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.157528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.128631 restraints weight = 7640.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132851 restraints weight = 4161.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.135616 restraints weight = 2825.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.137312 restraints weight = 2192.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.138683 restraints weight = 1848.793| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4752 Z= 0.151 Angle : 0.772 10.196 6448 Z= 0.375 Chirality : 0.043 0.155 759 Planarity : 0.003 0.032 786 Dihedral : 4.855 26.107 697 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 6.37 % Allowed : 37.07 % Favored : 56.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.35), residues: 569 helix: 2.46 (0.34), residues: 216 sheet: -1.40 (0.56), residues: 80 loop : -2.62 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 68 TYR 0.018 0.001 TYR n 295 PHE 0.010 0.001 PHE n 296 TRP 0.015 0.002 TRP g 55 HIS 0.005 0.001 HIS f 81 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4743) covalent geometry : angle 0.76376 ( 6430) SS BOND : bond 0.00703 ( 9) SS BOND : angle 2.25684 ( 18) hydrogen bonds : bond 0.03862 ( 214) hydrogen bonds : angle 3.80146 ( 615) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 892.16 seconds wall clock time: 15 minutes 59.62 seconds (959.62 seconds total)