Starting phenix.real_space_refine on Mon Jun 24 19:57:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy0_37914/06_2024/8wy0_37914_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy0_37914/06_2024/8wy0_37914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy0_37914/06_2024/8wy0_37914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy0_37914/06_2024/8wy0_37914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy0_37914/06_2024/8wy0_37914_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy0_37914/06_2024/8wy0_37914_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 3021 2.51 5 N 738 2.21 5 O 860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "d GLU 27": "OE1" <-> "OE2" Residue "e GLU 91": "OE1" <-> "OE2" Residue "e GLU 124": "OE1" <-> "OE2" Residue "f GLU 120": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 4656 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 234 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "b" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 243 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "d" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "e" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "f" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 933 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "g" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 890 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "m" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "n" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 302 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.45, per 1000 atoms: 0.74 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 855.5 milliseconds 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1094 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 10 helices and 7 sheets defined 36.6% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'a' and resid 28 through 51 removed outlier: 3.961A pdb=" N TYR a 33 " --> pdb=" O PRO a 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 55 Processing helix chain 'd' and resid 103 through 125 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 151 removed outlier: 4.195A pdb=" N ALA e 131 " --> pdb=" O MET e 128 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N THR e 132 " --> pdb=" O SER e 129 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR e 150 " --> pdb=" O LEU e 147 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TRP e 151 " --> pdb=" O VAL e 148 " (cutoff:3.500A) Processing helix chain 'f' and resid 105 through 107 No H-bonds generated for 'chain 'f' and resid 105 through 107' Processing helix chain 'f' and resid 127 through 153 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) Processing helix chain 'g' and resid 77 through 79 No H-bonds generated for 'chain 'g' and resid 77 through 79' Processing helix chain 'g' and resid 115 through 134 Processing helix chain 'm' and resid 261 through 290 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) Processing helix chain 'n' and resid 272 through 306 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= A, first strand: chain 'd' and resid 25 through 28 removed outlier: 4.597A pdb=" N GLY d 61 " --> pdb=" O VAL d 33 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL d 35 " --> pdb=" O ASP d 59 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ASP d 59 " --> pdb=" O VAL d 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'd' and resid 84 through 88 removed outlier: 3.815A pdb=" N SER d 84 " --> pdb=" O CYS d 73 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS d 73 " --> pdb=" O SER d 84 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL d 86 " --> pdb=" O TYR d 71 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR d 71 " --> pdb=" O VAL d 86 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG d 72 " --> pdb=" O TRP d 43 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N TRP d 43 " --> pdb=" O ARG d 72 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'e' and resid 36 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= D, first strand: chain 'e' and resid 58 through 61 removed outlier: 3.634A pdb=" N VAL e 97 " --> pdb=" O GLN e 60 " (cutoff:3.500A) Processing sheet with id= E, 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= F, first strand: chain 'g' and resid 31 through 33 Processing sheet with id= G, 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) 195 hydrogen bonds defined for protein. 519 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 2.03 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: 100.74 - 107.39: 132 107.39 - 114.04: 2712 114.04 - 120.69: 1900 120.69 - 127.35: 1655 127.35 - 134.00: 31 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: 4704 3.25 - 3.80: 7085 3.80 - 4.35: 8615 4.35 - 4.90: 14184 Nonbonded interactions: 34740 Sorted by model distance: nonbonded pdb=" O ILE d 24 " pdb=" OH TYR e 95 " model vdw 2.142 2.440 nonbonded pdb=" OG SER f 88 " pdb=" OE1 GLU f 91 " model vdw 2.155 2.440 nonbonded pdb=" O ASN e 121 " pdb=" ND2 ASN e 121 " model vdw 2.166 2.520 nonbonded pdb=" OD1 ASP e 126 " pdb=" OG SER e 129 " model vdw 2.186 2.440 nonbonded pdb=" O GLN e 92 " pdb=" OH TYR e 96 " model vdw 2.204 2.440 ... (remaining 34735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 1.850 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.190 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4743 Z= 0.202 Angle : 0.710 8.769 6430 Z= 0.363 Chirality : 0.041 0.237 759 Planarity : 0.004 0.038 786 Dihedral : 17.421 88.742 1776 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 1.16 % Allowed : 36.87 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.34), residues: 569 helix: 1.39 (0.35), residues: 215 sheet: -2.08 (0.55), residues: 84 loop : -2.88 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP f 59 HIS 0.004 0.001 HIS g 29 PHE 0.012 0.001 PHE n 296 TYR 0.025 0.002 TYR f 99 ARG 0.005 0.001 ARG e 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 190 time to evaluate : 0.553 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: 0.1770 time to fit residues: 42.2775 Evaluate side-chains 177 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 174 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 110 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 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 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4743 Z= 0.203 Angle : 0.647 7.817 6430 Z= 0.331 Chirality : 0.042 0.169 759 Planarity : 0.005 0.040 786 Dihedral : 5.378 49.261 701 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 7.53 % Allowed : 29.92 % Favored : 62.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.35), residues: 569 helix: 1.93 (0.34), residues: 215 sheet: -1.85 (0.54), residues: 89 loop : -2.84 (0.32), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP f 59 HIS 0.006 0.001 HIS f 81 PHE 0.015 0.002 PHE n 296 TYR 0.029 0.002 TYR f 99 ARG 0.003 0.001 ARG e 101 *********************** 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 218 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 179 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 52 ARG cc_start: 0.7475 (tpt170) cc_final: 0.6868 (ttm170) REVERT: d 22 PHE cc_start: 0.5041 (m-80) cc_final: 0.3844 (m-80) REVERT: d 27 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8042 (tt0) REVERT: d 43 TRP cc_start: 0.7836 (t60) cc_final: 0.7557 (t60) REVERT: e 40 ILE cc_start: 0.8553 (mt) cc_final: 0.8340 (mt) REVERT: e 72 ASP cc_start: 0.7073 (m-30) cc_final: 0.6812 (m-30) REVERT: e 74 ASN cc_start: 0.7998 (m-40) cc_final: 0.7740 (m110) REVERT: e 80 ASP cc_start: 0.7575 (m-30) cc_final: 0.7292 (m-30) REVERT: f 37 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6903 (tptt) REVERT: f 79 GLU cc_start: 0.3396 (OUTLIER) cc_final: 0.2354 (mm-30) REVERT: f 92 GLN cc_start: 0.6858 (mt0) cc_final: 0.6625 (mt0) REVERT: f 106 GLU cc_start: 0.8512 (pm20) cc_final: 0.8206 (pm20) REVERT: g 71 LYS cc_start: 0.6287 (mtmt) cc_final: 0.5965 (mmtm) REVERT: m 288 LYS cc_start: 0.8015 (tptt) cc_final: 0.7685 (tmtt) REVERT: n 275 GLN cc_start: 0.8394 (tm-30) cc_final: 0.8058 (tm-30) outliers start: 39 outliers final: 24 residues processed: 194 average time/residue: 0.1758 time to fit residues: 42.0612 Evaluate side-chains 192 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 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 97 VAL Chi-restraints excluded: chain f residue 37 LYS 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 61 MET Chi-restraints excluded: chain g residue 80 ASP 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 27 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 0.0980 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4743 Z= 0.178 Angle : 0.610 7.829 6430 Z= 0.313 Chirality : 0.041 0.135 759 Planarity : 0.004 0.041 786 Dihedral : 5.195 48.150 699 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 7.34 % Allowed : 31.85 % Favored : 60.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.35), residues: 569 helix: 2.17 (0.35), residues: 212 sheet: -2.04 (0.49), residues: 106 loop : -2.59 (0.34), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP f 59 HIS 0.004 0.001 HIS f 81 PHE 0.012 0.001 PHE g 135 TYR 0.021 0.001 TYR e 150 ARG 0.003 0.000 ARG f 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 176 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 26 LEU cc_start: 0.4767 (mm) cc_final: 0.4243 (tt) REVERT: b 52 ARG cc_start: 0.7456 (tpt170) cc_final: 0.6804 (tpp-160) REVERT: d 22 PHE cc_start: 0.4898 (m-80) cc_final: 0.4182 (m-80) REVERT: d 27 GLU cc_start: 0.8665 (mt-10) cc_final: 0.7944 (tt0) REVERT: d 34 PHE cc_start: 0.7211 (m-80) cc_final: 0.6851 (m-80) REVERT: d 43 TRP cc_start: 0.7558 (t60) cc_final: 0.7324 (t60) REVERT: d 79 TYR cc_start: 0.7938 (t80) cc_final: 0.7733 (t80) REVERT: e 72 ASP cc_start: 0.7072 (m-30) cc_final: 0.6770 (m-30) REVERT: e 74 ASN cc_start: 0.8003 (m-40) cc_final: 0.7634 (m110) REVERT: e 91 GLU cc_start: 0.7959 (tp30) cc_final: 0.7693 (tp30) REVERT: f 37 LYS cc_start: 0.7365 (ttpp) cc_final: 0.6950 (tptt) REVERT: f 92 GLN cc_start: 0.6891 (mt0) cc_final: 0.6636 (mt0) REVERT: f 106 GLU cc_start: 0.8503 (pm20) cc_final: 0.8225 (pm20) REVERT: f 117 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.7546 (ttp-110) REVERT: g 71 LYS cc_start: 0.6229 (mtmt) cc_final: 0.5964 (mmtm) REVERT: m 288 LYS cc_start: 0.7951 (tptt) cc_final: 0.7599 (tmtt) REVERT: m 289 LEU cc_start: 0.7913 (tp) cc_final: 0.7515 (tp) outliers start: 38 outliers final: 28 residues processed: 190 average time/residue: 0.1750 time to fit residues: 41.5995 Evaluate side-chains 194 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 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 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 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 80 ASP Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.0370 chunk 37 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4743 Z= 0.177 Angle : 0.601 7.564 6430 Z= 0.303 Chirality : 0.041 0.134 759 Planarity : 0.004 0.041 786 Dihedral : 5.064 45.820 699 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 8.11 % Allowed : 31.66 % Favored : 60.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.35), residues: 569 helix: 2.15 (0.34), residues: 215 sheet: -1.93 (0.50), residues: 106 loop : -2.62 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP g 55 HIS 0.004 0.001 HIS f 81 PHE 0.010 0.001 PHE g 135 TYR 0.022 0.001 TYR e 150 ARG 0.002 0.000 ARG f 115 *********************** 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 220 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 178 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 26 LEU cc_start: 0.4784 (mm) cc_final: 0.4190 (tt) REVERT: b 52 ARG cc_start: 0.7478 (tpt170) cc_final: 0.6822 (tpp-160) REVERT: d 22 PHE cc_start: 0.5153 (m-80) cc_final: 0.4395 (m-80) REVERT: d 27 GLU cc_start: 0.8561 (mt-10) cc_final: 0.7980 (tt0) REVERT: d 34 PHE cc_start: 0.7196 (m-80) cc_final: 0.6979 (m-10) REVERT: d 43 TRP cc_start: 0.7587 (t60) cc_final: 0.7285 (t60) REVERT: d 90 TYR cc_start: 0.8127 (m-80) cc_final: 0.7875 (m-80) REVERT: e 72 ASP cc_start: 0.7173 (m-30) cc_final: 0.6854 (m-30) REVERT: e 74 ASN cc_start: 0.8023 (m-40) cc_final: 0.7680 (m110) REVERT: f 37 LYS cc_start: 0.7376 (ttpp) cc_final: 0.6922 (tptp) REVERT: f 81 HIS cc_start: 0.7025 (OUTLIER) cc_final: 0.6683 (t70) REVERT: f 85 LYS cc_start: 0.8106 (tppt) cc_final: 0.7749 (mmmt) REVERT: f 92 GLN cc_start: 0.6889 (mt0) cc_final: 0.6616 (mt0) REVERT: f 104 LYS cc_start: 0.8495 (tptt) cc_final: 0.8193 (mmtm) REVERT: f 123 MET cc_start: 0.7080 (ttm) cc_final: 0.5921 (mtp) REVERT: f 125 MET cc_start: 0.8021 (mtp) cc_final: 0.7798 (mtt) REVERT: m 288 LYS cc_start: 0.8014 (tptt) cc_final: 0.7812 (tmtt) REVERT: m 289 LEU cc_start: 0.8028 (tp) cc_final: 0.7660 (tp) outliers start: 42 outliers final: 31 residues processed: 197 average time/residue: 0.1702 time to fit residues: 41.5498 Evaluate side-chains 196 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS 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 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 e residue 48 THR Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 136 VAL 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 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 80 ASP 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 44 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4743 Z= 0.218 Angle : 0.679 7.600 6430 Z= 0.337 Chirality : 0.041 0.130 759 Planarity : 0.004 0.041 786 Dihedral : 4.875 27.971 697 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 8.69 % Allowed : 32.63 % Favored : 58.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.35), residues: 569 helix: 2.16 (0.34), residues: 212 sheet: -1.83 (0.51), residues: 106 loop : -2.62 (0.34), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP g 55 HIS 0.004 0.001 HIS f 81 PHE 0.011 0.001 PHE n 296 TYR 0.020 0.001 TYR e 150 ARG 0.002 0.000 ARG d 68 *********************** 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 217 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 172 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 26 LEU cc_start: 0.4825 (mm) cc_final: 0.4213 (tt) REVERT: b 52 ARG cc_start: 0.7514 (tpt170) cc_final: 0.6889 (tpp-160) REVERT: d 22 PHE cc_start: 0.5314 (m-80) cc_final: 0.4525 (m-80) REVERT: d 27 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7931 (tt0) REVERT: d 43 TRP cc_start: 0.7563 (t60) cc_final: 0.7247 (t60) REVERT: d 79 TYR cc_start: 0.8028 (t80) cc_final: 0.7782 (t80) REVERT: e 72 ASP cc_start: 0.7226 (m-30) cc_final: 0.6898 (m-30) REVERT: e 74 ASN cc_start: 0.8020 (m-40) cc_final: 0.7720 (m110) REVERT: f 37 LYS cc_start: 0.7482 (ttpp) cc_final: 0.7229 (tptp) REVERT: f 81 HIS cc_start: 0.7084 (OUTLIER) cc_final: 0.6699 (t70) REVERT: f 92 GLN cc_start: 0.7130 (mt0) cc_final: 0.6794 (mt0) REVERT: f 125 MET cc_start: 0.8021 (mtp) cc_final: 0.7794 (mtt) REVERT: m 288 LYS cc_start: 0.8027 (tptt) cc_final: 0.7730 (tmtt) REVERT: m 289 LEU cc_start: 0.7959 (tp) cc_final: 0.7598 (tp) outliers start: 45 outliers final: 39 residues processed: 191 average time/residue: 0.1718 time to fit residues: 40.9289 Evaluate side-chains 204 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 164 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS 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 a residue 51 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 104 VAL 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 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 81 HIS 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 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 61 MET Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 111 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 44 optimal weight: 0.1980 chunk 24 optimal weight: 0.0970 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4743 Z= 0.172 Angle : 0.661 8.701 6430 Z= 0.325 Chirality : 0.041 0.157 759 Planarity : 0.004 0.040 786 Dihedral : 4.719 29.324 697 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 7.34 % Allowed : 33.78 % Favored : 58.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.35), residues: 569 helix: 2.18 (0.35), residues: 210 sheet: -1.71 (0.51), residues: 106 loop : -2.47 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP g 55 HIS 0.004 0.001 HIS f 81 PHE 0.009 0.001 PHE d 34 TYR 0.019 0.001 TYR e 150 ARG 0.002 0.000 ARG f 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 171 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 26 LEU cc_start: 0.4795 (mm) cc_final: 0.4252 (tt) REVERT: b 52 ARG cc_start: 0.7543 (tpt170) cc_final: 0.6887 (tpp-160) REVERT: d 27 GLU cc_start: 0.8527 (mt-10) cc_final: 0.7976 (tt0) REVERT: d 43 TRP cc_start: 0.7570 (t60) cc_final: 0.7258 (t60) REVERT: d 57 ARG cc_start: 0.8091 (tpp80) cc_final: 0.7614 (tpp80) REVERT: e 72 ASP cc_start: 0.7273 (m-30) cc_final: 0.6959 (m-30) REVERT: e 101 ARG cc_start: 0.8794 (ptp90) cc_final: 0.8441 (ptp90) REVERT: f 85 LYS cc_start: 0.8046 (tppt) cc_final: 0.7766 (mmmt) REVERT: f 92 GLN cc_start: 0.7134 (mt0) cc_final: 0.6751 (mt0) REVERT: m 289 LEU cc_start: 0.8003 (tp) cc_final: 0.7609 (tp) outliers start: 38 outliers final: 32 residues processed: 187 average time/residue: 0.1628 time to fit residues: 38.0844 Evaluate side-chains 196 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 d residue 52 LEU Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain m residue 259 GLU Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain m residue 268 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.1980 chunk 30 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 74 ASN ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4743 Z= 0.198 Angle : 0.676 8.825 6430 Z= 0.334 Chirality : 0.042 0.142 759 Planarity : 0.004 0.039 786 Dihedral : 4.789 27.472 697 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 8.49 % Allowed : 33.78 % Favored : 57.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.35), residues: 569 helix: 2.19 (0.35), residues: 209 sheet: -1.44 (0.54), residues: 96 loop : -2.46 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 55 HIS 0.005 0.001 HIS f 81 PHE 0.017 0.001 PHE n 296 TYR 0.018 0.002 TYR f 99 ARG 0.002 0.000 ARG f 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 168 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 26 LEU cc_start: 0.4870 (mm) cc_final: 0.4237 (tt) REVERT: b 52 ARG cc_start: 0.7535 (tpt170) cc_final: 0.6896 (tpp-160) REVERT: d 34 PHE cc_start: 0.7414 (m-10) cc_final: 0.7119 (m-10) REVERT: d 43 TRP cc_start: 0.7573 (t60) cc_final: 0.7245 (t60) REVERT: d 57 ARG cc_start: 0.8152 (tpp80) cc_final: 0.7682 (tpp80) REVERT: e 72 ASP cc_start: 0.7252 (m-30) cc_final: 0.6950 (m-30) REVERT: e 101 ARG cc_start: 0.8807 (ptp90) cc_final: 0.8509 (ptp90) REVERT: e 109 ASN cc_start: 0.7634 (m-40) cc_final: 0.7159 (p0) REVERT: f 85 LYS cc_start: 0.8047 (tppt) cc_final: 0.7745 (mmmt) REVERT: f 92 GLN cc_start: 0.7219 (mt0) cc_final: 0.6812 (mt0) REVERT: g 85 TYR cc_start: 0.8123 (m-80) cc_final: 0.7764 (m-80) REVERT: m 289 LEU cc_start: 0.8006 (tp) cc_final: 0.7644 (tp) outliers start: 44 outliers final: 39 residues processed: 191 average time/residue: 0.1738 time to fit residues: 41.1637 Evaluate side-chains 202 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 163 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS 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 a residue 51 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 111 ASN Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 259 GLU Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain m residue 284 LEU Chi-restraints excluded: chain n residue 279 THR Chi-restraints excluded: chain n residue 293 VAL 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 15 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 74 ASN ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4743 Z= 0.182 Angle : 0.687 9.729 6430 Z= 0.336 Chirality : 0.042 0.143 759 Planarity : 0.004 0.038 786 Dihedral : 4.795 33.325 697 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 6.37 % Allowed : 36.10 % Favored : 57.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.36), residues: 569 helix: 2.21 (0.35), residues: 209 sheet: -1.63 (0.50), residues: 106 loop : -2.29 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP g 55 HIS 0.005 0.001 HIS f 81 PHE 0.016 0.001 PHE n 296 TYR 0.019 0.001 TYR n 283 ARG 0.003 0.000 ARG g 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 52 ARG cc_start: 0.7542 (tpt170) cc_final: 0.6902 (tpp-160) REVERT: d 34 PHE cc_start: 0.7420 (m-10) cc_final: 0.7148 (m-10) REVERT: d 43 TRP cc_start: 0.7573 (t60) cc_final: 0.7208 (t60) REVERT: d 57 ARG cc_start: 0.8120 (tpp80) cc_final: 0.7666 (tpp80) REVERT: e 72 ASP cc_start: 0.7177 (m-30) cc_final: 0.6861 (m-30) REVERT: e 101 ARG cc_start: 0.8758 (ptp90) cc_final: 0.8453 (ptp90) REVERT: e 109 ASN cc_start: 0.7774 (m-40) cc_final: 0.7346 (p0) REVERT: e 149 TYR cc_start: 0.7319 (t80) cc_final: 0.6861 (t80) REVERT: f 85 LYS cc_start: 0.8015 (tppt) cc_final: 0.7700 (mmmt) REVERT: f 92 GLN cc_start: 0.7234 (mt0) cc_final: 0.6819 (mt0) REVERT: f 111 TYR cc_start: 0.7510 (m-80) cc_final: 0.6460 (m-80) REVERT: g 85 TYR cc_start: 0.8031 (m-80) cc_final: 0.7669 (m-80) REVERT: m 289 LEU cc_start: 0.8058 (tp) cc_final: 0.7667 (tp) outliers start: 33 outliers final: 31 residues processed: 185 average time/residue: 0.1679 time to fit residues: 38.8907 Evaluate side-chains 195 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 d residue 52 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 111 ASN Chi-restraints excluded: chain m residue 259 GLU Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain m residue 284 LEU Chi-restraints excluded: chain n residue 279 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4743 Z= 0.222 Angle : 0.727 10.752 6430 Z= 0.352 Chirality : 0.042 0.135 759 Planarity : 0.004 0.038 786 Dihedral : 4.944 32.217 697 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 8.11 % Allowed : 35.33 % Favored : 56.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.35), residues: 569 helix: 2.13 (0.34), residues: 209 sheet: -1.66 (0.51), residues: 102 loop : -2.38 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP g 55 HIS 0.005 0.001 HIS f 81 PHE 0.024 0.002 PHE e 110 TYR 0.022 0.002 TYR n 283 ARG 0.002 0.000 ARG d 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 170 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 52 ARG cc_start: 0.7578 (tpt170) cc_final: 0.6901 (tpp-160) REVERT: d 27 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7916 (tt0) REVERT: d 43 TRP cc_start: 0.7554 (t60) cc_final: 0.7192 (t60) REVERT: d 57 ARG cc_start: 0.8129 (tpp80) cc_final: 0.7601 (tpp80) REVERT: e 72 ASP cc_start: 0.7264 (m-30) cc_final: 0.6949 (m-30) REVERT: e 101 ARG cc_start: 0.8817 (ptp90) cc_final: 0.8505 (ptp90) REVERT: e 109 ASN cc_start: 0.7655 (m-40) cc_final: 0.7191 (p0) REVERT: e 149 TYR cc_start: 0.7319 (t80) cc_final: 0.6820 (t80) REVERT: f 85 LYS cc_start: 0.8113 (tppt) cc_final: 0.7813 (mmmt) REVERT: f 92 GLN cc_start: 0.7414 (mt0) cc_final: 0.6975 (mt0) REVERT: f 111 TYR cc_start: 0.7426 (m-80) cc_final: 0.6405 (m-80) REVERT: m 289 LEU cc_start: 0.7938 (tp) cc_final: 0.7594 (tp) outliers start: 42 outliers final: 38 residues processed: 188 average time/residue: 0.1640 time to fit residues: 38.5445 Evaluate side-chains 206 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 d residue 52 LEU Chi-restraints excluded: chain d residue 65 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 140 ILE Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 111 ASN Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 259 GLU Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain m residue 284 LEU Chi-restraints excluded: chain n residue 279 THR 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 24 optimal weight: 0.0040 chunk 36 optimal weight: 0.0980 chunk 54 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4743 Z= 0.180 Angle : 0.709 10.451 6430 Z= 0.344 Chirality : 0.042 0.167 759 Planarity : 0.004 0.037 786 Dihedral : 4.735 31.150 697 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 6.76 % Allowed : 37.07 % Favored : 56.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.35), residues: 569 helix: 2.15 (0.35), residues: 209 sheet: -1.51 (0.49), residues: 106 loop : -2.37 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP g 55 HIS 0.005 0.001 HIS f 81 PHE 0.023 0.001 PHE e 110 TYR 0.020 0.001 TYR d 71 ARG 0.002 0.000 ARG f 115 ********************** 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 200 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 165 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 52 ARG cc_start: 0.7519 (tpt170) cc_final: 0.6845 (ttm170) REVERT: d 22 PHE cc_start: 0.4947 (m-80) cc_final: 0.3692 (m-80) REVERT: d 43 TRP cc_start: 0.7535 (t60) cc_final: 0.7154 (t60) REVERT: d 57 ARG cc_start: 0.7906 (tpp80) cc_final: 0.7422 (tpp80) REVERT: d 79 TYR cc_start: 0.8166 (t80) cc_final: 0.7807 (t80) REVERT: e 72 ASP cc_start: 0.7164 (m-30) cc_final: 0.6851 (m-30) REVERT: e 101 ARG cc_start: 0.8695 (ptp90) cc_final: 0.8394 (ptp90) REVERT: e 109 ASN cc_start: 0.8012 (m-40) cc_final: 0.7548 (p0) REVERT: e 149 TYR cc_start: 0.7263 (t80) cc_final: 0.6794 (t80) REVERT: f 85 LYS cc_start: 0.8232 (tppt) cc_final: 0.7945 (mmmt) REVERT: f 92 GLN cc_start: 0.7285 (mt0) cc_final: 0.6916 (mt0) REVERT: f 111 TYR cc_start: 0.7371 (m-80) cc_final: 0.6399 (m-80) REVERT: g 85 TYR cc_start: 0.7986 (m-80) cc_final: 0.7635 (m-80) REVERT: m 289 LEU cc_start: 0.8037 (tp) cc_final: 0.7639 (tp) outliers start: 35 outliers final: 32 residues processed: 182 average time/residue: 0.1623 time to fit residues: 37.0054 Evaluate side-chains 192 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 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 123 MET Chi-restraints excluded: chain e residue 140 ILE 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 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 61 MET Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 111 ASN Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 259 GLU Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain m residue 284 LEU Chi-restraints excluded: chain n residue 279 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.160816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132895 restraints weight = 7390.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.136906 restraints weight = 4088.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.139678 restraints weight = 2818.833| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4743 Z= 0.186 Angle : 0.716 11.563 6430 Z= 0.346 Chirality : 0.042 0.163 759 Planarity : 0.004 0.038 786 Dihedral : 4.816 30.828 697 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 6.18 % Allowed : 37.45 % Favored : 56.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.35), residues: 569 helix: 2.17 (0.34), residues: 209 sheet: -1.35 (0.51), residues: 102 loop : -2.34 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP g 55 HIS 0.005 0.001 HIS f 81 PHE 0.023 0.002 PHE e 110 TYR 0.019 0.001 TYR d 71 ARG 0.002 0.000 ARG g 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1507.48 seconds wall clock time: 27 minutes 31.76 seconds (1651.76 seconds total)