Starting phenix.real_space_refine on Tue Feb 3 16:16:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pdx_71547/02_2026/9pdx_71547.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pdx_71547/02_2026/9pdx_71547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pdx_71547/02_2026/9pdx_71547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pdx_71547/02_2026/9pdx_71547.map" model { file = "/net/cci-nas-00/data/ceres_data/9pdx_71547/02_2026/9pdx_71547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pdx_71547/02_2026/9pdx_71547.cif" } resolution = 3.94 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= 0.031 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 28 5.16 5 C 2971 2.51 5 N 793 2.21 5 O 953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4745 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2901 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 373} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "C" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 945 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "B" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.25, per 1000 atoms: 0.26 Number of scatterers: 4745 At special positions: 0 Unit cell: (63.36, 108.24, 88, 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 28 16.00 O 953 8.00 N 793 7.00 C 2971 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS F 28 " - pdb=" SG CYS F 407 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 182 " distance=2.03 Simple disulfide: pdb=" SG CYS F 283 " - pdb=" SG CYS F 311 " distance=2.02 Simple disulfide: pdb=" SG CYS F 292 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 326 " - pdb=" SG CYS F 335 " distance=2.03 Simple disulfide: pdb=" SG CYS F 350 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 384 " - pdb=" SG CYS F 390 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " 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 Links applied ALPHA1-3 " BMA A 3 " - " MAN A 4 " ALPHA1-6 " BMA A 3 " - " MAN A 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN F 57 " " NAG F 501 " - " ASN F 172 " Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 274.7 milliseconds 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1138 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 8 sheets defined 21.9% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'F' and resid 65 through 89 removed outlier: 4.110A pdb=" N THR F 69 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG F 79 " --> pdb=" O LYS F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 130 removed outlier: 4.035A pdb=" N VAL F 118 " --> pdb=" O THR F 114 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 141 Processing helix chain 'F' and resid 163 through 177 removed outlier: 3.947A pdb=" N LEU F 173 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER F 175 " --> pdb=" O LYS F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 197 Processing helix chain 'F' and resid 197 through 210 removed outlier: 3.761A pdb=" N ASN F 210 " --> pdb=" O GLN F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 233 Processing helix chain 'F' and resid 237 through 247 Processing helix chain 'F' and resid 247 through 255 Processing helix chain 'F' and resid 338 through 340 No H-bonds generated for 'chain 'F' and resid 338 through 340' Processing helix chain 'F' and resid 411 through 415 Processing sheet with id=AA1, first strand: chain 'F' and resid 20 through 22 removed outlier: 3.528A pdb=" N LYS F 20 " --> pdb=" O GLU F 33 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU F 33 " --> pdb=" O LYS F 20 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 29 through 33 current: chain 'F' and resid 159 through 160 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 159 through 160 current: chain 'F' and resid 256 through 262 removed outlier: 3.870A pdb=" N PHE F 256 " --> pdb=" O GLN F 272 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE F 268 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS F 312 " --> pdb=" O PRO F 282 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TRP F 309 " --> pdb=" O TYR F 320 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 317 through 320 current: chain 'F' and resid 332 through 336 Processing sheet with id=AA2, first strand: chain 'F' and resid 293 through 295 removed outlier: 3.515A pdb=" N ALA F 300 " --> pdb=" O SER F 293 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN F 298 " --> pdb=" O LYS F 295 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 373 through 374 Processing sheet with id=AA4, first strand: chain 'F' and resid 390 through 392 removed outlier: 3.840A pdb=" N THR F 419 " --> pdb=" O SER F 391 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.861A pdb=" N VAL C 5 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA C 79 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 12 removed outlier: 4.107A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.559A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 63 " --> pdb=" O THR B 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 4.200A pdb=" N ILE B 48 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) 153 hydrogen bonds defined for protein. 417 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: 0.53 Time building geometry restraints manager: 0.68 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: 1521 1.34 - 1.46: 1172 1.46 - 1.59: 2098 1.59 - 1.71: 0 1.71 - 1.83: 38 Bond restraints: 4829 Sorted by residual: bond pdb=" C ASP C 52 " pdb=" N PRO C 53 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.45e+00 bond pdb=" N PRO F 235 " pdb=" CA PRO F 235 " ideal model delta sigma weight residual 1.469 1.482 -0.014 1.28e-02 6.10e+03 1.14e+00 bond pdb=" CA CYS F 407 " pdb=" C CYS F 407 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 9.01e-01 bond pdb=" CA VAL F 157 " pdb=" CB VAL F 157 " ideal model delta sigma weight residual 1.540 1.553 -0.013 1.36e-02 5.41e+03 8.51e-01 bond pdb=" CA VAL F 157 " pdb=" C VAL F 157 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.27e-02 6.20e+03 7.53e-01 ... (remaining 4824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 6349 1.56 - 3.12: 165 3.12 - 4.67: 25 4.67 - 6.23: 14 6.23 - 7.79: 2 Bond angle restraints: 6555 Sorted by residual: angle pdb=" N ARG F 348 " pdb=" CA ARG F 348 " pdb=" C ARG F 348 " ideal model delta sigma weight residual 114.39 108.37 6.02 1.45e+00 4.76e-01 1.73e+01 angle pdb=" CA VAL F 157 " pdb=" CB VAL F 157 " pdb=" CG1 VAL F 157 " ideal model delta sigma weight residual 110.40 116.25 -5.85 1.70e+00 3.46e-01 1.19e+01 angle pdb=" C TYR F 385 " pdb=" N LYS F 386 " pdb=" CA LYS F 386 " ideal model delta sigma weight residual 121.54 127.96 -6.42 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C VAL F 157 " pdb=" CA VAL F 157 " pdb=" CB VAL F 157 " ideal model delta sigma weight residual 111.29 116.72 -5.43 1.64e+00 3.72e-01 1.10e+01 angle pdb=" CA GLU F 25 " pdb=" C GLU F 25 " pdb=" N GLU F 26 " ideal model delta sigma weight residual 118.41 122.45 -4.04 1.34e+00 5.57e-01 9.09e+00 ... (remaining 6550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.27: 2720 25.27 - 50.54: 247 50.54 - 75.81: 29 75.81 - 101.08: 4 101.08 - 126.35: 3 Dihedral angle restraints: 3003 sinusoidal: 1230 harmonic: 1773 Sorted by residual: dihedral pdb=" CB CYS F 384 " pdb=" SG CYS F 384 " pdb=" SG CYS F 390 " pdb=" CB CYS F 390 " ideal model delta sinusoidal sigma weight residual 93.00 168.20 -75.20 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS F 283 " pdb=" SG CYS F 283 " pdb=" SG CYS F 311 " pdb=" CB CYS F 311 " ideal model delta sinusoidal sigma weight residual 93.00 146.47 -53.47 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 48.79 44.21 1 1.00e+01 1.00e-02 2.72e+01 ... (remaining 3000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 534 0.035 - 0.071: 162 0.071 - 0.106: 50 0.106 - 0.141: 28 0.141 - 0.177: 2 Chirality restraints: 776 Sorted by residual: chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN F 57 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" C1 NAG F 501 " pdb=" ND2 ASN F 172 " pdb=" C2 NAG F 501 " pdb=" O5 NAG F 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA ILE C 93 " pdb=" N ILE C 93 " pdb=" C ILE C 93 " pdb=" CB ILE C 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 773 not shown) Planarity restraints: 826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR F 359 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO F 360 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO F 360 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 360 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 52 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO C 53 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 386 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C LYS F 386 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS F 386 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY F 387 " 0.008 2.00e-02 2.50e+03 ... (remaining 823 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 2359 2.98 - 3.46: 4363 3.46 - 3.94: 7097 3.94 - 4.42: 7508 4.42 - 4.90: 12841 Nonbonded interactions: 34168 Sorted by model distance: nonbonded pdb=" N GLU F 133 " pdb=" OE1 GLU F 133 " model vdw 2.498 3.120 nonbonded pdb=" N GLU F 33 " pdb=" OE1 GLU F 33 " model vdw 2.542 3.120 nonbonded pdb=" C3 MAN A 5 " pdb=" O5 MAN A 5 " model vdw 2.588 2.776 nonbonded pdb=" N HIS C 99 " pdb=" O HIS C 99 " model vdw 2.591 2.496 nonbonded pdb=" N ARG F 348 " pdb=" N GLU F 349 " model vdw 2.594 2.560 ... (remaining 34163 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.220 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.180 Find NCS groups from input model: 0.020 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:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 0.037 4844 Z= 0.135 Angle : 0.651 7.790 6591 Z= 0.358 Chirality : 0.044 0.177 776 Planarity : 0.004 0.050 824 Dihedral : 18.202 126.346 1838 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.14 % Favored : 91.36 % Rotamer: Outliers : 3.48 % Allowed : 30.95 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: -1.37 (0.35), residues: 602 helix: 1.73 (0.49), residues: 122 sheet: -0.62 (0.42), residues: 173 loop : -2.28 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 329 TYR 0.010 0.001 TYR C 106 PHE 0.005 0.001 PHE B 71 TRP 0.017 0.001 TRP C 33 HIS 0.001 0.000 HIS F 332 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 4829) covalent geometry : angle 0.64346 ( 6555) SS BOND : bond 0.00297 ( 9) SS BOND : angle 1.61602 ( 18) hydrogen bonds : bond 0.20181 ( 153) hydrogen bonds : angle 7.75256 ( 417) link_ALPHA1-3 : bond 0.00736 ( 1) link_ALPHA1-3 : angle 1.36410 ( 3) link_ALPHA1-6 : bond 0.00671 ( 1) link_ALPHA1-6 : angle 1.22100 ( 3) link_BETA1-4 : bond 0.00319 ( 2) link_BETA1-4 : angle 1.48142 ( 6) link_NAG-ASN : bond 0.00282 ( 2) link_NAG-ASN : angle 1.10429 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: F 240 GLN cc_start: 0.7405 (mp10) cc_final: 0.6805 (mp10) REVERT: C 13 LYS cc_start: 0.8617 (mttt) cc_final: 0.8245 (mtmm) outliers start: 18 outliers final: 16 residues processed: 76 average time/residue: 0.0723 time to fit residues: 7.2143 Evaluate side-chains 77 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 311 CYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.0000 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.0170 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 overall best weight: 0.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.215117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.164723 restraints weight = 5497.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.161934 restraints weight = 8107.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.164799 restraints weight = 7885.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.163660 restraints weight = 5191.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.164715 restraints weight = 4855.215| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.0575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4844 Z= 0.118 Angle : 0.578 6.404 6591 Z= 0.302 Chirality : 0.043 0.177 776 Planarity : 0.004 0.048 824 Dihedral : 10.156 108.483 807 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.81 % Favored : 91.69 % Rotamer: Outliers : 5.22 % Allowed : 30.17 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: -1.19 (0.35), residues: 602 helix: 1.87 (0.48), residues: 122 sheet: -0.38 (0.44), residues: 165 loop : -2.21 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 329 TYR 0.010 0.001 TYR C 80 PHE 0.005 0.001 PHE F 256 TRP 0.019 0.001 TRP C 33 HIS 0.001 0.000 HIS F 332 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 4829) covalent geometry : angle 0.57253 ( 6555) SS BOND : bond 0.00174 ( 9) SS BOND : angle 0.88155 ( 18) hydrogen bonds : bond 0.04483 ( 153) hydrogen bonds : angle 5.92001 ( 417) link_ALPHA1-3 : bond 0.00633 ( 1) link_ALPHA1-3 : angle 1.31647 ( 3) link_ALPHA1-6 : bond 0.00961 ( 1) link_ALPHA1-6 : angle 2.09844 ( 3) link_BETA1-4 : bond 0.00296 ( 2) link_BETA1-4 : angle 1.56407 ( 6) link_NAG-ASN : bond 0.00295 ( 2) link_NAG-ASN : angle 1.08312 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.109 Fit side-chains REVERT: F 240 GLN cc_start: 0.7512 (mp10) cc_final: 0.6845 (mp10) REVERT: F 319 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.7246 (t80) REVERT: C 13 LYS cc_start: 0.8519 (mttt) cc_final: 0.8127 (mtmm) REVERT: C 33 TRP cc_start: 0.5822 (OUTLIER) cc_final: 0.4748 (p90) REVERT: B 2 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.7947 (mm) REVERT: B 97 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8371 (p) outliers start: 27 outliers final: 16 residues processed: 86 average time/residue: 0.0521 time to fit residues: 5.9868 Evaluate side-chains 78 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 311 CYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 319 TYR Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 34 optimal weight: 30.0000 chunk 47 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.206451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.153402 restraints weight = 5770.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.142470 restraints weight = 6827.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.145999 restraints weight = 8012.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.147374 restraints weight = 4321.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.147402 restraints weight = 3604.907| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 4844 Z= 0.326 Angle : 0.812 10.807 6591 Z= 0.418 Chirality : 0.050 0.189 776 Planarity : 0.005 0.043 824 Dihedral : 9.726 97.651 798 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.13 % Favored : 88.37 % Rotamer: Outliers : 8.70 % Allowed : 28.24 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: -1.87 (0.33), residues: 602 helix: 1.15 (0.46), residues: 121 sheet: -0.74 (0.42), residues: 164 loop : -2.60 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 329 TYR 0.019 0.003 TYR B 32 PHE 0.019 0.002 PHE F 256 TRP 0.033 0.003 TRP C 103 HIS 0.005 0.002 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00785 ( 4829) covalent geometry : angle 0.80163 ( 6555) SS BOND : bond 0.00537 ( 9) SS BOND : angle 2.13441 ( 18) hydrogen bonds : bond 0.05931 ( 153) hydrogen bonds : angle 5.83394 ( 417) link_ALPHA1-3 : bond 0.00762 ( 1) link_ALPHA1-3 : angle 1.25476 ( 3) link_ALPHA1-6 : bond 0.01329 ( 1) link_ALPHA1-6 : angle 2.57919 ( 3) link_BETA1-4 : bond 0.00133 ( 2) link_BETA1-4 : angle 1.82673 ( 6) link_NAG-ASN : bond 0.00203 ( 2) link_NAG-ASN : angle 1.08340 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 59 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: F 27 SER cc_start: 0.3273 (OUTLIER) cc_final: 0.2400 (m) REVERT: F 166 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7474 (tptm) REVERT: F 240 GLN cc_start: 0.7804 (mp10) cc_final: 0.7212 (mp10) REVERT: F 319 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.7242 (t80) REVERT: C 13 LYS cc_start: 0.8520 (mttt) cc_final: 0.8206 (mttm) REVERT: C 33 TRP cc_start: 0.6153 (OUTLIER) cc_final: 0.4689 (p90) REVERT: B 2 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8050 (mm) REVERT: B 96 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.6146 (mmt90) REVERT: B 97 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8419 (p) outliers start: 45 outliers final: 28 residues processed: 96 average time/residue: 0.0719 time to fit residues: 8.9991 Evaluate side-chains 94 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 59 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 311 CYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 319 TYR Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 409 TYR Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 0.0170 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.214776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.162207 restraints weight = 5663.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.156499 restraints weight = 8983.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.159773 restraints weight = 8156.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.160200 restraints weight = 4842.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.160429 restraints weight = 4331.070| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4844 Z= 0.120 Angle : 0.608 7.511 6591 Z= 0.313 Chirality : 0.044 0.177 776 Planarity : 0.004 0.044 824 Dihedral : 8.132 87.368 791 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.81 % Favored : 91.69 % Rotamer: Outliers : 6.00 % Allowed : 31.14 % Favored : 62.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: -1.39 (0.35), residues: 602 helix: 1.81 (0.47), residues: 122 sheet: -0.71 (0.42), residues: 175 loop : -2.30 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 329 TYR 0.011 0.001 TYR C 80 PHE 0.005 0.001 PHE B 71 TRP 0.018 0.001 TRP C 33 HIS 0.002 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 4829) covalent geometry : angle 0.59736 ( 6555) SS BOND : bond 0.00146 ( 9) SS BOND : angle 1.58619 ( 18) hydrogen bonds : bond 0.04129 ( 153) hydrogen bonds : angle 5.04678 ( 417) link_ALPHA1-3 : bond 0.00628 ( 1) link_ALPHA1-3 : angle 1.36924 ( 3) link_ALPHA1-6 : bond 0.01330 ( 1) link_ALPHA1-6 : angle 2.79708 ( 3) link_BETA1-4 : bond 0.00257 ( 2) link_BETA1-4 : angle 1.56355 ( 6) link_NAG-ASN : bond 0.00312 ( 2) link_NAG-ASN : angle 1.10161 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 59 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: F 84 VAL cc_start: 0.8461 (t) cc_final: 0.8191 (p) REVERT: F 240 GLN cc_start: 0.7411 (mp10) cc_final: 0.6595 (mp10) REVERT: F 319 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.7325 (t80) REVERT: C 13 LYS cc_start: 0.8465 (mttt) cc_final: 0.8214 (mttm) REVERT: C 33 TRP cc_start: 0.5703 (OUTLIER) cc_final: 0.4767 (p90) REVERT: C 102 SER cc_start: 0.9194 (p) cc_final: 0.8922 (p) REVERT: B 2 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8046 (mm) REVERT: B 97 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8386 (p) outliers start: 31 outliers final: 20 residues processed: 86 average time/residue: 0.0718 time to fit residues: 8.0677 Evaluate side-chains 80 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 311 CYS Chi-restraints excluded: chain F residue 319 TYR Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 409 TYR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 0.0470 chunk 19 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- 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 = 0.4314 r_free = 0.4314 target = 0.208156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.157833 restraints weight = 5466.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.153381 restraints weight = 7578.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.155770 restraints weight = 7821.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.156077 restraints weight = 4606.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156568 restraints weight = 4297.067| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4844 Z= 0.190 Angle : 0.650 8.182 6591 Z= 0.332 Chirality : 0.045 0.181 776 Planarity : 0.004 0.043 824 Dihedral : 7.682 77.805 790 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.63 % Favored : 88.87 % Rotamer: Outliers : 7.35 % Allowed : 29.40 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: -1.48 (0.34), residues: 602 helix: 1.71 (0.47), residues: 122 sheet: -0.62 (0.43), residues: 165 loop : -2.40 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 329 TYR 0.012 0.002 TYR C 105 PHE 0.010 0.001 PHE F 256 TRP 0.021 0.002 TRP C 103 HIS 0.002 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 4829) covalent geometry : angle 0.64029 ( 6555) SS BOND : bond 0.00378 ( 9) SS BOND : angle 1.50699 ( 18) hydrogen bonds : bond 0.04528 ( 153) hydrogen bonds : angle 4.97983 ( 417) link_ALPHA1-3 : bond 0.00641 ( 1) link_ALPHA1-3 : angle 1.26061 ( 3) link_ALPHA1-6 : bond 0.01514 ( 1) link_ALPHA1-6 : angle 2.91890 ( 3) link_BETA1-4 : bond 0.00221 ( 2) link_BETA1-4 : angle 1.61941 ( 6) link_NAG-ASN : bond 0.00229 ( 2) link_NAG-ASN : angle 1.08237 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 62 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: F 84 VAL cc_start: 0.8557 (t) cc_final: 0.8237 (p) REVERT: F 240 GLN cc_start: 0.7535 (mp10) cc_final: 0.7148 (mp10) REVERT: F 319 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.7291 (t80) REVERT: F 346 GLN cc_start: 0.6353 (OUTLIER) cc_final: 0.6113 (mm-40) REVERT: C 13 LYS cc_start: 0.8481 (mttt) cc_final: 0.8221 (mttm) REVERT: C 33 TRP cc_start: 0.5956 (OUTLIER) cc_final: 0.4770 (p90) REVERT: B 2 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8051 (mm) REVERT: B 97 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8437 (p) outliers start: 38 outliers final: 25 residues processed: 92 average time/residue: 0.0463 time to fit residues: 5.5831 Evaluate side-chains 89 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 59 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 311 CYS Chi-restraints excluded: chain F residue 319 TYR Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 409 TYR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 26 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.6340 ------------------------------------------------------------------------------- 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 = 0.4374 r_free = 0.4374 target = 0.215849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.165154 restraints weight = 5755.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.160371 restraints weight = 8449.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.162943 restraints weight = 8395.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.163009 restraints weight = 4420.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.163489 restraints weight = 4291.145| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4844 Z= 0.121 Angle : 0.594 8.099 6591 Z= 0.303 Chirality : 0.044 0.178 776 Planarity : 0.003 0.044 824 Dihedral : 6.702 54.289 790 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.81 % Favored : 91.69 % Rotamer: Outliers : 6.77 % Allowed : 29.40 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: -1.25 (0.34), residues: 602 helix: 1.93 (0.48), residues: 122 sheet: -0.52 (0.42), residues: 165 loop : -2.24 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 329 TYR 0.010 0.001 TYR C 106 PHE 0.006 0.001 PHE C 29 TRP 0.018 0.001 TRP C 33 HIS 0.002 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 4829) covalent geometry : angle 0.58571 ( 6555) SS BOND : bond 0.00161 ( 9) SS BOND : angle 1.27564 ( 18) hydrogen bonds : bond 0.03715 ( 153) hydrogen bonds : angle 4.62617 ( 417) link_ALPHA1-3 : bond 0.00608 ( 1) link_ALPHA1-3 : angle 1.34605 ( 3) link_ALPHA1-6 : bond 0.01886 ( 1) link_ALPHA1-6 : angle 2.72884 ( 3) link_BETA1-4 : bond 0.00253 ( 2) link_BETA1-4 : angle 1.49321 ( 6) link_NAG-ASN : bond 0.00310 ( 2) link_NAG-ASN : angle 1.13556 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 59 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: F 84 VAL cc_start: 0.8475 (t) cc_final: 0.8229 (p) REVERT: F 240 GLN cc_start: 0.7379 (mp10) cc_final: 0.6694 (mp10) REVERT: F 319 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.7266 (t80) REVERT: C 13 LYS cc_start: 0.8441 (mttt) cc_final: 0.8193 (mttm) REVERT: C 33 TRP cc_start: 0.5665 (OUTLIER) cc_final: 0.4725 (p90) REVERT: C 102 SER cc_start: 0.9216 (p) cc_final: 0.8924 (p) REVERT: B 2 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8009 (mm) REVERT: B 97 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8408 (p) outliers start: 35 outliers final: 25 residues processed: 90 average time/residue: 0.0683 time to fit residues: 8.2166 Evaluate side-chains 85 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 56 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 311 CYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 319 TYR Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 409 TYR Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 51 optimal weight: 0.0030 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.215056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.162971 restraints weight = 5646.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.158005 restraints weight = 7805.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.160040 restraints weight = 7788.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.160534 restraints weight = 4675.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.160810 restraints weight = 4044.654| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4844 Z= 0.129 Angle : 0.597 6.140 6591 Z= 0.305 Chirality : 0.044 0.178 776 Planarity : 0.003 0.044 824 Dihedral : 6.137 55.679 790 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.64 % Favored : 90.86 % Rotamer: Outliers : 7.16 % Allowed : 28.63 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: -1.17 (0.34), residues: 602 helix: 1.97 (0.48), residues: 121 sheet: -0.52 (0.42), residues: 170 loop : -2.15 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 329 TYR 0.010 0.001 TYR C 106 PHE 0.005 0.001 PHE F 256 TRP 0.018 0.001 TRP C 33 HIS 0.001 0.000 HIS F 332 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4829) covalent geometry : angle 0.58921 ( 6555) SS BOND : bond 0.00180 ( 9) SS BOND : angle 1.36986 ( 18) hydrogen bonds : bond 0.03779 ( 153) hydrogen bonds : angle 4.49740 ( 417) link_ALPHA1-3 : bond 0.00557 ( 1) link_ALPHA1-3 : angle 1.24522 ( 3) link_ALPHA1-6 : bond 0.01973 ( 1) link_ALPHA1-6 : angle 2.17723 ( 3) link_BETA1-4 : bond 0.00163 ( 2) link_BETA1-4 : angle 1.40436 ( 6) link_NAG-ASN : bond 0.00278 ( 2) link_NAG-ASN : angle 1.10529 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 59 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: F 240 GLN cc_start: 0.7442 (mp10) cc_final: 0.6769 (mp10) REVERT: F 319 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.7111 (t80) REVERT: C 13 LYS cc_start: 0.8454 (mttt) cc_final: 0.8183 (mttm) REVERT: C 33 TRP cc_start: 0.5764 (OUTLIER) cc_final: 0.4725 (p90) REVERT: B 2 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8022 (mm) outliers start: 37 outliers final: 28 residues processed: 91 average time/residue: 0.0656 time to fit residues: 8.0593 Evaluate side-chains 88 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 57 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 311 CYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 319 TYR Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 409 TYR Chi-restraints excluded: chain F residue 418 VAL Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 81 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 0.0970 chunk 4 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.1780 ------------------------------------------------------------------------------- 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 = 0.4349 r_free = 0.4349 target = 0.213314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.162491 restraints weight = 5663.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.157983 restraints weight = 9031.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.161115 restraints weight = 8513.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.160046 restraints weight = 4889.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.161032 restraints weight = 4797.182| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4844 Z= 0.162 Angle : 0.633 7.028 6591 Z= 0.324 Chirality : 0.045 0.179 776 Planarity : 0.004 0.043 824 Dihedral : 6.129 57.983 790 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.14 % Favored : 90.37 % Rotamer: Outliers : 6.77 % Allowed : 29.01 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: -1.26 (0.34), residues: 602 helix: 1.84 (0.48), residues: 122 sheet: -0.56 (0.42), residues: 170 loop : -2.20 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 329 TYR 0.010 0.001 TYR C 105 PHE 0.007 0.001 PHE F 256 TRP 0.019 0.002 TRP C 33 HIS 0.002 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 4829) covalent geometry : angle 0.62442 ( 6555) SS BOND : bond 0.00364 ( 9) SS BOND : angle 1.62908 ( 18) hydrogen bonds : bond 0.04021 ( 153) hydrogen bonds : angle 4.56155 ( 417) link_ALPHA1-3 : bond 0.00689 ( 1) link_ALPHA1-3 : angle 1.26861 ( 3) link_ALPHA1-6 : bond 0.01765 ( 1) link_ALPHA1-6 : angle 1.90240 ( 3) link_BETA1-4 : bond 0.00232 ( 2) link_BETA1-4 : angle 1.41236 ( 6) link_NAG-ASN : bond 0.00248 ( 2) link_NAG-ASN : angle 1.08615 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 57 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: F 88 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7540 (tp40) REVERT: F 240 GLN cc_start: 0.7434 (mp10) cc_final: 0.6736 (mp10) REVERT: F 319 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.7171 (t80) REVERT: C 13 LYS cc_start: 0.8426 (mttt) cc_final: 0.8200 (mttm) REVERT: C 33 TRP cc_start: 0.5783 (OUTLIER) cc_final: 0.4705 (p90) REVERT: C 102 SER cc_start: 0.9293 (p) cc_final: 0.8992 (p) REVERT: B 2 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8066 (mm) outliers start: 35 outliers final: 27 residues processed: 88 average time/residue: 0.0636 time to fit residues: 7.4943 Evaluate side-chains 88 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 57 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 311 CYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 319 TYR Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 409 TYR Chi-restraints excluded: chain F residue 418 VAL Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 81 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 0.0370 chunk 2 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.216135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.161184 restraints weight = 5629.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.157463 restraints weight = 7492.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.160366 restraints weight = 6995.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.160106 restraints weight = 4152.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.160764 restraints weight = 4049.932| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4844 Z= 0.118 Angle : 0.584 5.837 6591 Z= 0.301 Chirality : 0.044 0.176 776 Planarity : 0.003 0.043 824 Dihedral : 5.890 59.083 790 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.97 % Favored : 91.53 % Rotamer: Outliers : 6.38 % Allowed : 29.40 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: -1.15 (0.35), residues: 602 helix: 1.93 (0.48), residues: 122 sheet: -0.50 (0.42), residues: 170 loop : -2.12 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 329 TYR 0.010 0.001 TYR C 106 PHE 0.004 0.001 PHE F 200 TRP 0.018 0.001 TRP C 33 HIS 0.001 0.000 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 4829) covalent geometry : angle 0.57738 ( 6555) SS BOND : bond 0.00300 ( 9) SS BOND : angle 1.35025 ( 18) hydrogen bonds : bond 0.03507 ( 153) hydrogen bonds : angle 4.34189 ( 417) link_ALPHA1-3 : bond 0.00727 ( 1) link_ALPHA1-3 : angle 1.25153 ( 3) link_ALPHA1-6 : bond 0.01434 ( 1) link_ALPHA1-6 : angle 1.67657 ( 3) link_BETA1-4 : bond 0.00310 ( 2) link_BETA1-4 : angle 1.28790 ( 6) link_NAG-ASN : bond 0.00318 ( 2) link_NAG-ASN : angle 1.12725 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: F 240 GLN cc_start: 0.7455 (mp10) cc_final: 0.6756 (mp10) REVERT: F 319 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.7057 (t80) REVERT: C 13 LYS cc_start: 0.8445 (mttt) cc_final: 0.8180 (mttm) REVERT: C 33 TRP cc_start: 0.5733 (OUTLIER) cc_final: 0.4757 (p90) REVERT: C 37 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8287 (m) REVERT: B 2 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8129 (mm) outliers start: 33 outliers final: 26 residues processed: 87 average time/residue: 0.0632 time to fit residues: 7.4112 Evaluate side-chains 88 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 58 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 311 CYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 319 TYR Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 409 TYR Chi-restraints excluded: chain F residue 418 VAL Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 0.0070 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.216796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.162971 restraints weight = 5684.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.158168 restraints weight = 7903.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.160768 restraints weight = 7334.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.161119 restraints weight = 4115.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.161345 restraints weight = 3702.653| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4844 Z= 0.116 Angle : 0.586 7.488 6591 Z= 0.301 Chirality : 0.044 0.176 776 Planarity : 0.003 0.043 824 Dihedral : 5.705 54.893 790 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.80 % Favored : 90.70 % Rotamer: Outliers : 6.38 % Allowed : 29.59 % Favored : 64.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: -1.07 (0.35), residues: 602 helix: 2.01 (0.48), residues: 122 sheet: -0.45 (0.42), residues: 170 loop : -2.08 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 329 TYR 0.010 0.001 TYR C 106 PHE 0.004 0.001 PHE B 71 TRP 0.017 0.001 TRP C 33 HIS 0.001 0.000 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 4829) covalent geometry : angle 0.57976 ( 6555) SS BOND : bond 0.00253 ( 9) SS BOND : angle 1.34545 ( 18) hydrogen bonds : bond 0.03434 ( 153) hydrogen bonds : angle 4.26418 ( 417) link_ALPHA1-3 : bond 0.00783 ( 1) link_ALPHA1-3 : angle 1.20025 ( 3) link_ALPHA1-6 : bond 0.01219 ( 1) link_ALPHA1-6 : angle 1.55905 ( 3) link_BETA1-4 : bond 0.00319 ( 2) link_BETA1-4 : angle 1.25923 ( 6) link_NAG-ASN : bond 0.00318 ( 2) link_NAG-ASN : angle 1.09877 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 61 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: F 240 GLN cc_start: 0.7484 (mp10) cc_final: 0.6765 (mp10) REVERT: F 250 MET cc_start: 0.7932 (tpt) cc_final: 0.7666 (tpt) REVERT: F 319 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.6992 (t80) REVERT: C 13 LYS cc_start: 0.8449 (mttt) cc_final: 0.8189 (mttm) REVERT: C 33 TRP cc_start: 0.5697 (OUTLIER) cc_final: 0.4728 (p90) REVERT: C 37 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8295 (m) REVERT: C 102 SER cc_start: 0.9200 (p) cc_final: 0.8878 (p) REVERT: B 2 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8087 (mm) outliers start: 33 outliers final: 28 residues processed: 89 average time/residue: 0.0634 time to fit residues: 7.6441 Evaluate side-chains 91 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 182 CYS Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 311 CYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 319 TYR Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 409 TYR Chi-restraints excluded: chain F residue 418 VAL Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.215457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.160345 restraints weight = 5684.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156834 restraints weight = 7430.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.158079 restraints weight = 7435.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.159052 restraints weight = 5186.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.159487 restraints weight = 3919.139| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4844 Z= 0.130 Angle : 0.597 7.859 6591 Z= 0.305 Chirality : 0.044 0.175 776 Planarity : 0.003 0.043 824 Dihedral : 5.648 51.990 790 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.14 % Favored : 90.53 % Rotamer: Outliers : 6.19 % Allowed : 29.59 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 are not related in a simple way. whole: -1.11 (0.35), residues: 602 helix: 1.95 (0.48), residues: 122 sheet: -0.49 (0.41), residues: 170 loop : -2.08 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 329 TYR 0.010 0.001 TYR C 106 PHE 0.005 0.001 PHE F 256 TRP 0.017 0.001 TRP C 33 HIS 0.001 0.001 HIS F 332 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4829) covalent geometry : angle 0.59089 ( 6555) SS BOND : bond 0.00215 ( 9) SS BOND : angle 1.31504 ( 18) hydrogen bonds : bond 0.03619 ( 153) hydrogen bonds : angle 4.25616 ( 417) link_ALPHA1-3 : bond 0.00827 ( 1) link_ALPHA1-3 : angle 1.17738 ( 3) link_ALPHA1-6 : bond 0.01121 ( 1) link_ALPHA1-6 : angle 1.50061 ( 3) link_BETA1-4 : bond 0.00293 ( 2) link_BETA1-4 : angle 1.28621 ( 6) link_NAG-ASN : bond 0.00293 ( 2) link_NAG-ASN : angle 1.03743 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 888.92 seconds wall clock time: 16 minutes 8.65 seconds (968.65 seconds total)