Starting phenix.real_space_refine on Wed Sep 17 08:11:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chu_45602/09_2025/9chu_45602.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chu_45602/09_2025/9chu_45602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9chu_45602/09_2025/9chu_45602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chu_45602/09_2025/9chu_45602.map" model { file = "/net/cci-nas-00/data/ceres_data/9chu_45602/09_2025/9chu_45602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chu_45602/09_2025/9chu_45602.cif" } resolution = 3.49 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= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 4555 2.51 5 N 1151 2.21 5 O 1255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7009 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3326 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 9, 'TRANS': 418} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2806 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 20, 'TRANS': 331} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'GLU%COO:oxt': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'E5E': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'FK5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.82, per 1000 atoms: 0.26 Number of scatterers: 7009 At special positions: 0 Unit cell: (64.6, 84.15, 152.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1255 8.00 N 1151 7.00 C 4555 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 364.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 52.3% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 32 through 61 removed outlier: 3.891A pdb=" N PHE A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 97 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 102 through 137 removed outlier: 3.543A pdb=" N CYS A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 146 through 171 Proline residue: A 168 - end of helix removed outlier: 3.522A pdb=" N MET A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'A' and resid 198 through 208 Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.581A pdb=" N VAL A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.736A pdb=" N ILE A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.561A pdb=" N ILE A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 removed outlier: 3.797A pdb=" N LEU A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET A 333 " --> pdb=" O GLN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 356 Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 395 through 421 Proline residue: A 411 - end of helix removed outlier: 4.711A pdb=" N ILE A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 removed outlier: 3.536A pdb=" N ASN A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 452 removed outlier: 4.183A pdb=" N LEU A 447 " --> pdb=" O GLY A 443 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 56 through 73 removed outlier: 3.829A pdb=" N GLN B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 4.194A pdb=" N LYS B 99 " --> pdb=" O PHE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 153 through 159 removed outlier: 3.713A pdb=" N GLU B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.719A pdb=" N TYR B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 347 through 368 Proline residue: B 354 - end of helix Processing helix chain 'C' and resid 56 through 61 Processing sheet with id=AA1, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.142A pdb=" N LEU B 195 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 276 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ILE B 304 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG B 278 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 84 through 87 removed outlier: 3.591A pdb=" N LEU B 113 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR B 112 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 319 through 324 Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.607A pdb=" N THR C 21 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU C 106 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL C 23 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 35 through 38 removed outlier: 6.549A pdb=" N LYS C 35 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 30 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP C 37 " --> pdb=" O GLY C 28 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1848 1.33 - 1.45: 1331 1.45 - 1.57: 3925 1.57 - 1.69: 1 1.69 - 1.81: 73 Bond restraints: 7178 Sorted by residual: bond pdb=" C9 FK5 C 201 " pdb=" O4 FK5 C 201 " ideal model delta sigma weight residual 1.206 1.407 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C1 FK5 C 201 " pdb=" O2 FK5 C 201 " ideal model delta sigma weight residual 1.211 1.410 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" C22 FK5 C 201 " pdb=" O9 FK5 C 201 " ideal model delta sigma weight residual 1.215 1.408 -0.193 2.00e-02 2.50e+03 9.28e+01 bond pdb=" C8 FK5 C 201 " pdb=" O3 FK5 C 201 " ideal model delta sigma weight residual 1.232 1.408 -0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" C8 FK5 C 201 " pdb=" C9 FK5 C 201 " ideal model delta sigma weight residual 1.537 1.395 0.142 2.00e-02 2.50e+03 5.02e+01 ... (remaining 7173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 9446 2.32 - 4.64: 233 4.64 - 6.95: 46 6.95 - 9.27: 15 9.27 - 11.59: 3 Bond angle restraints: 9743 Sorted by residual: angle pdb=" N VAL A 206 " pdb=" CA VAL A 206 " pdb=" C VAL A 206 " ideal model delta sigma weight residual 113.20 101.61 11.59 9.60e-01 1.09e+00 1.46e+02 angle pdb=" N VAL A 420 " pdb=" CA VAL A 420 " pdb=" C VAL A 420 " ideal model delta sigma weight residual 110.30 103.53 6.77 9.70e-01 1.06e+00 4.87e+01 angle pdb=" N ASP A 423 " pdb=" CA ASP A 423 " pdb=" C ASP A 423 " ideal model delta sigma weight residual 111.33 103.40 7.93 1.21e+00 6.83e-01 4.30e+01 angle pdb=" N SER A 203 " pdb=" CA SER A 203 " pdb=" CB SER A 203 " ideal model delta sigma weight residual 110.20 119.73 -9.53 1.49e+00 4.50e-01 4.09e+01 angle pdb=" N GLN A 422 " pdb=" CA GLN A 422 " pdb=" C GLN A 422 " ideal model delta sigma weight residual 113.15 105.90 7.25 1.19e+00 7.06e-01 3.71e+01 ... (remaining 9738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 4221 35.78 - 71.56: 80 71.56 - 107.34: 8 107.34 - 143.13: 0 143.13 - 178.91: 4 Dihedral angle restraints: 4313 sinusoidal: 1734 harmonic: 2579 Sorted by residual: dihedral pdb=" CB CYS A 106 " pdb=" SG CYS A 106 " pdb=" SG CYS A 191 " pdb=" CB CYS A 191 " ideal model delta sinusoidal sigma weight residual -86.00 -174.25 88.25 1 1.00e+01 1.00e-02 9.31e+01 dihedral pdb=" N SER A 203 " pdb=" C SER A 203 " pdb=" CA SER A 203 " pdb=" CB SER A 203 " ideal model delta harmonic sigma weight residual 122.80 137.79 -14.99 0 2.50e+00 1.60e-01 3.60e+01 dihedral pdb=" C ARG A 175 " pdb=" N ARG A 175 " pdb=" CA ARG A 175 " pdb=" CB ARG A 175 " ideal model delta harmonic sigma weight residual -122.60 -136.04 13.44 0 2.50e+00 1.60e-01 2.89e+01 ... (remaining 4310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 1075 0.132 - 0.264: 22 0.264 - 0.396: 3 0.396 - 0.529: 2 0.529 - 0.661: 1 Chirality restraints: 1103 Sorted by residual: chirality pdb=" CA SER A 203 " pdb=" N SER A 203 " pdb=" C SER A 203 " pdb=" CB SER A 203 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA ARG A 175 " pdb=" N ARG A 175 " pdb=" C ARG A 175 " pdb=" CB ARG A 175 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CAL E5E A 501 " pdb=" CAH E5E A 501 " pdb=" CAK E5E A 501 " pdb=" OAD E5E A 501 " both_signs ideal model delta sigma weight residual False -2.31 -2.74 0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 1100 not shown) Planarity restraints: 1231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C26 FK5 C 201 " 0.111 2.00e-02 2.50e+03 1.22e-01 1.87e+02 pdb=" C27 FK5 C 201 " -0.039 2.00e-02 2.50e+03 pdb=" C28 FK5 C 201 " -0.193 2.00e-02 2.50e+03 pdb=" C29 FK5 C 201 " 0.151 2.00e-02 2.50e+03 pdb=" C42 FK5 C 201 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 FK5 C 201 " -0.052 2.00e-02 2.50e+03 5.92e-02 4.38e+01 pdb=" C19 FK5 C 201 " 0.014 2.00e-02 2.50e+03 pdb=" C20 FK5 C 201 " 0.095 2.00e-02 2.50e+03 pdb=" C21 FK5 C 201 " -0.072 2.00e-02 2.50e+03 pdb=" C37 FK5 C 201 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 430 " -0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C VAL A 430 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL A 430 " -0.025 2.00e-02 2.50e+03 pdb=" N TYR A 431 " -0.022 2.00e-02 2.50e+03 ... (remaining 1228 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 282 2.71 - 3.26: 7155 3.26 - 3.81: 10761 3.81 - 4.35: 12971 4.35 - 4.90: 22172 Nonbonded interactions: 53341 Sorted by model distance: nonbonded pdb=" OH TYR C 82 " pdb=" O3 FK5 C 201 " model vdw 2.165 3.040 nonbonded pdb=" OH TYR A 219 " pdb=" O LEU A 395 " model vdw 2.212 3.040 nonbonded pdb=" O GLY B 105 " pdb=" OH TYR B 112 " model vdw 2.221 3.040 nonbonded pdb=" O SER C 39 " pdb=" OG SER C 39 " model vdw 2.260 3.040 nonbonded pdb=" O PHE B 238 " pdb=" NH1 ARG B 291 " model vdw 2.279 3.120 ... (remaining 53336 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 individual isotropic 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: 3.900 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.960 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 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 : 0.008 0.201 7180 Z= 0.415 Angle : 0.893 11.588 9747 Z= 0.519 Chirality : 0.060 0.661 1103 Planarity : 0.006 0.122 1231 Dihedral : 16.113 178.907 2643 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.41 % Allowed : 1.22 % Favored : 98.37 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.29), residues: 877 helix: 0.22 (0.25), residues: 435 sheet: -2.37 (0.60), residues: 66 loop : -1.43 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.018 0.002 TYR A 449 PHE 0.025 0.002 PHE A 223 TRP 0.022 0.002 TRP C 59 HIS 0.014 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00834 ( 7178) covalent geometry : angle 0.89204 ( 9743) SS BOND : bond 0.00204 ( 2) SS BOND : angle 2.56779 ( 4) hydrogen bonds : bond 0.14401 ( 324) hydrogen bonds : angle 5.87809 ( 942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 193 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7186 (t80) REVERT: B 315 ASN cc_start: 0.8603 (t0) cc_final: 0.8339 (t0) REVERT: C 11 ASP cc_start: 0.8247 (t70) cc_final: 0.7864 (t70) outliers start: 3 outliers final: 0 residues processed: 125 average time/residue: 0.0836 time to fit residues: 14.1418 Evaluate side-chains 99 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 435 ASN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.172371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.148144 restraints weight = 8551.748| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.55 r_work: 0.3616 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7180 Z= 0.145 Angle : 0.601 6.066 9747 Z= 0.310 Chirality : 0.042 0.157 1103 Planarity : 0.004 0.031 1231 Dihedral : 13.787 175.727 1064 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.04 % Allowed : 9.10 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.30), residues: 877 helix: 0.64 (0.26), residues: 438 sheet: -2.33 (0.56), residues: 75 loop : -1.27 (0.36), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 291 TYR 0.017 0.001 TYR B 261 PHE 0.014 0.001 PHE A 242 TRP 0.009 0.002 TRP C 59 HIS 0.005 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7178) covalent geometry : angle 0.60057 ( 9743) SS BOND : bond 0.00091 ( 2) SS BOND : angle 1.00279 ( 4) hydrogen bonds : bond 0.04662 ( 324) hydrogen bonds : angle 4.42233 ( 942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8365 (mm) cc_final: 0.8136 (mm) REVERT: A 193 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7447 (t80) REVERT: A 259 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7414 (mpp) REVERT: B 315 ASN cc_start: 0.8847 (t0) cc_final: 0.8590 (t0) REVERT: C 5 GLU cc_start: 0.7419 (pm20) cc_final: 0.7184 (pm20) REVERT: C 11 ASP cc_start: 0.8233 (t70) cc_final: 0.7795 (t70) outliers start: 15 outliers final: 9 residues processed: 114 average time/residue: 0.0676 time to fit residues: 11.0420 Evaluate side-chains 106 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain C residue 8 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 84 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 435 ASN B 269 GLN B 366 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.167026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139015 restraints weight = 8783.417| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.99 r_work: 0.3457 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7180 Z= 0.137 Angle : 0.576 7.627 9747 Z= 0.296 Chirality : 0.041 0.132 1103 Planarity : 0.003 0.030 1231 Dihedral : 13.469 175.129 1064 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.72 % Allowed : 12.09 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.30), residues: 877 helix: 0.81 (0.26), residues: 440 sheet: -2.30 (0.56), residues: 75 loop : -1.21 (0.36), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 278 TYR 0.013 0.001 TYR B 261 PHE 0.013 0.001 PHE B 333 TRP 0.026 0.002 TRP A 173 HIS 0.002 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7178) covalent geometry : angle 0.57555 ( 9743) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.48767 ( 4) hydrogen bonds : bond 0.04379 ( 324) hydrogen bonds : angle 4.16498 ( 942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.277 Fit side-chains REVERT: A 72 ILE cc_start: 0.8234 (mm) cc_final: 0.7939 (mm) REVERT: A 99 TRP cc_start: 0.6722 (OUTLIER) cc_final: 0.5683 (t60) REVERT: A 193 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7478 (t80) REVERT: A 435 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7432 (t0) REVERT: B 98 MET cc_start: 0.7564 (mmm) cc_final: 0.7226 (mmm) REVERT: B 102 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: B 298 PHE cc_start: 0.7426 (m-80) cc_final: 0.6843 (t80) REVERT: B 315 ASN cc_start: 0.8735 (t0) cc_final: 0.8531 (t0) REVERT: C 11 ASP cc_start: 0.8207 (t70) cc_final: 0.7785 (t70) outliers start: 20 outliers final: 13 residues processed: 112 average time/residue: 0.0718 time to fit residues: 11.5850 Evaluate side-chains 108 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 14 optimal weight: 0.1980 chunk 54 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.169119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.141581 restraints weight = 8740.904| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.93 r_work: 0.3502 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7180 Z= 0.130 Angle : 0.571 13.595 9747 Z= 0.290 Chirality : 0.041 0.129 1103 Planarity : 0.003 0.029 1231 Dihedral : 13.272 174.921 1064 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.40 % Allowed : 14.27 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.30), residues: 877 helix: 0.95 (0.26), residues: 440 sheet: -2.21 (0.56), residues: 75 loop : -1.13 (0.36), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 278 TYR 0.011 0.001 TYR B 174 PHE 0.013 0.001 PHE B 333 TRP 0.027 0.002 TRP A 173 HIS 0.002 0.000 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7178) covalent geometry : angle 0.57088 ( 9743) SS BOND : bond 0.00042 ( 2) SS BOND : angle 0.42092 ( 4) hydrogen bonds : bond 0.04133 ( 324) hydrogen bonds : angle 4.03350 ( 942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.260 Fit side-chains REVERT: A 72 ILE cc_start: 0.8261 (mm) cc_final: 0.8003 (mm) REVERT: A 99 TRP cc_start: 0.6687 (OUTLIER) cc_final: 0.5694 (t60) REVERT: A 193 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7492 (t80) REVERT: B 98 MET cc_start: 0.7588 (mmm) cc_final: 0.7336 (mmm) REVERT: B 102 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: B 298 PHE cc_start: 0.7301 (m-80) cc_final: 0.6792 (t80) REVERT: C 5 GLU cc_start: 0.7156 (pm20) cc_final: 0.6894 (pm20) REVERT: C 11 ASP cc_start: 0.8237 (t70) cc_final: 0.7830 (t70) outliers start: 25 outliers final: 18 residues processed: 114 average time/residue: 0.0721 time to fit residues: 11.7889 Evaluate side-chains 115 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 99 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 56 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.0980 chunk 63 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN B 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.172110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.143834 restraints weight = 8657.750| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.92 r_work: 0.3526 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7180 Z= 0.116 Angle : 0.567 13.760 9747 Z= 0.285 Chirality : 0.040 0.127 1103 Planarity : 0.003 0.029 1231 Dihedral : 13.177 175.307 1064 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.12 % Allowed : 15.22 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.30), residues: 877 helix: 1.12 (0.26), residues: 439 sheet: -2.13 (0.56), residues: 75 loop : -1.09 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 278 TYR 0.011 0.001 TYR B 174 PHE 0.011 0.001 PHE B 333 TRP 0.024 0.001 TRP A 173 HIS 0.002 0.000 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7178) covalent geometry : angle 0.56736 ( 9743) SS BOND : bond 0.00029 ( 2) SS BOND : angle 0.38170 ( 4) hydrogen bonds : bond 0.03804 ( 324) hydrogen bonds : angle 3.89410 ( 942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.292 Fit side-chains REVERT: A 72 ILE cc_start: 0.8236 (mm) cc_final: 0.7977 (mm) REVERT: A 193 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7597 (t80) REVERT: B 98 MET cc_start: 0.7632 (mmm) cc_final: 0.7417 (mmm) REVERT: B 102 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: C 11 ASP cc_start: 0.8229 (t70) cc_final: 0.7831 (t70) outliers start: 23 outliers final: 15 residues processed: 119 average time/residue: 0.0735 time to fit residues: 12.3469 Evaluate side-chains 109 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 0.0000 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 chunk 57 optimal weight: 0.2980 chunk 81 optimal weight: 0.0870 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 0.0000 chunk 19 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 overall best weight: 0.0766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.177152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.148462 restraints weight = 8579.595| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.77 r_work: 0.3577 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7180 Z= 0.100 Angle : 0.527 13.990 9747 Z= 0.267 Chirality : 0.039 0.125 1103 Planarity : 0.003 0.028 1231 Dihedral : 12.994 175.239 1064 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.17 % Allowed : 14.95 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.30), residues: 877 helix: 1.26 (0.26), residues: 441 sheet: -1.86 (0.59), residues: 75 loop : -1.08 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 253 TYR 0.020 0.001 TYR B 287 PHE 0.010 0.001 PHE A 412 TRP 0.024 0.001 TRP A 173 HIS 0.003 0.000 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 7178) covalent geometry : angle 0.52726 ( 9743) SS BOND : bond 0.00079 ( 2) SS BOND : angle 0.30899 ( 4) hydrogen bonds : bond 0.03227 ( 324) hydrogen bonds : angle 3.75168 ( 942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.259 Fit side-chains REVERT: A 193 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7646 (t80) REVERT: A 435 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7538 (t0) REVERT: B 70 ILE cc_start: 0.7979 (tp) cc_final: 0.7698 (tt) REVERT: B 98 MET cc_start: 0.7698 (mmm) cc_final: 0.7381 (mmm) REVERT: B 102 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: B 298 PHE cc_start: 0.7411 (m-80) cc_final: 0.6918 (t80) REVERT: C 5 GLU cc_start: 0.6997 (pm20) cc_final: 0.6464 (pm20) outliers start: 16 outliers final: 9 residues processed: 118 average time/residue: 0.0749 time to fit residues: 12.4268 Evaluate side-chains 108 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 86 optimal weight: 0.0570 chunk 71 optimal weight: 0.0370 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN B 332 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.172725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142614 restraints weight = 8689.552| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.87 r_work: 0.3516 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7180 Z= 0.120 Angle : 0.574 14.960 9747 Z= 0.283 Chirality : 0.040 0.122 1103 Planarity : 0.003 0.028 1231 Dihedral : 13.038 175.857 1064 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.04 % Allowed : 16.98 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.30), residues: 877 helix: 1.32 (0.26), residues: 439 sheet: -1.70 (0.59), residues: 75 loop : -1.03 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 253 TYR 0.016 0.001 TYR B 287 PHE 0.011 0.001 PHE B 333 TRP 0.020 0.001 TRP A 173 HIS 0.003 0.000 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7178) covalent geometry : angle 0.57423 ( 9743) SS BOND : bond 0.00039 ( 2) SS BOND : angle 0.30605 ( 4) hydrogen bonds : bond 0.03590 ( 324) hydrogen bonds : angle 3.74243 ( 942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.260 Fit side-chains REVERT: A 193 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7560 (t80) REVERT: B 70 ILE cc_start: 0.8025 (tp) cc_final: 0.7723 (tt) REVERT: B 102 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: B 151 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: B 298 PHE cc_start: 0.7299 (m-80) cc_final: 0.6923 (t80) REVERT: C 5 GLU cc_start: 0.7003 (pm20) cc_final: 0.6657 (pm20) outliers start: 15 outliers final: 10 residues processed: 113 average time/residue: 0.0686 time to fit residues: 11.2418 Evaluate side-chains 111 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 8 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 53 optimal weight: 0.6980 chunk 62 optimal weight: 0.0030 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.171566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.143070 restraints weight = 8702.722| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.97 r_work: 0.3419 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7180 Z= 0.125 Angle : 0.590 17.416 9747 Z= 0.289 Chirality : 0.040 0.122 1103 Planarity : 0.003 0.028 1231 Dihedral : 13.067 176.015 1064 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.58 % Allowed : 16.98 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.30), residues: 877 helix: 1.27 (0.26), residues: 440 sheet: -1.79 (0.58), residues: 75 loop : -1.05 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 253 TYR 0.014 0.001 TYR B 287 PHE 0.012 0.001 PHE B 333 TRP 0.021 0.002 TRP A 173 HIS 0.003 0.000 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7178) covalent geometry : angle 0.58989 ( 9743) SS BOND : bond 0.00045 ( 2) SS BOND : angle 0.32232 ( 4) hydrogen bonds : bond 0.03699 ( 324) hydrogen bonds : angle 3.77532 ( 942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.303 Fit side-chains REVERT: A 193 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7613 (t80) REVERT: A 259 MET cc_start: 0.7766 (mmt) cc_final: 0.7526 (tmm) REVERT: B 70 ILE cc_start: 0.8038 (tp) cc_final: 0.7726 (tt) REVERT: B 98 MET cc_start: 0.8280 (mmp) cc_final: 0.8002 (mmm) REVERT: B 102 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: B 151 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: B 315 ASN cc_start: 0.8466 (t0) cc_final: 0.8240 (t0) REVERT: C 5 GLU cc_start: 0.7391 (pm20) cc_final: 0.6926 (pm20) outliers start: 19 outliers final: 16 residues processed: 113 average time/residue: 0.0724 time to fit residues: 11.7308 Evaluate side-chains 114 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 21 optimal weight: 0.0000 chunk 76 optimal weight: 0.0060 chunk 41 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 82 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 0.0870 overall best weight: 0.2178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.173339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.145458 restraints weight = 8721.291| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.87 r_work: 0.3541 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7180 Z= 0.103 Angle : 0.557 14.455 9747 Z= 0.275 Chirality : 0.039 0.121 1103 Planarity : 0.003 0.029 1231 Dihedral : 12.976 175.763 1064 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.45 % Allowed : 17.53 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.30), residues: 877 helix: 1.39 (0.26), residues: 440 sheet: -1.94 (0.60), residues: 65 loop : -1.03 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 253 TYR 0.014 0.001 TYR B 287 PHE 0.014 0.001 PHE A 297 TRP 0.025 0.002 TRP A 173 HIS 0.003 0.000 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 7178) covalent geometry : angle 0.55685 ( 9743) SS BOND : bond 0.00084 ( 2) SS BOND : angle 0.32431 ( 4) hydrogen bonds : bond 0.03264 ( 324) hydrogen bonds : angle 3.68260 ( 942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.323 Fit side-chains REVERT: A 193 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7502 (t80) REVERT: B 98 MET cc_start: 0.8161 (mmp) cc_final: 0.7570 (mmm) REVERT: B 102 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: B 151 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: B 298 PHE cc_start: 0.7289 (m-80) cc_final: 0.6916 (t80) REVERT: C 5 GLU cc_start: 0.7153 (pm20) cc_final: 0.6807 (pm20) REVERT: C 11 ASP cc_start: 0.8139 (t70) cc_final: 0.7880 (t70) outliers start: 18 outliers final: 14 residues processed: 111 average time/residue: 0.0700 time to fit residues: 11.2675 Evaluate side-chains 113 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 61 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 5 optimal weight: 0.0870 chunk 29 optimal weight: 0.9990 chunk 48 optimal weight: 0.0010 chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 71 optimal weight: 0.4980 chunk 86 optimal weight: 0.2980 chunk 54 optimal weight: 0.0050 chunk 2 optimal weight: 1.9990 overall best weight: 0.1578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 435 ASN B 150 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.175537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.145781 restraints weight = 8640.698| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.85 r_work: 0.3562 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7180 Z= 0.099 Angle : 0.556 14.298 9747 Z= 0.275 Chirality : 0.039 0.120 1103 Planarity : 0.003 0.028 1231 Dihedral : 12.923 176.597 1064 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.31 % Allowed : 17.80 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.30), residues: 877 helix: 1.52 (0.26), residues: 438 sheet: -2.03 (0.61), residues: 63 loop : -1.01 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 253 TYR 0.013 0.001 TYR B 287 PHE 0.012 0.001 PHE A 297 TRP 0.025 0.001 TRP A 173 HIS 0.002 0.000 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 7178) covalent geometry : angle 0.55574 ( 9743) SS BOND : bond 0.00084 ( 2) SS BOND : angle 0.29850 ( 4) hydrogen bonds : bond 0.03058 ( 324) hydrogen bonds : angle 3.59359 ( 942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.299 Fit side-chains REVERT: B 70 ILE cc_start: 0.8112 (tp) cc_final: 0.7755 (tt) REVERT: B 98 MET cc_start: 0.8266 (mmp) cc_final: 0.7701 (mmm) REVERT: B 102 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: B 151 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: B 298 PHE cc_start: 0.7377 (m-80) cc_final: 0.7023 (t80) REVERT: C 5 GLU cc_start: 0.7321 (pm20) cc_final: 0.6809 (pm20) REVERT: C 11 ASP cc_start: 0.8124 (t70) cc_final: 0.7856 (t70) outliers start: 17 outliers final: 15 residues processed: 113 average time/residue: 0.0680 time to fit residues: 11.1336 Evaluate side-chains 111 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 196 ASN A 435 ASN B 91 HIS B 315 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.169311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.144341 restraints weight = 8820.739| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.64 r_work: 0.3436 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7180 Z= 0.166 Angle : 0.641 14.200 9747 Z= 0.319 Chirality : 0.042 0.176 1103 Planarity : 0.003 0.030 1231 Dihedral : 13.053 176.151 1062 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.58 % Allowed : 18.75 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.30), residues: 877 helix: 1.33 (0.26), residues: 439 sheet: -2.04 (0.59), residues: 67 loop : -1.06 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 253 TYR 0.015 0.001 TYR B 174 PHE 0.019 0.002 PHE B 333 TRP 0.017 0.002 TRP A 173 HIS 0.002 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 7178) covalent geometry : angle 0.64148 ( 9743) SS BOND : bond 0.00154 ( 2) SS BOND : angle 0.55065 ( 4) hydrogen bonds : bond 0.03970 ( 324) hydrogen bonds : angle 3.77514 ( 942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1828.22 seconds wall clock time: 32 minutes 6.15 seconds (1926.15 seconds total)