Starting phenix.real_space_refine on Wed Sep 17 04:41:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c3b_45164/09_2025/9c3b_45164.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c3b_45164/09_2025/9c3b_45164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c3b_45164/09_2025/9c3b_45164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c3b_45164/09_2025/9c3b_45164.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c3b_45164/09_2025/9c3b_45164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c3b_45164/09_2025/9c3b_45164.map" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.076 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 10 5.16 5 C 2731 2.51 5 N 742 2.21 5 O 846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s 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: 4329 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3234 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 13, 'TRANS': 431} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 5, 'TYR:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1095 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 135} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.32, per 1000 atoms: 0.30 Number of scatterers: 4329 At special positions: 0 Unit cell: (108.528, 110.16, 84.048, 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 10 16.00 O 846 8.00 N 742 7.00 C 2731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.37 Conformation dependent library (CDL) restraints added in 193.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1096 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 6 sheets defined 32.3% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 43 through 51 removed outlier: 4.015A pdb=" N ASP A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 65 Processing helix chain 'A' and resid 103 through 107 removed outlier: 4.075A pdb=" N GLY A 106 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 107' Processing helix chain 'A' and resid 120 through 135 Processing helix chain 'A' and resid 149 through 153 removed outlier: 4.001A pdb=" N SER A 152 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 196 removed outlier: 3.640A pdb=" N TYR A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 removed outlier: 3.848A pdb=" N ALA A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.588A pdb=" N GLN A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 238' Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.647A pdb=" N LEU A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 252 " --> pdb=" O PRO A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 281 removed outlier: 3.577A pdb=" N TYR A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 345 through 369 removed outlier: 3.515A pdb=" N ASN A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 399 removed outlier: 3.570A pdb=" N ILE A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 415 removed outlier: 3.871A pdb=" N VAL A 415 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.594A pdb=" N ALA A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 12 removed outlier: 3.547A pdb=" N VAL B 12 " --> pdb=" O PRO B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 85 removed outlier: 3.779A pdb=" N ALA B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 41 removed outlier: 7.441A pdb=" N GLY A 77 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE A 27 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 202 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ALA A 229 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ALA A 204 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE A 326 " --> pdb=" O TRP A 263 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE A 325 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 293 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 146 removed outlier: 6.005A pdb=" N LYS A 159 " --> pdb=" O MET A 81 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N MET A 81 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 408 removed outlier: 6.692A pdb=" N ILE A 433 " --> pdb=" O SER A 403 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR A 405 " --> pdb=" O HIS A 431 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N HIS A 431 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL A 407 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR A 429 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 21 removed outlier: 4.387A pdb=" N CYS B 14 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N SER B 93 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN B 110 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ILE B 97 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA B 106 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP B 138 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE B 109 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 136 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 34 removed outlier: 6.817A pdb=" N ILE B 131 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 43 159 hydrogen bonds defined for protein. 441 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: 0.70 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1444 1.34 - 1.46: 655 1.46 - 1.57: 2287 1.57 - 1.69: 1 1.69 - 1.80: 16 Bond restraints: 4403 Sorted by residual: bond pdb=" CA SER B 71 " pdb=" CB SER B 71 " ideal model delta sigma weight residual 1.529 1.477 0.052 1.58e-02 4.01e+03 1.10e+01 bond pdb=" CB PRO A 136 " pdb=" CG PRO A 136 " ideal model delta sigma weight residual 1.492 1.644 -0.152 5.00e-02 4.00e+02 9.25e+00 bond pdb=" N ILE A 5 " pdb=" CA ILE A 5 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.95e+00 bond pdb=" CA SER A 357 " pdb=" CB SER A 357 " ideal model delta sigma weight residual 1.530 1.480 0.049 1.69e-02 3.50e+03 8.53e+00 bond pdb=" N PHE A 34 " pdb=" CA PHE A 34 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.23e-02 6.61e+03 8.11e+00 ... (remaining 4398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 5890 2.89 - 5.78: 108 5.78 - 8.67: 6 8.67 - 11.56: 1 11.56 - 14.45: 1 Bond angle restraints: 6006 Sorted by residual: angle pdb=" CA PRO A 136 " pdb=" N PRO A 136 " pdb=" CD PRO A 136 " ideal model delta sigma weight residual 112.00 97.55 14.45 1.40e+00 5.10e-01 1.07e+02 angle pdb=" N PRO A 88 " pdb=" CA PRO A 88 " pdb=" CB PRO A 88 " ideal model delta sigma weight residual 103.25 94.60 8.65 1.05e+00 9.07e-01 6.79e+01 angle pdb=" N LEU A 355 " pdb=" CA LEU A 355 " pdb=" C LEU A 355 " ideal model delta sigma weight residual 111.07 105.68 5.39 1.07e+00 8.73e-01 2.54e+01 angle pdb=" CA PRO A 88 " pdb=" N PRO A 88 " pdb=" CD PRO A 88 " ideal model delta sigma weight residual 112.00 105.01 6.99 1.40e+00 5.10e-01 2.49e+01 angle pdb=" N THR A 147 " pdb=" CA THR A 147 " pdb=" C THR A 147 " ideal model delta sigma weight residual 111.07 106.06 5.01 1.07e+00 8.73e-01 2.19e+01 ... (remaining 6001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 2296 17.47 - 34.93: 259 34.93 - 52.40: 49 52.40 - 69.86: 18 69.86 - 87.33: 8 Dihedral angle restraints: 2630 sinusoidal: 931 harmonic: 1699 Sorted by residual: dihedral pdb=" CD ARG A 308 " pdb=" NE ARG A 308 " pdb=" CZ ARG A 308 " pdb=" NH1 ARG A 308 " ideal model delta sinusoidal sigma weight residual 0.00 -62.69 62.69 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" CD ARG B 123 " pdb=" NE ARG B 123 " pdb=" CZ ARG B 123 " pdb=" NH1 ARG B 123 " ideal model delta sinusoidal sigma weight residual 0.00 -29.82 29.82 1 1.00e+01 1.00e-02 1.27e+01 dihedral pdb=" CB GLU B 22 " pdb=" CG GLU B 22 " pdb=" CD GLU B 22 " pdb=" OE1 GLU B 22 " ideal model delta sinusoidal sigma weight residual 0.00 87.33 -87.33 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 2627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 546 0.051 - 0.102: 133 0.102 - 0.153: 35 0.153 - 0.203: 3 0.203 - 0.254: 2 Chirality restraints: 719 Sorted by residual: chirality pdb=" CA VAL A 6 " pdb=" N VAL A 6 " pdb=" C VAL A 6 " pdb=" CB VAL A 6 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PRO A 136 " pdb=" N PRO A 136 " pdb=" C PRO A 136 " pdb=" CB PRO A 136 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASP A 427 " pdb=" N ASP A 427 " pdb=" C ASP A 427 " pdb=" CB ASP A 427 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 716 not shown) Planarity restraints: 775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 308 " 0.989 9.50e-02 1.11e+02 4.43e-01 1.19e+02 pdb=" NE ARG A 308 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A 308 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 308 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 308 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 123 " -0.546 9.50e-02 1.11e+02 2.45e-01 3.66e+01 pdb=" NE ARG B 123 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG B 123 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 123 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 123 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 135 " -0.070 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A 136 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 136 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 136 " -0.052 5.00e-02 4.00e+02 ... (remaining 772 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 695 2.75 - 3.29: 4142 3.29 - 3.83: 6855 3.83 - 4.36: 7848 4.36 - 4.90: 13683 Nonbonded interactions: 33223 Sorted by model distance: nonbonded pdb=" OH TYR A 200 " pdb=" OD2 ASP A 353 " model vdw 2.213 3.040 nonbonded pdb=" O ALA A 267 " pdb=" N PHE A 269 " model vdw 2.302 3.120 nonbonded pdb=" OG1 THR A 80 " pdb=" OD2 ASP A 183 " model vdw 2.310 3.040 nonbonded pdb=" OG SER A 217 " pdb=" OH TYR A 256 " model vdw 2.310 3.040 nonbonded pdb=" O ASP A 52 " pdb=" OG1 THR A 55 " model vdw 2.319 3.040 ... (remaining 33218 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: 20.470 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.400 Find NCS groups from input model: 0.010 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 : 0.007 0.152 4403 Z= 0.380 Angle : 0.885 14.453 6006 Z= 0.577 Chirality : 0.049 0.254 719 Planarity : 0.020 0.443 775 Dihedral : 16.525 87.326 1534 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 1.54 % Allowed : 8.22 % Favored : 90.24 % Rotamer: Outliers : 3.24 % Allowed : 19.21 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.94 (0.36), residues: 584 helix: 1.90 (0.45), residues: 139 sheet: -0.38 (0.49), residues: 122 loop : -1.98 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 364 TYR 0.009 0.001 TYR A 271 PHE 0.016 0.002 PHE A 165 TRP 0.008 0.001 TRP A 199 HIS 0.002 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00701 ( 4403) covalent geometry : angle 0.88484 ( 6006) hydrogen bonds : bond 0.18350 ( 159) hydrogen bonds : angle 6.69217 ( 441) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6122 (ptt180) REVERT: A 419 ASP cc_start: 0.8241 (m-30) cc_final: 0.7806 (m-30) REVERT: B 53 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.5141 (mtt90) outliers start: 14 outliers final: 0 residues processed: 146 average time/residue: 0.0827 time to fit residues: 14.9662 Evaluate side-chains 75 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain B residue 53 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN B 5 GLN B 72 ASN B 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.090157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.071756 restraints weight = 12258.861| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.70 r_work: 0.2945 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 4403 Z= 0.176 Angle : 0.645 7.916 6006 Z= 0.340 Chirality : 0.046 0.231 719 Planarity : 0.007 0.125 775 Dihedral : 5.303 54.192 634 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.86 % Allowed : 5.65 % Favored : 93.49 % Rotamer: Outliers : 6.71 % Allowed : 19.44 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.99 (0.35), residues: 584 helix: 1.42 (0.42), residues: 158 sheet: -0.21 (0.52), residues: 104 loop : -1.99 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 79 TYR 0.019 0.001 TYR A 200 PHE 0.018 0.002 PHE A 227 TRP 0.025 0.002 TRP A 65 HIS 0.002 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 4403) covalent geometry : angle 0.64468 ( 6006) hydrogen bonds : bond 0.04153 ( 159) hydrogen bonds : angle 4.86358 ( 441) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8420 (m-10) cc_final: 0.7951 (m-10) REVERT: A 155 MET cc_start: 0.6837 (tpt) cc_final: 0.5760 (tmm) REVERT: A 303 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8399 (mt0) REVERT: A 308 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7206 (mtm180) REVERT: A 332 VAL cc_start: 0.8397 (t) cc_final: 0.8072 (p) REVERT: A 368 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8971 (tt) REVERT: A 369 ASN cc_start: 0.9176 (m-40) cc_final: 0.8902 (m110) REVERT: B 81 LYS cc_start: 0.8897 (mttt) cc_final: 0.8697 (ttpp) REVERT: B 120 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8266 (tm-30) REVERT: B 123 ARG cc_start: 0.6240 (mtm-85) cc_final: 0.5705 (mtt90) outliers start: 29 outliers final: 15 residues processed: 100 average time/residue: 0.0698 time to fit residues: 9.0704 Evaluate side-chains 64 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 303 GLN Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 142 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.0970 chunk 43 optimal weight: 9.9990 chunk 17 optimal weight: 30.0000 chunk 14 optimal weight: 50.0000 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 11 optimal weight: 50.0000 chunk 16 optimal weight: 5.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.087178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.068675 restraints weight = 12244.388| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.65 r_work: 0.2885 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 4403 Z= 0.252 Angle : 0.662 6.254 6006 Z= 0.358 Chirality : 0.047 0.192 719 Planarity : 0.006 0.112 775 Dihedral : 5.153 50.907 630 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.86 % Allowed : 6.51 % Favored : 92.64 % Rotamer: Outliers : 5.56 % Allowed : 21.99 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.89 (0.35), residues: 584 helix: 1.58 (0.42), residues: 157 sheet: -0.19 (0.51), residues: 110 loop : -1.97 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 79 TYR 0.010 0.001 TYR B 98 PHE 0.010 0.002 PHE A 51 TRP 0.011 0.001 TRP A 65 HIS 0.002 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00585 ( 4403) covalent geometry : angle 0.66212 ( 6006) hydrogen bonds : bond 0.04357 ( 159) hydrogen bonds : angle 4.75756 ( 441) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 44 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.7108 (tpt) cc_final: 0.5904 (tmm) REVERT: A 308 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7272 (mtm180) REVERT: B 120 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8245 (tm-30) REVERT: B 123 ARG cc_start: 0.5746 (mtm-85) cc_final: 0.5137 (mpt180) outliers start: 24 outliers final: 15 residues processed: 67 average time/residue: 0.0695 time to fit residues: 6.1750 Evaluate side-chains 55 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 142 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 21 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** 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 = 0.3353 r_free = 0.3353 target = 0.086575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.067745 restraints weight = 11972.903| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.60 r_work: 0.2891 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4403 Z= 0.207 Angle : 0.604 6.927 6006 Z= 0.321 Chirality : 0.046 0.186 719 Planarity : 0.006 0.101 775 Dihedral : 5.255 59.110 630 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.86 % Allowed : 5.65 % Favored : 93.49 % Rotamer: Outliers : 4.40 % Allowed : 22.92 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.83 (0.35), residues: 584 helix: 1.82 (0.42), residues: 157 sheet: -0.09 (0.50), residues: 110 loop : -2.09 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 308 TYR 0.008 0.001 TYR B 98 PHE 0.007 0.001 PHE B 95 TRP 0.012 0.002 TRP A 65 HIS 0.003 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 4403) covalent geometry : angle 0.60363 ( 6006) hydrogen bonds : bond 0.03728 ( 159) hydrogen bonds : angle 4.51281 ( 441) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.7326 (tpt) cc_final: 0.6187 (tmm) REVERT: A 308 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7836 (mtp180) REVERT: B 89 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8352 (mp0) REVERT: B 120 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8330 (tm-30) outliers start: 19 outliers final: 14 residues processed: 58 average time/residue: 0.0651 time to fit residues: 5.0286 Evaluate side-chains 53 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 142 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 45 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 37 optimal weight: 0.0670 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 15 optimal weight: 30.0000 chunk 50 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 overall best weight: 4.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** 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 = 0.3344 r_free = 0.3344 target = 0.086010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.067141 restraints weight = 12169.662| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.59 r_work: 0.2869 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.7060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4403 Z= 0.208 Angle : 0.589 6.879 6006 Z= 0.313 Chirality : 0.045 0.188 719 Planarity : 0.006 0.099 775 Dihedral : 5.181 58.539 630 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.86 % Allowed : 5.65 % Favored : 93.49 % Rotamer: Outliers : 5.56 % Allowed : 21.53 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.83 (0.35), residues: 584 helix: 1.94 (0.42), residues: 157 sheet: -0.22 (0.52), residues: 104 loop : -2.07 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 79 TYR 0.007 0.001 TYR A 83 PHE 0.007 0.001 PHE B 132 TRP 0.008 0.001 TRP A 65 HIS 0.003 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 4403) covalent geometry : angle 0.58858 ( 6006) hydrogen bonds : bond 0.03640 ( 159) hydrogen bonds : angle 4.43319 ( 441) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 47 time to evaluate : 0.178 Fit side-chains REVERT: A 155 MET cc_start: 0.7543 (tpt) cc_final: 0.6438 (tmm) REVERT: A 308 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7734 (mtp180) REVERT: B 89 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8377 (mp0) REVERT: B 120 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8219 (tm-30) outliers start: 24 outliers final: 17 residues processed: 68 average time/residue: 0.0641 time to fit residues: 5.8068 Evaluate side-chains 56 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 142 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 53 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** 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 = 0.3376 r_free = 0.3376 target = 0.087703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.068874 restraints weight = 12242.909| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.62 r_work: 0.2909 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.7209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4403 Z= 0.120 Angle : 0.543 6.429 6006 Z= 0.291 Chirality : 0.043 0.184 719 Planarity : 0.005 0.096 775 Dihedral : 4.965 58.228 630 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.86 % Allowed : 4.62 % Favored : 94.52 % Rotamer: Outliers : 2.78 % Allowed : 24.07 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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 (0.35), residues: 584 helix: 2.09 (0.43), residues: 158 sheet: 0.12 (0.53), residues: 102 loop : -2.04 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 79 TYR 0.006 0.001 TYR A 271 PHE 0.019 0.001 PHE A 227 TRP 0.007 0.001 TRP A 290 HIS 0.001 0.000 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4403) covalent geometry : angle 0.54298 ( 6006) hydrogen bonds : bond 0.03297 ( 159) hydrogen bonds : angle 4.24564 ( 441) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.178 Fit side-chains REVERT: A 128 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7417 (m-80) REVERT: A 155 MET cc_start: 0.7526 (tpt) cc_final: 0.6412 (tmm) REVERT: A 308 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7724 (mtp180) REVERT: B 48 GLN cc_start: 0.8539 (mp10) cc_final: 0.8302 (mp10) REVERT: B 89 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8238 (mp0) REVERT: B 120 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8062 (tm-30) outliers start: 12 outliers final: 8 residues processed: 57 average time/residue: 0.0736 time to fit residues: 5.5089 Evaluate side-chains 51 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 127 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 40.0000 chunk 9 optimal weight: 50.0000 chunk 33 optimal weight: 0.0020 chunk 20 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** 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 = 0.3366 r_free = 0.3366 target = 0.087331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.068621 restraints weight = 12058.144| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.59 r_work: 0.2898 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.7351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4403 Z= 0.142 Angle : 0.560 6.385 6006 Z= 0.298 Chirality : 0.044 0.182 719 Planarity : 0.005 0.096 775 Dihedral : 4.914 58.507 630 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.86 % Allowed : 4.79 % Favored : 94.35 % Rotamer: Outliers : 3.24 % Allowed : 25.46 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -0.56 (0.35), residues: 584 helix: 2.16 (0.42), residues: 158 sheet: 0.13 (0.53), residues: 102 loop : -1.98 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 79 TYR 0.006 0.001 TYR B 98 PHE 0.013 0.001 PHE A 227 TRP 0.007 0.001 TRP A 65 HIS 0.002 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4403) covalent geometry : angle 0.55978 ( 6006) hydrogen bonds : bond 0.03299 ( 159) hydrogen bonds : angle 4.17559 ( 441) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.179 Fit side-chains REVERT: A 128 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7209 (m-80) REVERT: A 143 ASN cc_start: 0.8886 (m-40) cc_final: 0.8634 (m-40) REVERT: A 155 MET cc_start: 0.7601 (tpt) cc_final: 0.6410 (tmm) REVERT: A 308 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7730 (mtp180) REVERT: B 89 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8298 (mp0) REVERT: B 120 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8232 (tm-30) REVERT: B 123 ARG cc_start: 0.6009 (OUTLIER) cc_final: 0.3792 (mtm-85) outliers start: 14 outliers final: 10 residues processed: 52 average time/residue: 0.0725 time to fit residues: 5.0284 Evaluate side-chains 53 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 127 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 17 optimal weight: 30.0000 chunk 34 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** 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 = 0.3337 r_free = 0.3337 target = 0.085948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.067003 restraints weight = 12236.411| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.64 r_work: 0.2847 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.7580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4403 Z= 0.161 Angle : 0.571 6.307 6006 Z= 0.305 Chirality : 0.044 0.186 719 Planarity : 0.005 0.097 775 Dihedral : 4.909 57.631 630 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.86 % Allowed : 4.62 % Favored : 94.52 % Rotamer: Outliers : 3.47 % Allowed : 25.23 % Favored : 71.30 % 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: -0.57 (0.35), residues: 584 helix: 2.21 (0.42), residues: 158 sheet: 0.06 (0.54), residues: 102 loop : -1.99 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 79 TYR 0.007 0.001 TYR B 139 PHE 0.012 0.001 PHE A 227 TRP 0.008 0.001 TRP A 65 HIS 0.003 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 4403) covalent geometry : angle 0.57144 ( 6006) hydrogen bonds : bond 0.03303 ( 159) hydrogen bonds : angle 4.22064 ( 441) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.191 Fit side-chains REVERT: A 128 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7176 (m-80) REVERT: A 155 MET cc_start: 0.7692 (tpt) cc_final: 0.6516 (tmm) REVERT: A 308 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7761 (mtp180) REVERT: A 400 LYS cc_start: 0.9246 (mttp) cc_final: 0.8437 (tmtt) REVERT: B 73 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.9114 (mt0) REVERT: B 120 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8021 (tm-30) REVERT: B 123 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.3743 (mtm-85) outliers start: 15 outliers final: 11 residues processed: 52 average time/residue: 0.0756 time to fit residues: 5.1583 Evaluate side-chains 53 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 127 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 50.0000 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 20.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN A 398 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.087981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.069165 restraints weight = 12220.862| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.64 r_work: 0.2910 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.7656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4403 Z= 0.122 Angle : 0.545 6.315 6006 Z= 0.291 Chirality : 0.043 0.184 719 Planarity : 0.005 0.096 775 Dihedral : 4.696 55.406 630 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.68 % Allowed : 4.62 % Favored : 94.69 % Rotamer: Outliers : 3.24 % Allowed : 25.46 % Favored : 71.30 % 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: -0.50 (0.35), residues: 584 helix: 2.29 (0.42), residues: 158 sheet: -0.17 (0.51), residues: 110 loop : -1.89 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 79 TYR 0.005 0.001 TYR A 271 PHE 0.012 0.001 PHE A 227 TRP 0.007 0.001 TRP A 354 HIS 0.002 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4403) covalent geometry : angle 0.54480 ( 6006) hydrogen bonds : bond 0.03081 ( 159) hydrogen bonds : angle 4.12429 ( 441) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.192 Fit side-chains REVERT: A 128 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7153 (m-80) REVERT: A 155 MET cc_start: 0.7656 (tpt) cc_final: 0.6466 (tmm) REVERT: A 308 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7858 (mtp180) REVERT: A 400 LYS cc_start: 0.9229 (mttp) cc_final: 0.8401 (tmtt) REVERT: B 120 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8063 (tm-30) REVERT: B 123 ARG cc_start: 0.5756 (OUTLIER) cc_final: 0.3583 (mtm-85) outliers start: 14 outliers final: 10 residues processed: 53 average time/residue: 0.0718 time to fit residues: 5.0011 Evaluate side-chains 52 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 56 optimal weight: 0.0470 chunk 11 optimal weight: 50.0000 chunk 24 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** 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 = 0.3400 r_free = 0.3400 target = 0.089140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.070453 restraints weight = 12049.943| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.61 r_work: 0.2945 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.7757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 4403 Z= 0.111 Angle : 0.537 6.235 6006 Z= 0.287 Chirality : 0.043 0.180 719 Planarity : 0.005 0.096 775 Dihedral : 4.483 51.973 630 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.68 % Allowed : 3.94 % Favored : 95.38 % Rotamer: Outliers : 3.24 % Allowed : 24.31 % Favored : 72.45 % 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: -0.37 (0.36), residues: 584 helix: 2.43 (0.42), residues: 159 sheet: -0.05 (0.51), residues: 110 loop : -1.85 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 79 TYR 0.005 0.001 TYR A 271 PHE 0.012 0.001 PHE A 227 TRP 0.008 0.001 TRP A 354 HIS 0.001 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 4403) covalent geometry : angle 0.53685 ( 6006) hydrogen bonds : bond 0.02964 ( 159) hydrogen bonds : angle 4.01521 ( 441) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.139 Fit side-chains REVERT: A 65 TRP cc_start: 0.8674 (m-90) cc_final: 0.8201 (m-10) REVERT: A 128 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7007 (m-80) REVERT: A 155 MET cc_start: 0.7644 (tpt) cc_final: 0.6371 (tmm) REVERT: A 308 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7806 (mtp180) REVERT: A 400 LYS cc_start: 0.9232 (mttp) cc_final: 0.8400 (tmtt) REVERT: B 120 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8332 (tm-30) REVERT: B 123 ARG cc_start: 0.6103 (OUTLIER) cc_final: 0.3773 (mtm-85) outliers start: 14 outliers final: 9 residues processed: 52 average time/residue: 0.0750 time to fit residues: 5.0567 Evaluate side-chains 51 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 57 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 50.0000 chunk 24 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.084032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.065040 restraints weight = 12484.308| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.62 r_work: 0.2806 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.7879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 4403 Z= 0.296 Angle : 0.647 6.572 6006 Z= 0.343 Chirality : 0.047 0.191 719 Planarity : 0.006 0.097 775 Dihedral : 4.960 54.184 630 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.16 % Favored : 93.15 % Rotamer: Outliers : 3.24 % Allowed : 24.54 % Favored : 72.22 % 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: -0.50 (0.36), residues: 584 helix: 2.27 (0.41), residues: 158 sheet: -0.31 (0.51), residues: 112 loop : -1.81 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 386 TYR 0.009 0.001 TYR A 377 PHE 0.008 0.001 PHE A 227 TRP 0.008 0.002 TRP A 65 HIS 0.005 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00685 ( 4403) covalent geometry : angle 0.64660 ( 6006) hydrogen bonds : bond 0.03642 ( 159) hydrogen bonds : angle 4.43432 ( 441) =============================================================================== Job complete usr+sys time: 1599.86 seconds wall clock time: 28 minutes 12.87 seconds (1692.87 seconds total)