Starting phenix.real_space_refine on Fri Aug 22 15:51:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ghb_40039/08_2025/8ghb_40039.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghb_40039/08_2025/8ghb_40039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ghb_40039/08_2025/8ghb_40039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghb_40039/08_2025/8ghb_40039.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ghb_40039/08_2025/8ghb_40039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghb_40039/08_2025/8ghb_40039.map" } resolution = 2.76 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= 0.034 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: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 34 5.16 5 C 3379 2.51 5 N 920 2.21 5 O 955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5289 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5288 Classifications: {'peptide': 658} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 614} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.50, per 1000 atoms: 0.28 Number of scatterers: 5289 At special positions: 0 Unit cell: (75.44, 62.32, 107.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 34 16.00 O 955 8.00 N 920 7.00 C 3379 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: 0.50 Conformation dependent library (CDL) restraints added in 208.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 5 sheets defined 50.0% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 122 through 139 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.534A pdb=" N LEU A 160 " --> pdb=" O LYS A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 167 through 192 removed outlier: 3.519A pdb=" N TYR A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 224 through 235 removed outlier: 4.168A pdb=" N PHE A 232 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 271 Processing helix chain 'A' and resid 279 through 282 Processing helix chain 'A' and resid 336 through 357 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 395 through 407 Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'A' and resid 423 through 436 removed outlier: 3.621A pdb=" N ALA A 434 " --> pdb=" O ARG A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 458 through 483 Processing helix chain 'A' and resid 485 through 491 Processing helix chain 'A' and resid 492 through 504 Processing helix chain 'A' and resid 521 through 537 Processing helix chain 'A' and resid 537 through 545 Processing helix chain 'A' and resid 545 through 552 removed outlier: 4.513A pdb=" N ASP A 549 " --> pdb=" O GLN A 545 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 573 through 581 Processing helix chain 'A' and resid 583 through 597 Processing helix chain 'A' and resid 617 through 643 removed outlier: 3.846A pdb=" N LYS A 621 " --> pdb=" O GLY A 617 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.500A pdb=" N GLU A 47 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG A 5 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL A 83 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG A 7 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE A 81 " --> pdb=" O ARG A 7 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 9 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE A 77 " --> pdb=" O GLY A 11 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TRP A 13 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA A 75 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N PHE A 77 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG A 98 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP A 79 " --> pdb=" O CYS A 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 39 removed outlier: 3.808A pdb=" N LEU A 24 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 37 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 243 removed outlier: 3.569A pdb=" N VAL A 301 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU A 300 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE A 316 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET A 302 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 288 through 289 264 hydrogen bonds defined for protein. 744 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: 0.65 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1689 1.34 - 1.46: 882 1.46 - 1.57: 2806 1.57 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 5428 Sorted by residual: bond pdb=" CG1 ILE A 357 " pdb=" CD1 ILE A 357 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.21e+00 bond pdb=" CB PRO A 555 " pdb=" CG PRO A 555 " ideal model delta sigma weight residual 1.492 1.425 0.067 5.00e-02 4.00e+02 1.81e+00 bond pdb=" C ILE A 390 " pdb=" N PRO A 391 " ideal model delta sigma weight residual 1.337 1.353 -0.016 1.24e-02 6.50e+03 1.66e+00 bond pdb=" CA ILE A 390 " pdb=" C ILE A 390 " ideal model delta sigma weight residual 1.524 1.538 -0.013 1.05e-02 9.07e+03 1.62e+00 bond pdb=" CG GLU A 267 " pdb=" CD GLU A 267 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.54e+00 ... (remaining 5423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 7107 1.97 - 3.95: 228 3.95 - 5.92: 34 5.92 - 7.89: 7 7.89 - 9.87: 2 Bond angle restraints: 7378 Sorted by residual: angle pdb=" N PRO A 443 " pdb=" CA PRO A 443 " pdb=" C PRO A 443 " ideal model delta sigma weight residual 110.70 115.33 -4.63 1.22e+00 6.72e-01 1.44e+01 angle pdb=" CA ILE A 390 " pdb=" C ILE A 390 " pdb=" N PRO A 391 " ideal model delta sigma weight residual 118.88 124.08 -5.20 1.54e+00 4.22e-01 1.14e+01 angle pdb=" CA PRO A 443 " pdb=" C PRO A 443 " pdb=" N PRO A 444 " ideal model delta sigma weight residual 117.93 121.92 -3.99 1.20e+00 6.94e-01 1.11e+01 angle pdb=" CA PRO A 391 " pdb=" N PRO A 391 " pdb=" CD PRO A 391 " ideal model delta sigma weight residual 112.00 107.64 4.36 1.40e+00 5.10e-01 9.70e+00 angle pdb=" CA THR A 327 " pdb=" CB THR A 327 " pdb=" CG2 THR A 327 " ideal model delta sigma weight residual 110.50 115.56 -5.06 1.70e+00 3.46e-01 8.86e+00 ... (remaining 7373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 2968 17.33 - 34.66: 236 34.66 - 51.99: 37 51.99 - 69.32: 16 69.32 - 86.65: 4 Dihedral angle restraints: 3261 sinusoidal: 1348 harmonic: 1913 Sorted by residual: dihedral pdb=" CA ASP A 335 " pdb=" C ASP A 335 " pdb=" N PRO A 336 " pdb=" CA PRO A 336 " ideal model delta harmonic sigma weight residual 180.00 160.18 19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA THR A 537 " pdb=" C THR A 537 " pdb=" N ALA A 538 " pdb=" CA ALA A 538 " ideal model delta harmonic sigma weight residual -180.00 -161.47 -18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA LEU A 382 " pdb=" C LEU A 382 " pdb=" N HIS A 383 " pdb=" CA HIS A 383 " ideal model delta harmonic sigma weight residual -180.00 -163.63 -16.37 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 3258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 669 0.067 - 0.133: 117 0.133 - 0.200: 7 0.200 - 0.266: 2 0.266 - 0.333: 1 Chirality restraints: 796 Sorted by residual: chirality pdb=" CB THR A 327 " pdb=" CA THR A 327 " pdb=" OG1 THR A 327 " pdb=" CG2 THR A 327 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CB ILE A 390 " pdb=" CA ILE A 390 " pdb=" CG1 ILE A 390 " pdb=" CG2 ILE A 390 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CG LEU A 303 " pdb=" CB LEU A 303 " pdb=" CD1 LEU A 303 " pdb=" CD2 LEU A 303 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 793 not shown) Planarity restraints: 959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 185 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C MET A 185 " -0.051 2.00e-02 2.50e+03 pdb=" O MET A 185 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 186 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 335 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.31e+00 pdb=" N PRO A 336 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 336 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 336 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 80 " -0.227 9.50e-02 1.11e+02 1.02e-01 6.76e+00 pdb=" NE ARG A 80 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 80 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 80 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 80 " -0.005 2.00e-02 2.50e+03 ... (remaining 956 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 60 2.64 - 3.20: 4469 3.20 - 3.77: 9220 3.77 - 4.33: 12610 4.33 - 4.90: 20277 Nonbonded interactions: 46636 Sorted by model distance: nonbonded pdb=" OXT ILE A 663 " pdb="FE FE2 A 901 " model vdw 2.072 3.000 nonbonded pdb=" NE2 HIS A 360 " pdb="FE FE2 A 901 " model vdw 2.150 3.080 nonbonded pdb=" NE2 HIS A 365 " pdb="FE FE2 A 901 " model vdw 2.222 3.080 nonbonded pdb=" O SER A 594 " pdb=" OG SER A 598 " model vdw 2.289 3.040 nonbonded pdb=" O ILE A 371 " pdb=" OG1 THR A 375 " model vdw 2.302 3.040 ... (remaining 46631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.230 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 : 0.006 0.067 5428 Z= 0.238 Angle : 0.821 9.866 7378 Z= 0.425 Chirality : 0.052 0.333 796 Planarity : 0.009 0.102 959 Dihedral : 13.616 86.652 2021 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.29), residues: 654 helix: -1.16 (0.25), residues: 291 sheet: 0.65 (0.56), residues: 78 loop : -0.55 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 98 TYR 0.013 0.002 TYR A 97 PHE 0.023 0.002 PHE A 94 TRP 0.013 0.002 TRP A 208 HIS 0.014 0.002 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00576 ( 5428) covalent geometry : angle 0.82059 ( 7378) hydrogen bonds : bond 0.17136 ( 264) hydrogen bonds : angle 7.87422 ( 744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.229 Fit side-chains REVERT: A 5 ARG cc_start: 0.8615 (ttm-80) cc_final: 0.8174 (tpt-90) REVERT: A 32 GLU cc_start: 0.8477 (pt0) cc_final: 0.8234 (pt0) REVERT: A 68 HIS cc_start: 0.7788 (t70) cc_final: 0.7329 (t70) REVERT: A 110 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7204 (tm-30) REVERT: A 435 GLN cc_start: 0.8766 (tt0) cc_final: 0.8428 (mp10) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.6334 time to fit residues: 70.2575 Evaluate side-chains 58 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 220 GLN A 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.105015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.090990 restraints weight = 9884.488| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.75 r_work: 0.3206 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5428 Z= 0.152 Angle : 0.577 7.212 7378 Z= 0.299 Chirality : 0.041 0.163 796 Planarity : 0.005 0.052 959 Dihedral : 4.480 18.501 715 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.64 % Allowed : 10.02 % Favored : 87.35 % 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: 0.19 (0.31), residues: 654 helix: 0.45 (0.29), residues: 293 sheet: 0.41 (0.54), residues: 72 loop : -0.13 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 3 TYR 0.015 0.002 TYR A 460 PHE 0.009 0.001 PHE A 482 TRP 0.007 0.001 TRP A 498 HIS 0.013 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5428) covalent geometry : angle 0.57735 ( 7378) hydrogen bonds : bond 0.04411 ( 264) hydrogen bonds : angle 5.99755 ( 744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.151 Fit side-chains REVERT: A 5 ARG cc_start: 0.8953 (ttm-80) cc_final: 0.8308 (tpt-90) REVERT: A 21 ARG cc_start: 0.7374 (tpt90) cc_final: 0.7139 (tpt170) REVERT: A 32 GLU cc_start: 0.8612 (pt0) cc_final: 0.8387 (pt0) REVERT: A 68 HIS cc_start: 0.8092 (t70) cc_final: 0.7847 (t-170) REVERT: A 82 THR cc_start: 0.9260 (p) cc_final: 0.8917 (t) REVERT: A 110 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7627 (tm-30) REVERT: A 133 LYS cc_start: 0.8684 (mttt) cc_final: 0.8331 (mtpp) REVERT: A 159 ASP cc_start: 0.8651 (m-30) cc_final: 0.8272 (m-30) REVERT: A 168 GLU cc_start: 0.8287 (tp30) cc_final: 0.7905 (tp30) REVERT: A 185 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8141 (mtm) REVERT: A 435 GLN cc_start: 0.8970 (tt0) cc_final: 0.8610 (mp10) REVERT: A 589 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8417 (tt) outliers start: 15 outliers final: 3 residues processed: 72 average time/residue: 0.6622 time to fit residues: 49.5143 Evaluate side-chains 64 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 13 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.104731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.090632 restraints weight = 9742.047| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.74 r_work: 0.3192 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5428 Z= 0.153 Angle : 0.550 7.748 7378 Z= 0.276 Chirality : 0.041 0.148 796 Planarity : 0.005 0.049 959 Dihedral : 4.251 14.115 715 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.81 % Allowed : 12.83 % Favored : 84.36 % 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: 0.74 (0.32), residues: 654 helix: 0.98 (0.30), residues: 293 sheet: 0.44 (0.55), residues: 72 loop : 0.15 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 156 TYR 0.014 0.002 TYR A 460 PHE 0.010 0.001 PHE A 482 TRP 0.007 0.001 TRP A 197 HIS 0.010 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 5428) covalent geometry : angle 0.55045 ( 7378) hydrogen bonds : bond 0.04228 ( 264) hydrogen bonds : angle 5.69563 ( 744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.219 Fit side-chains REVERT: A 32 GLU cc_start: 0.8599 (pt0) cc_final: 0.8370 (pt0) REVERT: A 68 HIS cc_start: 0.8106 (t70) cc_final: 0.7855 (t-170) REVERT: A 133 LYS cc_start: 0.8679 (mttt) cc_final: 0.8267 (tppt) REVERT: A 159 ASP cc_start: 0.8651 (m-30) cc_final: 0.8327 (m-30) REVERT: A 168 GLU cc_start: 0.8241 (tp30) cc_final: 0.8007 (mm-30) REVERT: A 219 ARG cc_start: 0.8376 (tmt-80) cc_final: 0.7744 (tpt90) REVERT: A 435 GLN cc_start: 0.8984 (tt0) cc_final: 0.8611 (mp10) REVERT: A 589 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8398 (tt) REVERT: A 603 ASP cc_start: 0.8562 (t0) cc_final: 0.8138 (t0) outliers start: 16 outliers final: 4 residues processed: 77 average time/residue: 0.5701 time to fit residues: 45.8449 Evaluate side-chains 68 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 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 231 GLN A 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.102652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.088765 restraints weight = 9778.243| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.72 r_work: 0.3171 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5428 Z= 0.170 Angle : 0.554 7.291 7378 Z= 0.277 Chirality : 0.041 0.145 796 Planarity : 0.004 0.048 959 Dihedral : 4.192 14.137 715 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.16 % Allowed : 13.18 % Favored : 83.66 % 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: 0.92 (0.32), residues: 654 helix: 1.19 (0.30), residues: 294 sheet: 0.34 (0.54), residues: 72 loop : 0.22 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 156 TYR 0.014 0.002 TYR A 460 PHE 0.011 0.001 PHE A 278 TRP 0.007 0.001 TRP A 197 HIS 0.007 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 5428) covalent geometry : angle 0.55390 ( 7378) hydrogen bonds : bond 0.04110 ( 264) hydrogen bonds : angle 5.52561 ( 744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.184 Fit side-chains REVERT: A 32 GLU cc_start: 0.8641 (pt0) cc_final: 0.8379 (pt0) REVERT: A 68 HIS cc_start: 0.8135 (t70) cc_final: 0.7906 (t-170) REVERT: A 110 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7582 (tm-30) REVERT: A 133 LYS cc_start: 0.8683 (mttt) cc_final: 0.8257 (tppt) REVERT: A 156 ARG cc_start: 0.8333 (ttp-110) cc_final: 0.7814 (ptm-80) REVERT: A 158 ASP cc_start: 0.8577 (m-30) cc_final: 0.8235 (m-30) REVERT: A 159 ASP cc_start: 0.8640 (m-30) cc_final: 0.8347 (m-30) REVERT: A 168 GLU cc_start: 0.8228 (tp30) cc_final: 0.7877 (tp30) REVERT: A 435 GLN cc_start: 0.9032 (tt0) cc_final: 0.8623 (mp10) REVERT: A 589 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8456 (tt) REVERT: A 603 ASP cc_start: 0.8634 (t0) cc_final: 0.8137 (t0) outliers start: 18 outliers final: 5 residues processed: 77 average time/residue: 0.5275 time to fit residues: 42.5428 Evaluate side-chains 67 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 33 optimal weight: 0.0470 chunk 51 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.102902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.088435 restraints weight = 9977.866| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.83 r_work: 0.3162 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5428 Z= 0.160 Angle : 0.557 8.525 7378 Z= 0.277 Chirality : 0.042 0.252 796 Planarity : 0.004 0.047 959 Dihedral : 4.129 14.485 715 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.51 % Allowed : 14.41 % Favored : 82.07 % 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: 0.99 (0.32), residues: 654 helix: 1.26 (0.30), residues: 295 sheet: 0.25 (0.54), residues: 72 loop : 0.28 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 485 TYR 0.014 0.001 TYR A 460 PHE 0.012 0.001 PHE A 278 TRP 0.008 0.001 TRP A 176 HIS 0.006 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 5428) covalent geometry : angle 0.55716 ( 7378) hydrogen bonds : bond 0.03991 ( 264) hydrogen bonds : angle 5.39319 ( 744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.215 Fit side-chains REVERT: A 30 ARG cc_start: 0.8146 (ptp-170) cc_final: 0.7880 (ptt-90) REVERT: A 32 GLU cc_start: 0.8672 (pt0) cc_final: 0.8417 (pt0) REVERT: A 98 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8395 (ptp-110) REVERT: A 110 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7702 (tm-30) REVERT: A 133 LYS cc_start: 0.8701 (mttt) cc_final: 0.8283 (tppt) REVERT: A 146 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: A 156 ARG cc_start: 0.8325 (ttp-110) cc_final: 0.7779 (ptm-80) REVERT: A 159 ASP cc_start: 0.8640 (m-30) cc_final: 0.8310 (m-30) REVERT: A 168 GLU cc_start: 0.8232 (tp30) cc_final: 0.7946 (tp30) REVERT: A 435 GLN cc_start: 0.9040 (tt0) cc_final: 0.8591 (mp10) REVERT: A 589 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8450 (tt) REVERT: A 603 ASP cc_start: 0.8652 (t0) cc_final: 0.8139 (t0) outliers start: 20 outliers final: 6 residues processed: 79 average time/residue: 0.5845 time to fit residues: 48.0923 Evaluate side-chains 69 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 27 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 15 optimal weight: 0.0970 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.103987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.089567 restraints weight = 9911.125| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.81 r_work: 0.3181 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5428 Z= 0.136 Angle : 0.562 9.087 7378 Z= 0.276 Chirality : 0.041 0.209 796 Planarity : 0.004 0.046 959 Dihedral : 4.080 13.813 715 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.34 % Allowed : 15.82 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.32), residues: 654 helix: 1.31 (0.30), residues: 295 sheet: 0.13 (0.54), residues: 74 loop : 0.32 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 485 TYR 0.013 0.001 TYR A 460 PHE 0.012 0.001 PHE A 278 TRP 0.010 0.001 TRP A 70 HIS 0.006 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5428) covalent geometry : angle 0.56158 ( 7378) hydrogen bonds : bond 0.03895 ( 264) hydrogen bonds : angle 5.33504 ( 744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.235 Fit side-chains REVERT: A 30 ARG cc_start: 0.8119 (ptp-170) cc_final: 0.7849 (ptt-90) REVERT: A 32 GLU cc_start: 0.8653 (pt0) cc_final: 0.8389 (pt0) REVERT: A 98 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8375 (ptp-110) REVERT: A 110 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7610 (tm-30) REVERT: A 133 LYS cc_start: 0.8684 (mttt) cc_final: 0.8275 (tppt) REVERT: A 146 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: A 156 ARG cc_start: 0.8329 (ttp-110) cc_final: 0.7793 (ptm-80) REVERT: A 159 ASP cc_start: 0.8643 (m-30) cc_final: 0.8304 (m-30) REVERT: A 168 GLU cc_start: 0.8254 (tp30) cc_final: 0.7980 (mm-30) REVERT: A 414 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: A 435 GLN cc_start: 0.9031 (tt0) cc_final: 0.8597 (mp10) REVERT: A 589 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8464 (tt) REVERT: A 603 ASP cc_start: 0.8632 (t0) cc_final: 0.8094 (t0) outliers start: 19 outliers final: 5 residues processed: 76 average time/residue: 0.5404 time to fit residues: 43.0641 Evaluate side-chains 70 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 26 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.104246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.089910 restraints weight = 9926.915| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.79 r_work: 0.3187 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5428 Z= 0.132 Angle : 0.547 7.885 7378 Z= 0.271 Chirality : 0.040 0.189 796 Planarity : 0.004 0.046 959 Dihedral : 4.022 14.574 715 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.87 % Allowed : 16.17 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.32), residues: 654 helix: 1.39 (0.30), residues: 294 sheet: 0.05 (0.55), residues: 74 loop : 0.32 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 485 TYR 0.013 0.001 TYR A 460 PHE 0.009 0.001 PHE A 278 TRP 0.011 0.001 TRP A 70 HIS 0.006 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 5428) covalent geometry : angle 0.54713 ( 7378) hydrogen bonds : bond 0.03833 ( 264) hydrogen bonds : angle 5.24088 ( 744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.242 Fit side-chains REVERT: A 32 GLU cc_start: 0.8647 (pt0) cc_final: 0.8373 (pt0) REVERT: A 98 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8302 (ptp-110) REVERT: A 110 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7575 (tm-30) REVERT: A 146 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: A 156 ARG cc_start: 0.8328 (ttp-110) cc_final: 0.7805 (ptm-80) REVERT: A 158 ASP cc_start: 0.8597 (m-30) cc_final: 0.8238 (m-30) REVERT: A 159 ASP cc_start: 0.8661 (m-30) cc_final: 0.8326 (m-30) REVERT: A 168 GLU cc_start: 0.8264 (tp30) cc_final: 0.8000 (mm-30) REVERT: A 414 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8198 (m-80) REVERT: A 435 GLN cc_start: 0.9006 (tt0) cc_final: 0.8584 (mp10) REVERT: A 485 ARG cc_start: 0.8428 (mtp85) cc_final: 0.7694 (mtp85) REVERT: A 589 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8490 (tt) REVERT: A 603 ASP cc_start: 0.8595 (t0) cc_final: 0.8048 (t0) outliers start: 22 outliers final: 5 residues processed: 79 average time/residue: 0.5856 time to fit residues: 48.2689 Evaluate side-chains 69 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 24 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 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 231 GLN A 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.103919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.089434 restraints weight = 9917.843| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.83 r_work: 0.3185 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5428 Z= 0.146 Angle : 0.595 10.044 7378 Z= 0.288 Chirality : 0.041 0.179 796 Planarity : 0.004 0.046 959 Dihedral : 4.019 14.673 715 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.99 % Allowed : 17.40 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.32), residues: 654 helix: 1.36 (0.30), residues: 295 sheet: 0.07 (0.54), residues: 74 loop : 0.38 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 485 TYR 0.014 0.001 TYR A 460 PHE 0.010 0.001 PHE A 278 TRP 0.010 0.001 TRP A 176 HIS 0.006 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 5428) covalent geometry : angle 0.59457 ( 7378) hydrogen bonds : bond 0.03859 ( 264) hydrogen bonds : angle 5.22820 ( 744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.8082 (ptp-170) cc_final: 0.7866 (ptt-90) REVERT: A 32 GLU cc_start: 0.8465 (pt0) cc_final: 0.8211 (pt0) REVERT: A 98 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8240 (ptp-110) REVERT: A 110 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7445 (tm-30) REVERT: A 146 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: A 156 ARG cc_start: 0.8276 (ttp-110) cc_final: 0.7781 (ptm-80) REVERT: A 158 ASP cc_start: 0.8534 (m-30) cc_final: 0.8177 (m-30) REVERT: A 159 ASP cc_start: 0.8590 (m-30) cc_final: 0.8269 (m-30) REVERT: A 168 GLU cc_start: 0.8103 (tp30) cc_final: 0.7793 (tp30) REVERT: A 435 GLN cc_start: 0.8884 (tt0) cc_final: 0.8560 (mp10) REVERT: A 589 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8431 (tt) REVERT: A 603 ASP cc_start: 0.8492 (t0) cc_final: 0.7978 (t0) outliers start: 17 outliers final: 7 residues processed: 76 average time/residue: 0.5495 time to fit residues: 43.7460 Evaluate side-chains 71 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 47 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.096818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.081744 restraints weight = 9549.983| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.74 r_work: 0.3016 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5428 Z= 0.167 Angle : 0.594 7.826 7378 Z= 0.293 Chirality : 0.042 0.176 796 Planarity : 0.004 0.045 959 Dihedral : 4.080 15.426 715 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.81 % Allowed : 17.40 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.32), residues: 654 helix: 1.34 (0.30), residues: 295 sheet: 0.10 (0.54), residues: 74 loop : 0.37 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 485 TYR 0.014 0.001 TYR A 460 PHE 0.012 0.001 PHE A 278 TRP 0.011 0.001 TRP A 176 HIS 0.006 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 5428) covalent geometry : angle 0.59394 ( 7378) hydrogen bonds : bond 0.03915 ( 264) hydrogen bonds : angle 5.23537 ( 744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8519 (pt0) cc_final: 0.8219 (pt0) REVERT: A 98 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8072 (ptp-110) REVERT: A 110 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7441 (tm-30) REVERT: A 146 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: A 156 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7638 (ptm-80) REVERT: A 159 ASP cc_start: 0.8614 (m-30) cc_final: 0.8211 (m-30) REVERT: A 168 GLU cc_start: 0.8109 (tp30) cc_final: 0.7718 (tp30) REVERT: A 267 GLU cc_start: 0.7325 (pt0) cc_final: 0.7123 (pt0) REVERT: A 414 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8210 (m-80) REVERT: A 435 GLN cc_start: 0.8865 (tt0) cc_final: 0.8450 (mp10) REVERT: A 589 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8326 (tt) REVERT: A 603 ASP cc_start: 0.8615 (t0) cc_final: 0.8054 (t0) outliers start: 16 outliers final: 6 residues processed: 74 average time/residue: 0.5394 time to fit residues: 41.6375 Evaluate side-chains 71 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 56 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.097696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.082662 restraints weight = 9572.288| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.76 r_work: 0.3032 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5428 Z= 0.146 Angle : 0.595 8.090 7378 Z= 0.293 Chirality : 0.041 0.175 796 Planarity : 0.004 0.046 959 Dihedral : 4.063 15.608 715 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.81 % Allowed : 17.57 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.32), residues: 654 helix: 1.37 (0.30), residues: 294 sheet: 0.03 (0.54), residues: 74 loop : 0.38 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 485 TYR 0.013 0.001 TYR A 460 PHE 0.010 0.001 PHE A 278 TRP 0.012 0.001 TRP A 176 HIS 0.006 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 5428) covalent geometry : angle 0.59464 ( 7378) hydrogen bonds : bond 0.03838 ( 264) hydrogen bonds : angle 5.19853 ( 744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.216 Fit side-chains REVERT: A 30 ARG cc_start: 0.8122 (ptp-170) cc_final: 0.7904 (ptt-90) REVERT: A 32 GLU cc_start: 0.8499 (pt0) cc_final: 0.8186 (pt0) REVERT: A 98 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8092 (ptp-110) REVERT: A 110 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7401 (tm-30) REVERT: A 146 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: A 156 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7642 (ptm-80) REVERT: A 158 ASP cc_start: 0.8506 (m-30) cc_final: 0.8116 (m-30) REVERT: A 159 ASP cc_start: 0.8595 (m-30) cc_final: 0.8190 (m-30) REVERT: A 168 GLU cc_start: 0.8095 (tp30) cc_final: 0.7736 (tp30) REVERT: A 185 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7965 (mmt) REVERT: A 414 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.8219 (m-80) REVERT: A 435 GLN cc_start: 0.8873 (tt0) cc_final: 0.8470 (mp10) REVERT: A 589 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8147 (tt) REVERT: A 603 ASP cc_start: 0.8599 (t0) cc_final: 0.8053 (t0) outliers start: 16 outliers final: 5 residues processed: 75 average time/residue: 0.5291 time to fit residues: 41.6074 Evaluate side-chains 73 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 23 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 49 optimal weight: 0.0010 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 547 GLN A 556 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.098288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.083122 restraints weight = 9563.529| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.79 r_work: 0.3038 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5428 Z= 0.139 Angle : 0.600 9.654 7378 Z= 0.292 Chirality : 0.041 0.172 796 Planarity : 0.004 0.046 959 Dihedral : 4.039 15.319 715 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.46 % Allowed : 18.10 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.33), residues: 654 helix: 1.41 (0.30), residues: 293 sheet: 0.08 (0.54), residues: 74 loop : 0.39 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 485 TYR 0.013 0.001 TYR A 460 PHE 0.009 0.001 PHE A 278 TRP 0.012 0.001 TRP A 25 HIS 0.006 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5428) covalent geometry : angle 0.60034 ( 7378) hydrogen bonds : bond 0.03804 ( 264) hydrogen bonds : angle 5.14884 ( 744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1816.55 seconds wall clock time: 31 minutes 44.63 seconds (1904.63 seconds total)