Starting phenix.real_space_refine on Thu Mar 6 07:28:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ghb_40039/03_2025/8ghb_40039.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghb_40039/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ghb_40039/03_2025/8ghb_40039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghb_40039/03_2025/8ghb_40039.map" model { file = "/net/cci-nas-00/data/ceres_data/8ghb_40039/03_2025/8ghb_40039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghb_40039/03_2025/8ghb_40039.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.62, per 1000 atoms: 0.87 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: 1.57 Conformation dependent library (CDL) restraints added in 706.2 milliseconds 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: 0.61 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: 1.47 Time building geometry restraints manager: 1.60 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: 2.340 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.640 Find NCS groups from input model: 0.040 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:14.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.180 ------------------------------------------------------------------------------- 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= 0.382 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 : 4.28 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (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 TRP 0.013 0.002 TRP A 208 HIS 0.014 0.002 HIS A 360 PHE 0.023 0.002 PHE A 94 TYR 0.013 0.002 TYR A 97 ARG 0.020 0.001 ARG A 98 *********************** 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 : 0.665 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: 1.4799 time to fit residues: 164.1805 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 : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 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 = 0.3494 r_free = 0.3494 target = 0.104093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.090138 restraints weight = 9729.727| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.72 r_work: 0.3193 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5428 Z= 0.261 Angle : 0.580 7.132 7378 Z= 0.299 Chirality : 0.042 0.153 796 Planarity : 0.005 0.051 959 Dihedral : 4.462 17.862 715 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.46 % Allowed : 10.37 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.31), residues: 654 helix: 0.41 (0.29), residues: 294 sheet: 0.44 (0.54), residues: 72 loop : -0.07 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 197 HIS 0.011 0.001 HIS A 51 PHE 0.009 0.001 PHE A 278 TYR 0.015 0.002 TYR A 460 ARG 0.005 0.001 ARG A 3 *********************** 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: 14 poor density : 64 time to evaluate : 0.614 Fit side-chains REVERT: A 21 ARG cc_start: 0.7404 (tpt90) cc_final: 0.7149 (tpt170) REVERT: A 32 GLU cc_start: 0.8608 (pt0) cc_final: 0.8363 (pt0) REVERT: A 68 HIS cc_start: 0.8119 (t70) cc_final: 0.7856 (t-170) REVERT: A 82 THR cc_start: 0.9273 (p) cc_final: 0.8911 (t) REVERT: A 110 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 133 LYS cc_start: 0.8690 (mttt) cc_final: 0.8332 (mtpp) REVERT: A 159 ASP cc_start: 0.8654 (m-30) cc_final: 0.8279 (m-30) REVERT: A 168 GLU cc_start: 0.8292 (tp30) cc_final: 0.8027 (mm-30) REVERT: A 185 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8085 (mtm) REVERT: A 435 GLN cc_start: 0.8974 (tt0) cc_final: 0.8634 (mp10) REVERT: A 589 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8427 (tt) REVERT: A 603 ASP cc_start: 0.8567 (t0) cc_final: 0.8209 (t0) outliers start: 14 outliers final: 4 residues processed: 72 average time/residue: 1.2798 time to fit residues: 96.2978 Evaluate side-chains 68 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU 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 20 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3463 r_free = 0.3463 target = 0.101911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.087918 restraints weight = 9763.151| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.71 r_work: 0.3156 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 5428 Z= 0.306 Angle : 0.577 7.744 7378 Z= 0.289 Chirality : 0.042 0.143 796 Planarity : 0.005 0.048 959 Dihedral : 4.291 14.340 715 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.34 % Allowed : 12.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.32), residues: 654 helix: 0.96 (0.30), residues: 293 sheet: 0.44 (0.55), residues: 72 loop : 0.13 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 197 HIS 0.009 0.001 HIS A 51 PHE 0.013 0.001 PHE A 482 TYR 0.014 0.002 TYR A 460 ARG 0.007 0.001 ARG A 156 *********************** 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: 19 poor density : 65 time to evaluate : 0.583 Fit side-chains REVERT: A 32 GLU cc_start: 0.8659 (pt0) cc_final: 0.8413 (pt0) REVERT: A 68 HIS cc_start: 0.8120 (t70) cc_final: 0.7866 (t-170) REVERT: A 110 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7911 (tm-30) REVERT: A 133 LYS cc_start: 0.8690 (mttt) cc_final: 0.8263 (tppt) REVERT: A 156 ARG cc_start: 0.8319 (ttp-110) cc_final: 0.7896 (ptm-80) REVERT: A 159 ASP cc_start: 0.8618 (m-30) cc_final: 0.8345 (m-30) REVERT: A 168 GLU cc_start: 0.8244 (tp30) cc_final: 0.7891 (tp30) REVERT: A 435 GLN cc_start: 0.9033 (tt0) cc_final: 0.8617 (mp10) REVERT: A 589 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8413 (tt) REVERT: A 603 ASP cc_start: 0.8687 (t0) cc_final: 0.8291 (t0) outliers start: 19 outliers final: 5 residues processed: 77 average time/residue: 1.2242 time to fit residues: 98.5291 Evaluate side-chains 64 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 45 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.102524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088143 restraints weight = 10062.901| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.82 r_work: 0.3155 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2188 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= 0.260 Angle : 0.553 8.102 7378 Z= 0.278 Chirality : 0.041 0.220 796 Planarity : 0.004 0.048 959 Dihedral : 4.213 14.528 715 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.34 % Allowed : 13.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.32), residues: 654 helix: 1.23 (0.30), residues: 295 sheet: 0.29 (0.55), residues: 72 loop : 0.19 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 176 HIS 0.009 0.001 HIS A 51 PHE 0.012 0.001 PHE A 482 TYR 0.014 0.001 TYR A 460 ARG 0.005 0.000 ARG A 21 *********************** 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 85 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.609 Fit side-chains REVERT: A 32 GLU cc_start: 0.8669 (pt0) cc_final: 0.8397 (pt0) REVERT: A 98 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8407 (ptp-110) REVERT: A 133 LYS cc_start: 0.8695 (mttt) cc_final: 0.8273 (tppt) REVERT: A 156 ARG cc_start: 0.8297 (ttp-110) cc_final: 0.7766 (ptm-80) REVERT: A 159 ASP cc_start: 0.8637 (m-30) cc_final: 0.8340 (m-30) REVERT: A 168 GLU cc_start: 0.8230 (tp30) cc_final: 0.7992 (mm-30) REVERT: A 435 GLN cc_start: 0.9059 (tt0) cc_final: 0.8603 (mp10) REVERT: A 589 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8475 (tt) REVERT: A 603 ASP cc_start: 0.8691 (t0) cc_final: 0.8220 (t0) outliers start: 19 outliers final: 6 residues processed: 79 average time/residue: 1.2404 time to fit residues: 102.5205 Evaluate side-chains 68 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 184 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 0.0050 chunk 59 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.103434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.089071 restraints weight = 9850.473| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.82 r_work: 0.3170 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2324 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= 0.202 Angle : 0.556 9.310 7378 Z= 0.274 Chirality : 0.041 0.188 796 Planarity : 0.004 0.048 959 Dihedral : 4.116 13.574 715 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.87 % Allowed : 14.76 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.32), residues: 654 helix: 1.33 (0.30), residues: 296 sheet: 0.04 (0.55), residues: 71 loop : 0.26 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 70 HIS 0.007 0.001 HIS A 51 PHE 0.011 0.001 PHE A 278 TYR 0.013 0.001 TYR A 460 ARG 0.005 0.000 ARG A 485 *********************** 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 86 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.579 Fit side-chains REVERT: A 32 GLU cc_start: 0.8656 (pt0) cc_final: 0.8382 (pt0) REVERT: A 98 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8387 (ptp-110) REVERT: A 110 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 133 LYS cc_start: 0.8688 (mttt) cc_final: 0.8282 (tppt) REVERT: A 156 ARG cc_start: 0.8302 (ttp-110) cc_final: 0.7791 (ptm-80) REVERT: A 159 ASP cc_start: 0.8643 (m-30) cc_final: 0.8348 (m-30) REVERT: A 435 GLN cc_start: 0.9007 (tt0) cc_final: 0.8581 (mp10) REVERT: A 589 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8486 (tt) REVERT: A 603 ASP cc_start: 0.8675 (t0) cc_final: 0.8202 (t0) outliers start: 22 outliers final: 7 residues processed: 79 average time/residue: 1.1965 time to fit residues: 98.9222 Evaluate side-chains 68 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 25 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.102707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.088373 restraints weight = 9853.212| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.78 r_work: 0.3169 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5428 Z= 0.242 Angle : 0.562 7.816 7378 Z= 0.278 Chirality : 0.041 0.171 796 Planarity : 0.004 0.045 959 Dihedral : 4.069 14.026 715 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.51 % Allowed : 15.99 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.32), residues: 654 helix: 1.35 (0.30), residues: 296 sheet: -0.06 (0.55), residues: 73 loop : 0.30 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 70 HIS 0.007 0.001 HIS A 51 PHE 0.012 0.001 PHE A 278 TYR 0.013 0.001 TYR A 460 ARG 0.006 0.000 ARG A 485 *********************** 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 82 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.595 Fit side-chains REVERT: A 32 GLU cc_start: 0.8673 (pt0) cc_final: 0.8387 (pt0) REVERT: A 98 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8376 (ptp-110) REVERT: A 110 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7669 (tm-30) REVERT: A 133 LYS cc_start: 0.8680 (mttt) cc_final: 0.8280 (tppt) REVERT: A 146 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: A 156 ARG cc_start: 0.8294 (ttp-110) cc_final: 0.7771 (ptm-80) REVERT: A 159 ASP cc_start: 0.8652 (m-30) cc_final: 0.8368 (m-30) REVERT: A 414 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.8145 (m-80) REVERT: A 589 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8476 (tt) REVERT: A 603 ASP cc_start: 0.8680 (t0) cc_final: 0.8184 (t0) outliers start: 20 outliers final: 5 residues processed: 75 average time/residue: 1.1881 time to fit residues: 93.2716 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 : 0.565 ------------------------------------------------------------------------------- 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 137 GLN Chi-restraints excluded: chain A residue 146 GLU 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 37 optimal weight: 2.9990 chunk 6 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.0770 chunk 60 optimal weight: 1.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.103248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.088818 restraints weight = 9886.303| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.81 r_work: 0.3174 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5428 Z= 0.211 Angle : 0.553 7.572 7378 Z= 0.274 Chirality : 0.040 0.159 796 Planarity : 0.004 0.046 959 Dihedral : 4.037 13.981 715 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.61 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.33), residues: 654 helix: 1.43 (0.30), residues: 295 sheet: -0.08 (0.55), residues: 73 loop : 0.34 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 176 HIS 0.007 0.001 HIS A 51 PHE 0.010 0.001 PHE A 278 TYR 0.013 0.001 TYR A 460 ARG 0.008 0.000 ARG A 485 *********************** 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 : 0.637 Fit side-chains REVERT: A 30 ARG cc_start: 0.8215 (ptp-170) cc_final: 0.7934 (ptt-90) REVERT: A 32 GLU cc_start: 0.8681 (pt0) cc_final: 0.8387 (pt0) REVERT: A 98 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8354 (ttp-110) REVERT: A 110 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7582 (tm-30) REVERT: A 146 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: A 156 ARG cc_start: 0.8330 (ttp-110) cc_final: 0.7858 (ptm-80) REVERT: A 159 ASP cc_start: 0.8660 (m-30) cc_final: 0.8346 (m-30) REVERT: A 168 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7910 (tp30) REVERT: A 435 GLN cc_start: 0.9164 (tt0) cc_final: 0.8578 (mp10) REVERT: A 589 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8495 (tt) REVERT: A 603 ASP cc_start: 0.8651 (t0) cc_final: 0.8149 (t0) outliers start: 22 outliers final: 6 residues processed: 80 average time/residue: 1.3536 time to fit residues: 113.1152 Evaluate side-chains 68 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 137 GLN Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 168 GLU 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 3 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3471 r_free = 0.3471 target = 0.102484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.088004 restraints weight = 9968.793| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.78 r_work: 0.3151 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5428 Z= 0.271 Angle : 0.588 9.111 7378 Z= 0.289 Chirality : 0.041 0.150 796 Planarity : 0.004 0.045 959 Dihedral : 4.059 14.282 715 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.39 % Allowed : 16.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.32), residues: 654 helix: 1.39 (0.30), residues: 294 sheet: -0.08 (0.55), residues: 73 loop : 0.35 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 70 HIS 0.006 0.001 HIS A 51 PHE 0.013 0.001 PHE A 278 TYR 0.014 0.001 TYR A 460 ARG 0.008 0.000 ARG A 485 *********************** 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 87 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8698 (pt0) cc_final: 0.8389 (pt0) REVERT: A 98 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8335 (ptp-110) REVERT: A 110 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7662 (tm-30) REVERT: A 146 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: A 156 ARG cc_start: 0.8303 (ttp-110) cc_final: 0.7823 (ptm-80) REVERT: A 159 ASP cc_start: 0.8673 (m-30) cc_final: 0.8309 (m-30) REVERT: A 414 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8269 (m-80) REVERT: A 435 GLN cc_start: 0.9177 (tt0) cc_final: 0.8590 (mp10) REVERT: A 485 ARG cc_start: 0.8477 (mtp85) cc_final: 0.7990 (mtp85) REVERT: A 589 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8503 (tt) REVERT: A 603 ASP cc_start: 0.8635 (t0) cc_final: 0.8153 (t0) outliers start: 25 outliers final: 8 residues processed: 80 average time/residue: 1.2324 time to fit residues: 103.1632 Evaluate side-chains 71 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 121 LEU 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 354 LEU 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 2 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 0.0470 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 0.0570 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 A 400 ASN A 547 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.103800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.089438 restraints weight = 9806.924| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.78 r_work: 0.3181 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2664 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= 0.194 Angle : 0.576 9.229 7378 Z= 0.282 Chirality : 0.040 0.148 796 Planarity : 0.004 0.046 959 Dihedral : 4.045 14.020 715 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.99 % Allowed : 17.93 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.33), residues: 654 helix: 1.46 (0.30), residues: 294 sheet: -0.13 (0.54), residues: 73 loop : 0.40 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 176 HIS 0.007 0.001 HIS A 51 PHE 0.009 0.001 PHE A 278 TYR 0.013 0.001 TYR A 460 ARG 0.007 0.000 ARG A 485 *********************** 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 79 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.646 Fit side-chains REVERT: A 30 ARG cc_start: 0.8129 (ptp-170) cc_final: 0.7877 (ptt-90) REVERT: A 32 GLU cc_start: 0.8666 (pt0) cc_final: 0.8354 (pt0) REVERT: A 98 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8238 (ttp-110) REVERT: A 110 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7532 (tm-30) REVERT: A 146 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7962 (mp0) REVERT: A 156 ARG cc_start: 0.8318 (ttp-110) cc_final: 0.7857 (ptm-80) REVERT: A 159 ASP cc_start: 0.8656 (m-30) cc_final: 0.8314 (m-30) REVERT: A 414 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: A 435 GLN cc_start: 0.9135 (tt0) cc_final: 0.8538 (mp10) REVERT: A 589 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8502 (tt) REVERT: A 603 ASP cc_start: 0.8604 (t0) cc_final: 0.8117 (t0) outliers start: 17 outliers final: 8 residues processed: 74 average time/residue: 1.2169 time to fit residues: 94.2259 Evaluate side-chains 71 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 121 LEU Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 354 LEU 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 51 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 64 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 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 231 GLN A 287 ASN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 ASN ** 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 = 0.3487 r_free = 0.3487 target = 0.103309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.089365 restraints weight = 9926.546| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.72 r_work: 0.3174 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2660 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= 0.221 Angle : 0.599 9.520 7378 Z= 0.293 Chirality : 0.040 0.149 796 Planarity : 0.004 0.046 959 Dihedral : 4.030 14.120 715 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 : 3.16 % Allowed : 17.75 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.33), residues: 654 helix: 1.42 (0.30), residues: 293 sheet: -0.08 (0.54), residues: 73 loop : 0.42 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 176 HIS 0.007 0.001 HIS A 51 PHE 0.011 0.001 PHE A 278 TYR 0.013 0.001 TYR A 460 ARG 0.010 0.001 ARG A 485 ********************** 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 76 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.673 Fit side-chains REVERT: A 32 GLU cc_start: 0.8650 (pt0) cc_final: 0.8358 (pt0) REVERT: A 110 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7555 (tm-30) REVERT: A 146 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: A 156 ARG cc_start: 0.8331 (ttp-110) cc_final: 0.7882 (ptm-80) REVERT: A 159 ASP cc_start: 0.8660 (m-30) cc_final: 0.8318 (m-30) REVERT: A 414 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8205 (m-80) REVERT: A 435 GLN cc_start: 0.9133 (tt0) cc_final: 0.8562 (mp10) REVERT: A 589 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8549 (tt) REVERT: A 603 ASP cc_start: 0.8582 (t0) cc_final: 0.8094 (t0) outliers start: 18 outliers final: 10 residues processed: 71 average time/residue: 1.1478 time to fit residues: 85.9048 Evaluate side-chains 70 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 137 GLN Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 354 LEU 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 Chi-restraints excluded: chain A residue 597 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 0.0770 chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 55 optimal weight: 0.0000 overall best weight: 0.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.104339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.090089 restraints weight = 9914.935| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.79 r_work: 0.3156 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5428 Z= 0.183 Angle : 0.589 9.460 7378 Z= 0.287 Chirality : 0.040 0.146 796 Planarity : 0.004 0.046 959 Dihedral : 4.026 15.006 715 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.28 % Allowed : 18.80 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.33), residues: 654 helix: 1.47 (0.30), residues: 293 sheet: -0.15 (0.54), residues: 73 loop : 0.44 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 176 HIS 0.007 0.001 HIS A 51 PHE 0.009 0.001 PHE A 352 TYR 0.012 0.001 TYR A 460 ARG 0.010 0.000 ARG A 485 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3944.44 seconds wall clock time: 68 minutes 8.66 seconds (4088.66 seconds total)