Starting phenix.real_space_refine on Sat May 10 06:17:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ghb_40039/05_2025/8ghb_40039.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghb_40039/05_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_40039/05_2025/8ghb_40039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghb_40039/05_2025/8ghb_40039.map" model { file = "/net/cci-nas-00/data/ceres_data/8ghb_40039/05_2025/8ghb_40039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghb_40039/05_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 3.89, per 1000 atoms: 0.74 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: 1.21 Conformation dependent library (CDL) restraints added in 584.7 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: 0.54 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: 1.49 Time building geometry restraints manager: 1.39 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: 2.290 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.750 Find NCS groups from input model: 0.180 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:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.170 ------------------------------------------------------------------------------- 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 : 4.28 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 Details of bonding type rmsd hydrogen bonds : bond 0.17136 ( 264) hydrogen bonds : angle 7.87422 ( 744) covalent geometry : bond 0.00576 ( 5428) covalent geometry : angle 0.82059 ( 7378) *********************** 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 : 0.619 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: 1.3640 time to fit residues: 151.5782 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 : 0.614 ------------------------------------------------------------------------------- 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 = 0.104034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.090110 restraints weight = 9730.120| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.72 r_work: 0.3193 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1658 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= 0.172 Angle : 0.580 7.118 7378 Z= 0.299 Chirality : 0.042 0.154 796 Planarity : 0.005 0.051 959 Dihedral : 4.461 17.850 715 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: 0.42 (0.29), residues: 294 sheet: 0.44 (0.54), residues: 72 loop : -0.06 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 Details of bonding type rmsd hydrogen bonds : bond 0.04496 ( 264) hydrogen bonds : angle 5.99177 ( 744) covalent geometry : bond 0.00388 ( 5428) covalent geometry : angle 0.57977 ( 7378) *********************** 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 : 0.576 Fit side-chains REVERT: A 21 ARG cc_start: 0.7405 (tpt90) cc_final: 0.7153 (tpt170) REVERT: A 32 GLU cc_start: 0.8603 (pt0) cc_final: 0.8359 (pt0) REVERT: A 68 HIS cc_start: 0.8120 (t70) cc_final: 0.7857 (t-170) REVERT: A 82 THR cc_start: 0.9271 (p) cc_final: 0.8910 (t) REVERT: A 110 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7795 (tm-30) REVERT: A 133 LYS cc_start: 0.8689 (mttt) cc_final: 0.8332 (mtpp) REVERT: A 159 ASP cc_start: 0.8652 (m-30) cc_final: 0.8280 (m-30) REVERT: A 168 GLU cc_start: 0.8294 (tp30) cc_final: 0.8030 (mm-30) REVERT: A 185 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8116 (mtm) REVERT: A 435 GLN cc_start: 0.8976 (tt0) cc_final: 0.8633 (mp10) REVERT: A 589 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8428 (tt) REVERT: A 603 ASP cc_start: 0.8563 (t0) cc_final: 0.8201 (t0) outliers start: 14 outliers final: 4 residues processed: 72 average time/residue: 1.2182 time to fit residues: 91.7142 Evaluate side-chains 66 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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: 0.8980 chunk 64 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 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 287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.089069 restraints weight = 9758.016| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.70 r_work: 0.3170 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1968 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= 0.176 Angle : 0.562 7.817 7378 Z= 0.282 Chirality : 0.041 0.145 796 Planarity : 0.005 0.048 959 Dihedral : 4.265 14.231 715 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.81 % Allowed : 13.01 % Favored : 84.18 % 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: 0.75 (0.32), residues: 654 helix: 0.99 (0.30), residues: 293 sheet: 0.42 (0.55), residues: 72 loop : 0.16 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 176 HIS 0.010 0.001 HIS A 51 PHE 0.012 0.001 PHE A 482 TYR 0.014 0.002 TYR A 460 ARG 0.005 0.000 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.04279 ( 264) hydrogen bonds : angle 5.69898 ( 744) covalent geometry : bond 0.00400 ( 5428) covalent geometry : angle 0.56206 ( 7378) *********************** 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 81 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.578 Fit side-chains REVERT: A 32 GLU cc_start: 0.8645 (pt0) cc_final: 0.8396 (pt0) REVERT: A 68 HIS cc_start: 0.8103 (t70) cc_final: 0.7860 (t-170) REVERT: A 110 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7812 (tm-30) REVERT: A 133 LYS cc_start: 0.8683 (mttt) cc_final: 0.8262 (tppt) REVERT: A 159 ASP cc_start: 0.8644 (m-30) cc_final: 0.8335 (m-30) REVERT: A 168 GLU cc_start: 0.8239 (tp30) cc_final: 0.8019 (mm-30) REVERT: A 219 ARG cc_start: 0.8388 (tmt-80) cc_final: 0.7731 (tpt90) REVERT: A 435 GLN cc_start: 0.9000 (tt0) cc_final: 0.8633 (mp10) REVERT: A 589 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8411 (tt) REVERT: A 603 ASP cc_start: 0.8612 (t0) cc_final: 0.8195 (t0) outliers start: 16 outliers final: 3 residues processed: 75 average time/residue: 1.2439 time to fit residues: 97.5622 Evaluate side-chains 66 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 64 optimal weight: 0.0970 chunk 58 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.103412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089405 restraints weight = 9957.262| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.75 r_work: 0.3176 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2125 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= 0.149 Angle : 0.538 7.191 7378 Z= 0.271 Chirality : 0.040 0.145 796 Planarity : 0.004 0.048 959 Dihedral : 4.172 14.314 715 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.51 % Allowed : 12.83 % 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: 0.93 (0.32), residues: 654 helix: 1.23 (0.30), residues: 294 sheet: 0.30 (0.55), residues: 72 loop : 0.20 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 176 HIS 0.008 0.001 HIS A 51 PHE 0.011 0.001 PHE A 482 TYR 0.014 0.001 TYR A 460 ARG 0.005 0.000 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 264) hydrogen bonds : angle 5.49858 ( 744) covalent geometry : bond 0.00340 ( 5428) covalent geometry : angle 0.53827 ( 7378) *********************** 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 86 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.590 Fit side-chains REVERT: A 21 ARG cc_start: 0.7337 (tmt170) cc_final: 0.7126 (tpt170) REVERT: A 32 GLU cc_start: 0.8645 (pt0) cc_final: 0.8370 (pt0) REVERT: A 133 LYS cc_start: 0.8678 (mttt) cc_final: 0.8259 (tppt) REVERT: A 156 ARG cc_start: 0.8317 (ttp-110) cc_final: 0.7918 (ptm-80) REVERT: A 159 ASP cc_start: 0.8625 (m-30) cc_final: 0.8354 (m-30) REVERT: A 168 GLU cc_start: 0.8223 (tp30) cc_final: 0.8015 (mm-30) REVERT: A 435 GLN cc_start: 0.9020 (tt0) cc_final: 0.8600 (mp10) REVERT: A 589 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8452 (tt) REVERT: A 603 ASP cc_start: 0.8635 (t0) cc_final: 0.8138 (t0) outliers start: 20 outliers final: 7 residues processed: 79 average time/residue: 1.1748 time to fit residues: 97.0022 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 : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 184 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3463 r_free = 0.3463 target = 0.102153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.087800 restraints weight = 9915.325| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.79 r_work: 0.3157 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5428 Z= 0.178 Angle : 0.562 8.504 7378 Z= 0.281 Chirality : 0.042 0.230 796 Planarity : 0.004 0.047 959 Dihedral : 4.151 14.156 715 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.04 % Allowed : 14.41 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.97 (0.32), residues: 654 helix: 1.26 (0.30), residues: 294 sheet: 0.31 (0.56), residues: 72 loop : 0.23 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 176 HIS 0.007 0.001 HIS A 51 PHE 0.013 0.001 PHE A 278 TYR 0.014 0.001 TYR A 460 ARG 0.005 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 264) hydrogen bonds : angle 5.40667 ( 744) covalent geometry : bond 0.00408 ( 5428) covalent geometry : angle 0.56228 ( 7378) *********************** 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: 23 poor density : 63 time to evaluate : 0.584 Fit side-chains REVERT: A 30 ARG cc_start: 0.8162 (ptp-170) cc_final: 0.7873 (ptt-90) REVERT: A 32 GLU cc_start: 0.8664 (pt0) cc_final: 0.8388 (pt0) REVERT: A 98 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8364 (ptp-110) REVERT: A 110 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7699 (tm-30) REVERT: A 133 LYS cc_start: 0.8704 (mttt) cc_final: 0.8284 (tppt) REVERT: A 156 ARG cc_start: 0.8328 (ttp-110) cc_final: 0.7941 (ptm-80) REVERT: A 159 ASP cc_start: 0.8619 (m-30) cc_final: 0.8313 (m-30) REVERT: A 168 GLU cc_start: 0.8234 (tp30) cc_final: 0.7960 (tp30) REVERT: A 435 GLN cc_start: 0.9031 (tt0) cc_final: 0.8584 (mp10) REVERT: A 589 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8435 (tt) REVERT: A 603 ASP cc_start: 0.8646 (t0) cc_final: 0.8130 (t0) outliers start: 23 outliers final: 7 residues processed: 77 average time/residue: 1.1975 time to fit residues: 96.3811 Evaluate side-chains 72 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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: 0.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 0.0980 chunk 52 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3478 r_free = 0.3478 target = 0.103033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.088644 restraints weight = 9876.447| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.80 r_work: 0.3172 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5428 Z= 0.144 Angle : 0.560 7.695 7378 Z= 0.277 Chirality : 0.041 0.206 796 Planarity : 0.004 0.046 959 Dihedral : 4.092 13.687 715 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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 (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: 1.30 (0.30), residues: 294 sheet: 0.11 (0.56), residues: 73 loop : 0.31 (0.37), residues: 287 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 0.007 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 264) hydrogen bonds : angle 5.33780 ( 744) covalent geometry : bond 0.00331 ( 5428) covalent geometry : angle 0.55986 ( 7378) *********************** 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 86 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.627 Fit side-chains REVERT: A 32 GLU cc_start: 0.8683 (pt0) cc_final: 0.8393 (pt0) REVERT: A 98 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8306 (ptp-110) REVERT: A 110 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7625 (tm-30) REVERT: A 146 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: A 156 ARG cc_start: 0.8306 (ttp-110) cc_final: 0.7781 (ptm-80) REVERT: A 158 ASP cc_start: 0.8560 (m-30) cc_final: 0.8217 (m-30) REVERT: A 159 ASP cc_start: 0.8651 (m-30) cc_final: 0.8319 (m-30) REVERT: A 168 GLU cc_start: 0.8262 (tp30) cc_final: 0.7962 (tp30) REVERT: A 414 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.8179 (m-80) REVERT: A 435 GLN cc_start: 0.9006 (tt0) cc_final: 0.8555 (mp10) REVERT: A 589 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8463 (tt) REVERT: A 603 ASP cc_start: 0.8636 (t0) cc_final: 0.8104 (t0) outliers start: 19 outliers final: 5 residues processed: 79 average time/residue: 1.1742 time to fit residues: 97.2001 Evaluate side-chains 67 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 0.0050 chunk 60 optimal weight: 0.6980 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.104019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.089625 restraints weight = 9864.439| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.81 r_work: 0.3188 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5428 Z= 0.127 Angle : 0.556 8.349 7378 Z= 0.274 Chirality : 0.040 0.191 796 Planarity : 0.004 0.046 959 Dihedral : 4.047 14.118 715 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.51 % Allowed : 17.05 % 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: 1.09 (0.33), residues: 654 helix: 1.41 (0.30), residues: 294 sheet: 0.06 (0.56), residues: 73 loop : 0.32 (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 0.008 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 264) hydrogen bonds : angle 5.24616 ( 744) covalent geometry : bond 0.00288 ( 5428) covalent geometry : angle 0.55582 ( 7378) *********************** 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 84 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.582 Fit side-chains REVERT: A 30 ARG cc_start: 0.8151 (ptp-170) cc_final: 0.7911 (ptt-90) REVERT: A 32 GLU cc_start: 0.8643 (pt0) cc_final: 0.8357 (pt0) REVERT: A 98 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8298 (ptp-110) REVERT: A 110 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7543 (tm-30) REVERT: A 146 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: A 156 ARG cc_start: 0.8317 (ttp-110) cc_final: 0.7783 (ptm-80) REVERT: A 159 ASP cc_start: 0.8634 (m-30) cc_final: 0.8310 (m-30) REVERT: A 168 GLU cc_start: 0.8239 (tp30) cc_final: 0.7980 (mm-30) REVERT: A 414 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.8220 (m-80) REVERT: A 589 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8474 (tt) REVERT: A 603 ASP cc_start: 0.8589 (t0) cc_final: 0.8076 (t0) outliers start: 20 outliers final: 5 residues processed: 77 average time/residue: 1.2070 time to fit residues: 97.3188 Evaluate side-chains 71 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 3 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.0970 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.0020 chunk 5 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.104186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.089746 restraints weight = 9941.786| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.83 r_work: 0.3186 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5428 Z= 0.135 Angle : 0.572 8.295 7378 Z= 0.281 Chirality : 0.040 0.181 796 Planarity : 0.004 0.046 959 Dihedral : 4.030 14.103 715 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.34 % Allowed : 17.75 % 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: 1.17 (0.33), residues: 654 helix: 1.47 (0.30), residues: 294 sheet: 0.05 (0.55), 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 0.010 0.001 PHE A 278 TYR 0.013 0.001 TYR A 460 ARG 0.008 0.001 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 264) hydrogen bonds : angle 5.19943 ( 744) covalent geometry : bond 0.00312 ( 5428) covalent geometry : angle 0.57223 ( 7378) *********************** 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 85 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.8029 (ptp-170) cc_final: 0.7790 (ptt-90) REVERT: A 32 GLU cc_start: 0.8463 (pt0) cc_final: 0.8221 (pt0) REVERT: A 98 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8227 (ptp-110) REVERT: A 110 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: A 146 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: A 156 ARG cc_start: 0.8277 (ttp-110) cc_final: 0.7807 (ptm-80) REVERT: A 159 ASP cc_start: 0.8556 (m-30) cc_final: 0.8275 (m-30) REVERT: A 168 GLU cc_start: 0.8087 (tp30) cc_final: 0.7791 (tp30) REVERT: A 414 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: A 435 GLN cc_start: 0.9045 (tt0) cc_final: 0.8553 (mp10) REVERT: A 589 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8442 (tt) REVERT: A 603 ASP cc_start: 0.8488 (t0) cc_final: 0.7999 (t0) outliers start: 19 outliers final: 7 residues processed: 78 average time/residue: 1.1585 time to fit residues: 94.6758 Evaluate side-chains 73 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 110 GLU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 185 MET 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 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: 2.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 24 optimal weight: 0.0170 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.5820 ------------------------------------------------------------------------------- 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 ** 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 = 0.3485 r_free = 0.3485 target = 0.103132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.088740 restraints weight = 9825.810| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.78 r_work: 0.3180 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5428 Z= 0.144 Angle : 0.577 8.752 7378 Z= 0.283 Chirality : 0.041 0.178 796 Planarity : 0.004 0.046 959 Dihedral : 4.047 14.140 715 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.34 % Allowed : 17.93 % Favored : 78.73 % 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: 1.18 (0.33), residues: 654 helix: 1.45 (0.30), residues: 295 sheet: 0.06 (0.55), residues: 73 loop : 0.44 (0.37), residues: 286 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 0.010 0.001 PHE A 278 TYR 0.014 0.001 TYR A 460 ARG 0.009 0.001 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 264) hydrogen bonds : angle 5.19407 ( 744) covalent geometry : bond 0.00332 ( 5428) covalent geometry : angle 0.57708 ( 7378) *********************** 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 84 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.580 Fit side-chains REVERT: A 32 GLU cc_start: 0.8651 (pt0) cc_final: 0.8354 (pt0) REVERT: A 98 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8282 (ptp-110) REVERT: A 110 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7572 (tm-30) REVERT: A 146 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: A 156 ARG cc_start: 0.8323 (ttp-110) cc_final: 0.7809 (ptm-80) REVERT: A 159 ASP cc_start: 0.8639 (m-30) cc_final: 0.8297 (m-30) REVERT: A 168 GLU cc_start: 0.8265 (tp30) cc_final: 0.7946 (tp30) REVERT: A 185 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8034 (mmt) REVERT: A 414 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8267 (m-80) REVERT: A 435 GLN cc_start: 0.9152 (tt0) cc_final: 0.8530 (mp10) REVERT: A 485 ARG cc_start: 0.8525 (mtp85) cc_final: 0.8158 (mtp85) REVERT: A 589 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8365 (tt) REVERT: A 597 LEU cc_start: 0.8536 (mt) cc_final: 0.8294 (mt) REVERT: A 603 ASP cc_start: 0.8622 (t0) cc_final: 0.8073 (t0) outliers start: 19 outliers final: 7 residues processed: 78 average time/residue: 1.1842 time to fit residues: 96.6014 Evaluate side-chains 75 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 110 GLU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 185 MET 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 414 PHE Chi-restraints excluded: chain A residue 449 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 42 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 231 GLN ** 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 = 0.3482 r_free = 0.3482 target = 0.103036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.088668 restraints weight = 10028.030| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.80 r_work: 0.3175 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5428 Z= 0.153 Angle : 0.595 8.909 7378 Z= 0.291 Chirality : 0.041 0.175 796 Planarity : 0.004 0.046 959 Dihedral : 4.056 14.421 715 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.34 % Allowed : 17.93 % Favored : 78.73 % 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: 1.44 (0.30), residues: 295 sheet: 0.06 (0.55), residues: 73 loop : 0.41 (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 0.014 0.001 TYR A 460 ARG 0.009 0.001 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 264) hydrogen bonds : angle 5.19448 ( 744) covalent geometry : bond 0.00355 ( 5428) covalent geometry : angle 0.59529 ( 7378) ********************** 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 83 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.636 Fit side-chains REVERT: A 30 ARG cc_start: 0.8153 (ptp-170) cc_final: 0.7904 (ptt-90) REVERT: A 32 GLU cc_start: 0.8656 (pt0) cc_final: 0.8350 (pt0) REVERT: A 98 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8276 (ptp-110) REVERT: A 110 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7566 (tm-30) REVERT: A 146 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: A 156 ARG cc_start: 0.8314 (ttp-110) cc_final: 0.7806 (ptm-80) REVERT: A 159 ASP cc_start: 0.8648 (m-30) cc_final: 0.8290 (m-30) REVERT: A 168 GLU cc_start: 0.8251 (tp30) cc_final: 0.7948 (tp30) REVERT: A 185 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8049 (mmt) REVERT: A 414 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8285 (m-80) REVERT: A 435 GLN cc_start: 0.9149 (tt0) cc_final: 0.8524 (mp10) REVERT: A 589 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8371 (tt) REVERT: A 597 LEU cc_start: 0.8519 (mt) cc_final: 0.8262 (mt) REVERT: A 603 ASP cc_start: 0.8627 (t0) cc_final: 0.8080 (t0) outliers start: 19 outliers final: 8 residues processed: 76 average time/residue: 1.1264 time to fit residues: 89.9476 Evaluate side-chains 75 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 110 GLU Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 185 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 33 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 64 optimal weight: 0.0870 chunk 55 optimal weight: 0.4980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN ** 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 = 0.3495 r_free = 0.3495 target = 0.104061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.089710 restraints weight = 9976.487| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.81 r_work: 0.3186 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2683 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= 0.137 Angle : 0.591 9.009 7378 Z= 0.290 Chirality : 0.041 0.175 796 Planarity : 0.005 0.046 959 Dihedral : 4.054 14.406 715 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.16 % Allowed : 18.45 % Favored : 78.38 % 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: 1.19 (0.33), residues: 654 helix: 1.47 (0.30), residues: 295 sheet: 0.05 (0.55), residues: 73 loop : 0.43 (0.37), residues: 286 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 0.009 0.001 PHE A 278 TYR 0.013 0.001 TYR A 460 ARG 0.012 0.001 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 264) hydrogen bonds : angle 5.17262 ( 744) covalent geometry : bond 0.00317 ( 5428) covalent geometry : angle 0.59100 ( 7378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3910.25 seconds wall clock time: 68 minutes 8.47 seconds (4088.47 seconds total)