Starting phenix.real_space_refine on Sat May 10 00:04:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k7n_62150/05_2025/9k7n_62150.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k7n_62150/05_2025/9k7n_62150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k7n_62150/05_2025/9k7n_62150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k7n_62150/05_2025/9k7n_62150.map" model { file = "/net/cci-nas-00/data/ceres_data/9k7n_62150/05_2025/9k7n_62150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k7n_62150/05_2025/9k7n_62150.cif" } resolution = 3.3 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= 0.001 sd= 0.053 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 S 33 5.16 5 Cl 1 4.86 5 C 2900 2.51 5 N 658 2.21 5 O 740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 4332 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4324 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 518} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {' CL': 1, 'TAU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.10, per 1000 atoms: 0.72 Number of scatterers: 4332 At special positions: 0 Unit cell: (81.76, 68.62, 82.49, 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) Cl 1 17.00 S 33 16.00 O 740 8.00 N 658 7.00 C 2900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.05 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: 1.11 Conformation dependent library (CDL) restraints added in 510.5 milliseconds 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 994 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 83.5% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.578A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 removed outlier: 3.726A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.713A pdb=" N TRP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 153 removed outlier: 3.885A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.953A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 238 Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.620A pdb=" N GLY A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 244' Processing helix chain 'A' and resid 245 through 267 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.722A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 287 removed outlier: 3.612A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 287' Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.429A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.535A pdb=" N SER A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.567A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 removed outlier: 4.566A pdb=" N PHE A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.960A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 425 removed outlier: 3.704A pdb=" N GLY A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 444 removed outlier: 3.924A pdb=" N ILE A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 448 removed outlier: 3.779A pdb=" N THR A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 448' Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.654A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 482 Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 568 removed outlier: 4.025A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL A 557 " --> pdb=" O SER A 553 " (cutoff:3.500A) Proline residue: A 558 - end of helix Processing helix chain 'A' and resid 571 through 581 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 298 hydrogen bonds defined for protein. 885 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: 1.19 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 639 1.31 - 1.44: 1361 1.44 - 1.56: 2424 1.56 - 1.69: 0 1.69 - 1.82: 47 Bond restraints: 4471 Sorted by residual: bond pdb=" C ALA A 78 " pdb=" O ALA A 78 " ideal model delta sigma weight residual 1.236 1.185 0.051 1.24e-02 6.50e+03 1.70e+01 bond pdb=" C LEU A 267 " pdb=" N PRO A 268 " ideal model delta sigma weight residual 1.330 1.364 -0.034 1.22e-02 6.72e+03 7.89e+00 bond pdb=" C TYR A 538 " pdb=" N PRO A 539 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.31e-02 5.83e+03 6.40e+00 bond pdb=" CA SER A 365 " pdb=" C SER A 365 " ideal model delta sigma weight residual 1.526 1.497 0.029 1.20e-02 6.94e+03 5.83e+00 bond pdb=" C VAL A 528 " pdb=" N PRO A 529 " ideal model delta sigma weight residual 1.331 1.362 -0.031 1.31e-02 5.83e+03 5.66e+00 ... (remaining 4466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 5849 2.72 - 5.45: 206 5.45 - 8.17: 34 8.17 - 10.90: 9 10.90 - 13.62: 1 Bond angle restraints: 6099 Sorted by residual: angle pdb=" N SER A 121 " pdb=" CA SER A 121 " pdb=" C SER A 121 " ideal model delta sigma weight residual 113.38 103.97 9.41 1.23e+00 6.61e-01 5.85e+01 angle pdb=" N TRP A 65 " pdb=" CA TRP A 65 " pdb=" C TRP A 65 " ideal model delta sigma weight residual 111.14 119.01 -7.87 1.08e+00 8.57e-01 5.31e+01 angle pdb=" N ILE A 511 " pdb=" CA ILE A 511 " pdb=" C ILE A 511 " ideal model delta sigma weight residual 110.42 117.34 -6.92 9.60e-01 1.09e+00 5.20e+01 angle pdb=" N TYR A 461 " pdb=" CA TYR A 461 " pdb=" C TYR A 461 " ideal model delta sigma weight residual 111.36 119.16 -7.80 1.09e+00 8.42e-01 5.12e+01 angle pdb=" N ARG A 66 " pdb=" CA ARG A 66 " pdb=" C ARG A 66 " ideal model delta sigma weight residual 111.14 118.73 -7.59 1.08e+00 8.57e-01 4.94e+01 ... (remaining 6094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 2303 16.01 - 32.03: 167 32.03 - 48.04: 44 48.04 - 64.05: 11 64.05 - 80.07: 2 Dihedral angle restraints: 2527 sinusoidal: 956 harmonic: 1571 Sorted by residual: dihedral pdb=" C TYR A 137 " pdb=" N TYR A 137 " pdb=" CA TYR A 137 " pdb=" CB TYR A 137 " ideal model delta harmonic sigma weight residual -122.60 -137.40 14.80 0 2.50e+00 1.60e-01 3.51e+01 dihedral pdb=" N TYR A 137 " pdb=" C TYR A 137 " pdb=" CA TYR A 137 " pdb=" CB TYR A 137 " ideal model delta harmonic sigma weight residual 122.80 136.78 -13.98 0 2.50e+00 1.60e-01 3.13e+01 dihedral pdb=" C TYR A 461 " pdb=" N TYR A 461 " pdb=" CA TYR A 461 " pdb=" CB TYR A 461 " ideal model delta harmonic sigma weight residual -122.60 -133.16 10.56 0 2.50e+00 1.60e-01 1.79e+01 ... (remaining 2524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 567 0.122 - 0.244: 96 0.244 - 0.366: 8 0.366 - 0.488: 2 0.488 - 0.609: 2 Chirality restraints: 675 Sorted by residual: chirality pdb=" CA TYR A 137 " pdb=" N TYR A 137 " pdb=" C TYR A 137 " pdb=" CB TYR A 137 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.29e+00 chirality pdb=" CA TYR A 461 " pdb=" N TYR A 461 " pdb=" C TYR A 461 " pdb=" CB TYR A 461 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.08e+00 chirality pdb=" CA PHE A 345 " pdb=" N PHE A 345 " pdb=" C PHE A 345 " pdb=" CB PHE A 345 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 672 not shown) Planarity restraints: 741 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 252 " -0.073 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO A 253 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 81 " 0.051 5.00e-02 4.00e+02 7.71e-02 9.50e+00 pdb=" N PRO A 82 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 374 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.41e+00 pdb=" N PRO A 375 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.039 5.00e-02 4.00e+02 ... (remaining 738 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 54 2.67 - 3.23: 4463 3.23 - 3.79: 7337 3.79 - 4.34: 10113 4.34 - 4.90: 15931 Nonbonded interactions: 37898 Sorted by model distance: nonbonded pdb=" OH TYR A 83 " pdb="CL CL A 702 " model vdw 2.115 3.190 nonbonded pdb=" OD1 ASP A 219 " pdb=" N LEU A 220 " model vdw 2.288 3.120 nonbonded pdb=" N SER A 464 " pdb=" O SER A 464 " model vdw 2.416 2.496 nonbonded pdb=" N SER A 121 " pdb=" N GLY A 122 " model vdw 2.448 2.560 nonbonded pdb=" O PHE A 58 " pdb=" O3 TAU A 701 " model vdw 2.461 3.040 ... (remaining 37893 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: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 14.610 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 4472 Z= 0.508 Angle : 1.229 13.622 6101 Z= 0.862 Chirality : 0.094 0.609 675 Planarity : 0.009 0.110 741 Dihedral : 12.281 80.066 1530 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.08 % Allowed : 6.24 % Favored : 92.69 % Cbeta Deviations : 0.20 % 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: 2.30 (0.36), residues: 543 helix: 2.34 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -0.69 (0.49), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 387 HIS 0.001 0.000 HIS A 170 PHE 0.020 0.002 PHE A 522 TYR 0.026 0.002 TYR A 137 ARG 0.002 0.000 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.21751 ( 298) hydrogen bonds : angle 7.22434 ( 885) SS BOND : bond 0.01563 ( 1) SS BOND : angle 2.12603 ( 2) covalent geometry : bond 0.00669 ( 4471) covalent geometry : angle 1.22860 ( 6099) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 202 ASN cc_start: 0.8247 (t0) cc_final: 0.7901 (t0) REVERT: A 286 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7560 (mm-30) REVERT: A 302 TYR cc_start: 0.7948 (m-80) cc_final: 0.7210 (m-80) REVERT: A 350 PHE cc_start: 0.8349 (t80) cc_final: 0.8039 (t80) REVERT: A 452 MET cc_start: 0.7462 (tpp) cc_final: 0.7238 (tpt) outliers start: 5 outliers final: 3 residues processed: 134 average time/residue: 0.1437 time to fit residues: 24.8208 Evaluate side-chains 79 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 418 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 GLN A 353 GLN A 355 GLN A 456 GLN A 533 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.175690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145440 restraints weight = 5393.542| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.37 r_work: 0.3619 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4472 Z= 0.183 Angle : 0.669 9.216 6101 Z= 0.357 Chirality : 0.044 0.175 675 Planarity : 0.006 0.058 741 Dihedral : 6.169 59.345 599 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.58 % Allowed : 12.04 % Favored : 85.38 % 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: 1.64 (0.35), residues: 543 helix: 1.72 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -0.49 (0.48), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 113 HIS 0.007 0.002 HIS A 212 PHE 0.035 0.002 PHE A 58 TYR 0.024 0.002 TYR A 498 ARG 0.003 0.000 ARG A 201 Details of bonding type rmsd hydrogen bonds : bond 0.06190 ( 298) hydrogen bonds : angle 5.33264 ( 885) SS BOND : bond 0.00361 ( 1) SS BOND : angle 3.41047 ( 2) covalent geometry : bond 0.00387 ( 4471) covalent geometry : angle 0.66576 ( 6099) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.458 Fit side-chains REVERT: A 47 LYS cc_start: 0.7610 (mmtp) cc_final: 0.7370 (pttt) REVERT: A 51 VAL cc_start: 0.7365 (t) cc_final: 0.7152 (t) REVERT: A 202 ASN cc_start: 0.8598 (t0) cc_final: 0.8305 (t0) REVERT: A 256 MET cc_start: 0.7676 (tpp) cc_final: 0.7266 (tpt) REVERT: A 302 TYR cc_start: 0.8604 (m-80) cc_final: 0.8146 (m-80) REVERT: A 324 ARG cc_start: 0.6040 (ttp-170) cc_final: 0.5616 (mmp-170) REVERT: A 350 PHE cc_start: 0.8519 (t80) cc_final: 0.8169 (t80) outliers start: 12 outliers final: 7 residues processed: 98 average time/residue: 0.1134 time to fit residues: 15.3656 Evaluate side-chains 89 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 540 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 52 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 36 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 63 ASN A 74 ASN ** A 167 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 = 0.4057 r_free = 0.4057 target = 0.175385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144871 restraints weight = 5372.920| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.37 r_work: 0.3606 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4472 Z= 0.154 Angle : 0.599 11.029 6101 Z= 0.309 Chirality : 0.040 0.151 675 Planarity : 0.005 0.058 741 Dihedral : 5.899 59.567 597 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.23 % Allowed : 12.69 % Favored : 84.09 % 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: 1.47 (0.35), residues: 543 helix: 1.55 (0.25), residues: 396 sheet: None (None), residues: 0 loop : -0.52 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 113 HIS 0.004 0.001 HIS A 212 PHE 0.033 0.002 PHE A 58 TYR 0.019 0.001 TYR A 69 ARG 0.002 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.05495 ( 298) hydrogen bonds : angle 5.08082 ( 885) SS BOND : bond 0.00093 ( 1) SS BOND : angle 2.04354 ( 2) covalent geometry : bond 0.00345 ( 4471) covalent geometry : angle 0.59753 ( 6099) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7618 (mmtp) cc_final: 0.7393 (pttt) REVERT: A 202 ASN cc_start: 0.8600 (t0) cc_final: 0.8287 (t0) REVERT: A 302 TYR cc_start: 0.8584 (m-80) cc_final: 0.8239 (m-80) REVERT: A 324 ARG cc_start: 0.6039 (ttp-170) cc_final: 0.5648 (mmp-170) REVERT: A 350 PHE cc_start: 0.8663 (t80) cc_final: 0.8052 (t80) REVERT: A 408 GLU cc_start: 0.7903 (tp30) cc_final: 0.7671 (tp30) REVERT: A 498 TYR cc_start: 0.7136 (p90) cc_final: 0.6927 (p90) outliers start: 15 outliers final: 11 residues processed: 90 average time/residue: 0.1145 time to fit residues: 14.1816 Evaluate side-chains 83 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 548 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 151 GLN ** A 167 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 = 0.4052 r_free = 0.4052 target = 0.174820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.144175 restraints weight = 5394.159| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.38 r_work: 0.3599 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4472 Z= 0.140 Angle : 0.555 8.104 6101 Z= 0.288 Chirality : 0.039 0.184 675 Planarity : 0.005 0.054 741 Dihedral : 5.877 59.751 597 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.23 % Allowed : 13.33 % Favored : 83.44 % 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: 1.53 (0.35), residues: 543 helix: 1.57 (0.25), residues: 401 sheet: None (None), residues: 0 loop : -0.50 (0.49), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 113 HIS 0.003 0.001 HIS A 212 PHE 0.031 0.002 PHE A 58 TYR 0.018 0.001 TYR A 69 ARG 0.001 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04975 ( 298) hydrogen bonds : angle 4.81009 ( 885) SS BOND : bond 0.00071 ( 1) SS BOND : angle 1.92967 ( 2) covalent geometry : bond 0.00312 ( 4471) covalent geometry : angle 0.55413 ( 6099) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 202 ASN cc_start: 0.8627 (t0) cc_final: 0.8278 (t0) REVERT: A 302 TYR cc_start: 0.8624 (m-80) cc_final: 0.8314 (m-80) REVERT: A 324 ARG cc_start: 0.6014 (ttp-170) cc_final: 0.5646 (mmp-170) REVERT: A 350 PHE cc_start: 0.8432 (t80) cc_final: 0.8094 (t80) REVERT: A 493 GLU cc_start: 0.7259 (pt0) cc_final: 0.6882 (pt0) outliers start: 15 outliers final: 10 residues processed: 86 average time/residue: 0.1182 time to fit residues: 13.9840 Evaluate side-chains 79 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 555 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 14 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 167 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 = 0.4028 r_free = 0.4028 target = 0.171581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.140773 restraints weight = 5609.445| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.37 r_work: 0.3568 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4472 Z= 0.150 Angle : 0.550 7.610 6101 Z= 0.285 Chirality : 0.039 0.188 675 Planarity : 0.005 0.052 741 Dihedral : 5.888 59.496 597 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.44 % Allowed : 14.84 % Favored : 81.72 % 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: 1.62 (0.35), residues: 543 helix: 1.64 (0.25), residues: 405 sheet: None (None), residues: 0 loop : -0.57 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 113 HIS 0.003 0.001 HIS A 212 PHE 0.025 0.002 PHE A 232 TYR 0.019 0.001 TYR A 69 ARG 0.001 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.04842 ( 298) hydrogen bonds : angle 4.75725 ( 885) SS BOND : bond 0.00296 ( 1) SS BOND : angle 1.65398 ( 2) covalent geometry : bond 0.00344 ( 4471) covalent geometry : angle 0.54896 ( 6099) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8671 (m-80) cc_final: 0.8351 (m-80) REVERT: A 324 ARG cc_start: 0.6085 (ttp-170) cc_final: 0.5708 (mmp-170) REVERT: A 350 PHE cc_start: 0.8485 (t80) cc_final: 0.8120 (t80) outliers start: 16 outliers final: 10 residues processed: 82 average time/residue: 0.1172 time to fit residues: 13.1981 Evaluate side-chains 76 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.171319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.140166 restraints weight = 5557.245| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.40 r_work: 0.3562 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4472 Z= 0.155 Angle : 0.560 7.607 6101 Z= 0.289 Chirality : 0.040 0.180 675 Planarity : 0.005 0.050 741 Dihedral : 5.922 59.632 597 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.23 % Allowed : 16.56 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.50 (0.36), residues: 543 helix: 1.56 (0.25), residues: 407 sheet: None (None), residues: 0 loop : -0.66 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 113 HIS 0.003 0.001 HIS A 212 PHE 0.026 0.002 PHE A 232 TYR 0.019 0.001 TYR A 69 ARG 0.001 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.04694 ( 298) hydrogen bonds : angle 4.76862 ( 885) SS BOND : bond 0.00118 ( 1) SS BOND : angle 1.61457 ( 2) covalent geometry : bond 0.00360 ( 4471) covalent geometry : angle 0.55935 ( 6099) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8723 (m-80) cc_final: 0.8309 (m-80) REVERT: A 324 ARG cc_start: 0.6106 (ttp-170) cc_final: 0.5729 (mmp-170) REVERT: A 408 GLU cc_start: 0.7932 (tp30) cc_final: 0.7665 (tp30) outliers start: 15 outliers final: 13 residues processed: 81 average time/residue: 0.1235 time to fit residues: 13.6792 Evaluate side-chains 77 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 19 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 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.171089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.140649 restraints weight = 5500.635| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.30 r_work: 0.3568 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4472 Z= 0.141 Angle : 0.540 7.219 6101 Z= 0.278 Chirality : 0.039 0.180 675 Planarity : 0.004 0.048 741 Dihedral : 5.860 58.399 597 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.87 % Allowed : 16.99 % Favored : 79.14 % 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: 1.53 (0.36), residues: 543 helix: 1.60 (0.25), residues: 411 sheet: None (None), residues: 0 loop : -0.78 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 113 HIS 0.003 0.001 HIS A 212 PHE 0.031 0.002 PHE A 232 TYR 0.018 0.001 TYR A 69 ARG 0.001 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 298) hydrogen bonds : angle 4.65474 ( 885) SS BOND : bond 0.00100 ( 1) SS BOND : angle 1.73339 ( 2) covalent geometry : bond 0.00326 ( 4471) covalent geometry : angle 0.53901 ( 6099) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.451 Fit side-chains REVERT: A 302 TYR cc_start: 0.8735 (m-80) cc_final: 0.8316 (m-80) REVERT: A 324 ARG cc_start: 0.6082 (ttp-170) cc_final: 0.5693 (mmp-170) REVERT: A 350 PHE cc_start: 0.8654 (t80) cc_final: 0.8324 (t80) REVERT: A 408 GLU cc_start: 0.7910 (tp30) cc_final: 0.7633 (tp30) outliers start: 18 outliers final: 14 residues processed: 85 average time/residue: 0.1227 time to fit residues: 14.2220 Evaluate side-chains 78 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 0.0570 chunk 1 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.172184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.141639 restraints weight = 5466.794| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.34 r_work: 0.3577 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4472 Z= 0.131 Angle : 0.531 6.890 6101 Z= 0.275 Chirality : 0.039 0.204 675 Planarity : 0.005 0.047 741 Dihedral : 5.827 57.146 597 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.58 % Allowed : 18.28 % Favored : 79.14 % 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: 1.58 (0.36), residues: 543 helix: 1.64 (0.25), residues: 411 sheet: None (None), residues: 0 loop : -0.80 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 113 HIS 0.003 0.001 HIS A 212 PHE 0.034 0.002 PHE A 232 TYR 0.017 0.001 TYR A 69 ARG 0.001 0.000 ARG A 201 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 298) hydrogen bonds : angle 4.61560 ( 885) SS BOND : bond 0.00231 ( 1) SS BOND : angle 1.65767 ( 2) covalent geometry : bond 0.00296 ( 4471) covalent geometry : angle 0.53050 ( 6099) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.467 Fit side-chains REVERT: A 302 TYR cc_start: 0.8715 (m-80) cc_final: 0.8241 (m-80) REVERT: A 324 ARG cc_start: 0.6011 (ttp-170) cc_final: 0.5625 (mmp-170) REVERT: A 350 PHE cc_start: 0.8643 (t80) cc_final: 0.8237 (t80) REVERT: A 408 GLU cc_start: 0.7867 (tp30) cc_final: 0.7617 (tp30) outliers start: 12 outliers final: 10 residues processed: 78 average time/residue: 0.1351 time to fit residues: 14.3418 Evaluate side-chains 75 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 555 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.171597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.140871 restraints weight = 5574.568| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.37 r_work: 0.3566 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4472 Z= 0.145 Angle : 0.555 7.254 6101 Z= 0.285 Chirality : 0.039 0.207 675 Planarity : 0.005 0.046 741 Dihedral : 5.831 56.500 597 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.80 % Allowed : 18.28 % Favored : 78.92 % 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: 1.59 (0.36), residues: 543 helix: 1.66 (0.25), residues: 411 sheet: None (None), residues: 0 loop : -0.81 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 113 HIS 0.003 0.001 HIS A 212 PHE 0.033 0.002 PHE A 232 TYR 0.018 0.001 TYR A 69 ARG 0.001 0.000 ARG A 201 Details of bonding type rmsd hydrogen bonds : bond 0.04420 ( 298) hydrogen bonds : angle 4.60006 ( 885) SS BOND : bond 0.00245 ( 1) SS BOND : angle 1.66461 ( 2) covalent geometry : bond 0.00337 ( 4471) covalent geometry : angle 0.55456 ( 6099) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.479 Fit side-chains REVERT: A 302 TYR cc_start: 0.8704 (m-80) cc_final: 0.8194 (m-80) REVERT: A 324 ARG cc_start: 0.6006 (ttp-170) cc_final: 0.5646 (mmp-170) REVERT: A 408 GLU cc_start: 0.7880 (tp30) cc_final: 0.7628 (tp30) REVERT: A 493 GLU cc_start: 0.7380 (pt0) cc_final: 0.7032 (pt0) outliers start: 13 outliers final: 12 residues processed: 77 average time/residue: 0.1251 time to fit residues: 13.2264 Evaluate side-chains 77 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.171596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.140921 restraints weight = 5432.032| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.35 r_work: 0.3563 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4472 Z= 0.142 Angle : 0.547 7.109 6101 Z= 0.283 Chirality : 0.039 0.211 675 Planarity : 0.005 0.045 741 Dihedral : 5.801 56.490 597 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.37 % Allowed : 19.14 % Favored : 78.49 % 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: 1.56 (0.36), residues: 543 helix: 1.63 (0.25), residues: 411 sheet: None (None), residues: 0 loop : -0.82 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 113 HIS 0.003 0.001 HIS A 212 PHE 0.036 0.002 PHE A 232 TYR 0.018 0.001 TYR A 69 ARG 0.001 0.000 ARG A 201 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 298) hydrogen bonds : angle 4.59911 ( 885) SS BOND : bond 0.00263 ( 1) SS BOND : angle 1.68849 ( 2) covalent geometry : bond 0.00329 ( 4471) covalent geometry : angle 0.54645 ( 6099) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.505 Fit side-chains REVERT: A 302 TYR cc_start: 0.8732 (m-80) cc_final: 0.8314 (m-80) REVERT: A 324 ARG cc_start: 0.6049 (ttp-170) cc_final: 0.5656 (mmp-170) REVERT: A 408 GLU cc_start: 0.7873 (tp30) cc_final: 0.7619 (tp30) REVERT: A 493 GLU cc_start: 0.7389 (pt0) cc_final: 0.7033 (pt0) outliers start: 11 outliers final: 11 residues processed: 73 average time/residue: 0.1330 time to fit residues: 13.1468 Evaluate side-chains 74 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.0670 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.172279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141601 restraints weight = 5503.495| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.37 r_work: 0.3578 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4472 Z= 0.135 Angle : 0.548 7.164 6101 Z= 0.281 Chirality : 0.038 0.209 675 Planarity : 0.004 0.044 741 Dihedral : 5.763 56.361 597 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.80 % Allowed : 18.49 % Favored : 78.71 % 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: 1.59 (0.36), residues: 543 helix: 1.69 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -0.91 (0.50), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 113 HIS 0.003 0.001 HIS A 212 PHE 0.036 0.002 PHE A 232 TYR 0.017 0.001 TYR A 69 ARG 0.001 0.000 ARG A 201 Details of bonding type rmsd hydrogen bonds : bond 0.04311 ( 298) hydrogen bonds : angle 4.56065 ( 885) SS BOND : bond 0.00208 ( 1) SS BOND : angle 1.57974 ( 2) covalent geometry : bond 0.00308 ( 4471) covalent geometry : angle 0.54698 ( 6099) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2085.11 seconds wall clock time: 37 minutes 3.69 seconds (2223.69 seconds total)