Starting phenix.real_space_refine on Thu Mar 6 01:07:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k7n_62150/03_2025/9k7n_62150.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k7n_62150/03_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_62150/03_2025/9k7n_62150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k7n_62150/03_2025/9k7n_62150.map" model { file = "/net/cci-nas-00/data/ceres_data/9k7n_62150/03_2025/9k7n_62150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k7n_62150/03_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-5624/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: 3.73, per 1000 atoms: 0.86 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: 1.36 Conformation dependent library (CDL) restraints added in 567.0 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: 0.47 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: 1.34 Time building geometry restraints manager: 1.44 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: 1.790 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.810 Find NCS groups from input model: 0.050 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- 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 4471 Z= 0.436 Angle : 1.229 13.622 6099 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 *********************** 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 : 0.487 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: 0.1431 time to fit residues: 24.6618 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 : 0.466 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145439 restraints weight = 5393.542| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.37 r_work: 0.3618 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 4471 Z= 0.256 Angle : 0.666 9.216 6099 Z= 0.356 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 *********************** 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 : 0.431 Fit side-chains REVERT: A 47 LYS cc_start: 0.7607 (mmtp) cc_final: 0.7368 (pttt) REVERT: A 51 VAL cc_start: 0.7359 (t) cc_final: 0.7145 (t) REVERT: A 202 ASN cc_start: 0.8601 (t0) cc_final: 0.8306 (t0) REVERT: A 256 MET cc_start: 0.7671 (tpp) cc_final: 0.7260 (tpt) REVERT: A 302 TYR cc_start: 0.8604 (m-80) cc_final: 0.8145 (m-80) REVERT: A 324 ARG cc_start: 0.6041 (ttp-170) cc_final: 0.5613 (mmp-170) REVERT: A 350 PHE cc_start: 0.8517 (t80) cc_final: 0.8168 (t80) outliers start: 12 outliers final: 7 residues processed: 98 average time/residue: 0.1120 time to fit residues: 15.1558 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 : 0.438 ------------------------------------------------------------------------------- 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: 4.9990 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 0.0040 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.175093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.144504 restraints weight = 5377.365| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.38 r_work: 0.3601 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4471 Z= 0.230 Angle : 0.590 11.060 6099 Z= 0.307 Chirality : 0.040 0.155 675 Planarity : 0.005 0.059 741 Dihedral : 5.900 59.827 597 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.44 % Allowed : 11.83 % Favored : 84.73 % 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: 1.55 (0.35), residues: 543 helix: 1.59 (0.25), residues: 395 sheet: None (None), residues: 0 loop : -0.41 (0.51), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 113 HIS 0.004 0.002 HIS A 212 PHE 0.037 0.002 PHE A 58 TYR 0.018 0.001 TYR A 69 ARG 0.002 0.000 ARG A 564 *********************** 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 96 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7626 (mmtp) cc_final: 0.7405 (pttt) REVERT: A 202 ASN cc_start: 0.8605 (t0) cc_final: 0.8299 (t0) REVERT: A 302 TYR cc_start: 0.8606 (m-80) cc_final: 0.8266 (m-80) REVERT: A 324 ARG cc_start: 0.6072 (ttp-170) cc_final: 0.5670 (mmp-170) REVERT: A 350 PHE cc_start: 0.8708 (t80) cc_final: 0.8085 (t80) REVERT: A 408 GLU cc_start: 0.7904 (tp30) cc_final: 0.7666 (tp30) REVERT: A 498 TYR cc_start: 0.7220 (p90) cc_final: 0.6998 (p90) outliers start: 16 outliers final: 11 residues processed: 93 average time/residue: 0.1196 time to fit residues: 15.2654 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 : 0.468 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 4 optimal weight: 0.0870 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN ** 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 = 0.4054 r_free = 0.4054 target = 0.173958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.142801 restraints weight = 5486.070| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.36 r_work: 0.3592 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4471 Z= 0.205 Angle : 0.552 8.174 6099 Z= 0.286 Chirality : 0.039 0.185 675 Planarity : 0.005 0.056 741 Dihedral : 5.854 59.752 597 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.44 % Allowed : 13.76 % Favored : 82.80 % 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: 1.49 (0.35), residues: 543 helix: 1.58 (0.25), residues: 399 sheet: None (None), residues: 0 loop : -0.60 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 113 HIS 0.003 0.001 HIS A 212 PHE 0.033 0.002 PHE A 58 TYR 0.018 0.001 TYR A 69 ARG 0.001 0.000 ARG A 66 *********************** 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 85 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8622 (m-80) cc_final: 0.8310 (m-80) REVERT: A 324 ARG cc_start: 0.5996 (ttp-170) cc_final: 0.5647 (mmp-170) REVERT: A 350 PHE cc_start: 0.8444 (t80) cc_final: 0.8088 (t80) REVERT: A 498 TYR cc_start: 0.7262 (p90) cc_final: 0.7043 (p90) outliers start: 16 outliers final: 10 residues processed: 82 average time/residue: 0.1434 time to fit residues: 16.0117 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 : 0.461 ------------------------------------------------------------------------------- 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 540 ASN Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 20.0000 chunk 34 optimal weight: 0.0870 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 0.0020 overall best weight: 0.4166 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.174764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.143843 restraints weight = 5559.266| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.40 r_work: 0.3607 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4471 Z= 0.180 Angle : 0.524 7.329 6099 Z= 0.272 Chirality : 0.039 0.193 675 Planarity : 0.005 0.052 741 Dihedral : 5.796 57.909 597 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.80 % Allowed : 15.48 % 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: 1.70 (0.35), residues: 543 helix: 1.74 (0.26), residues: 399 sheet: None (None), residues: 0 loop : -0.53 (0.50), residues: 144 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 0.025 0.002 PHE A 232 TYR 0.016 0.001 TYR A 69 ARG 0.001 0.000 ARG A 66 *********************** 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 84 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8639 (m-80) cc_final: 0.8340 (m-80) REVERT: A 324 ARG cc_start: 0.6030 (ttp-170) cc_final: 0.5659 (mmp-170) REVERT: A 350 PHE cc_start: 0.8424 (t80) cc_final: 0.8072 (t80) REVERT: A 498 TYR cc_start: 0.7286 (p90) cc_final: 0.7051 (p90) outliers start: 13 outliers final: 8 residues processed: 81 average time/residue: 0.1559 time to fit residues: 17.2325 Evaluate side-chains 75 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 574 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.0570 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.173234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.142242 restraints weight = 5533.816| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.40 r_work: 0.3591 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4471 Z= 0.208 Angle : 0.539 7.290 6099 Z= 0.279 Chirality : 0.039 0.193 675 Planarity : 0.005 0.049 741 Dihedral : 5.773 56.467 597 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.66 % Allowed : 16.13 % 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: 1.74 (0.36), residues: 543 helix: 1.74 (0.25), residues: 405 sheet: None (None), residues: 0 loop : -0.54 (0.51), residues: 138 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 0.028 0.002 PHE A 232 TYR 0.018 0.001 TYR A 69 ARG 0.001 0.000 ARG A 564 *********************** 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 88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 1.533 Fit side-chains REVERT: A 302 TYR cc_start: 0.8680 (m-80) cc_final: 0.8289 (m-80) REVERT: A 324 ARG cc_start: 0.6088 (ttp-170) cc_final: 0.5717 (mmp-170) REVERT: A 350 PHE cc_start: 0.8583 (t80) cc_final: 0.8219 (t80) REVERT: A 408 GLU cc_start: 0.7918 (tp30) cc_final: 0.7652 (tp30) REVERT: A 498 TYR cc_start: 0.7318 (p90) cc_final: 0.7057 (p90) outliers start: 17 outliers final: 13 residues processed: 84 average time/residue: 0.2142 time to fit residues: 24.9414 Evaluate side-chains 81 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 338 PHE 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 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: 3.9990 chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.173604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.143020 restraints weight = 5506.973| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.37 r_work: 0.3602 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4471 Z= 0.189 Angle : 0.524 6.941 6099 Z= 0.271 Chirality : 0.038 0.197 675 Planarity : 0.004 0.047 741 Dihedral : 5.745 56.059 597 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.01 % Allowed : 16.99 % Favored : 80.00 % 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: 1.76 (0.36), residues: 543 helix: 1.77 (0.25), residues: 405 sheet: None (None), residues: 0 loop : -0.61 (0.51), residues: 138 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 0.030 0.002 PHE A 232 TYR 0.016 0.001 TYR A 69 ARG 0.001 0.000 ARG A 263 *********************** 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 84 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.432 Fit side-chains REVERT: A 302 TYR cc_start: 0.8672 (m-80) cc_final: 0.8281 (m-80) REVERT: A 324 ARG cc_start: 0.6066 (ttp-170) cc_final: 0.5643 (mmp-170) REVERT: A 350 PHE cc_start: 0.8541 (t80) cc_final: 0.8262 (t80) REVERT: A 408 GLU cc_start: 0.7904 (tp30) cc_final: 0.7618 (tp30) outliers start: 14 outliers final: 10 residues processed: 81 average time/residue: 0.1220 time to fit residues: 13.5938 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 : 0.421 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.172609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.142097 restraints weight = 5464.105| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.35 r_work: 0.3583 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4471 Z= 0.206 Angle : 0.542 7.103 6099 Z= 0.276 Chirality : 0.038 0.196 675 Planarity : 0.004 0.045 741 Dihedral : 5.800 56.697 597 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.58 % Allowed : 17.42 % Favored : 80.00 % 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: 1.75 (0.36), residues: 543 helix: 1.76 (0.25), residues: 407 sheet: None (None), residues: 0 loop : -0.64 (0.52), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 387 HIS 0.003 0.001 HIS A 212 PHE 0.034 0.002 PHE A 232 TYR 0.018 0.001 TYR A 69 ARG 0.001 0.000 ARG A 66 *********************** 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 84 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.444 Fit side-chains REVERT: A 302 TYR cc_start: 0.8708 (m-80) cc_final: 0.8248 (m-80) REVERT: A 324 ARG cc_start: 0.5965 (ttp-170) cc_final: 0.5585 (mmp-170) REVERT: A 350 PHE cc_start: 0.8576 (t80) cc_final: 0.8236 (t80) REVERT: A 408 GLU cc_start: 0.7853 (tp30) cc_final: 0.7610 (tp30) REVERT: A 504 MET cc_start: 0.7618 (mtp) cc_final: 0.7319 (mtp) outliers start: 12 outliers final: 11 residues processed: 82 average time/residue: 0.1268 time to fit residues: 14.3332 Evaluate side-chains 77 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 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 = 0.4041 r_free = 0.4041 target = 0.172990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.142162 restraints weight = 5583.169| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.41 r_work: 0.3583 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4471 Z= 0.205 Angle : 0.542 6.882 6099 Z= 0.278 Chirality : 0.039 0.207 675 Planarity : 0.005 0.045 741 Dihedral : 5.819 56.615 597 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.80 % Allowed : 17.85 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.79 (0.36), residues: 543 helix: 1.78 (0.25), residues: 406 sheet: None (None), residues: 0 loop : -0.55 (0.52), residues: 137 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 0.035 0.002 PHE A 232 TYR 0.017 0.001 TYR A 69 ARG 0.002 0.000 ARG A 177 *********************** 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 : 0.441 Fit side-chains REVERT: A 302 TYR cc_start: 0.8685 (m-80) cc_final: 0.8340 (m-80) REVERT: A 324 ARG cc_start: 0.6023 (ttp-170) cc_final: 0.5593 (mmp-170) REVERT: A 350 PHE cc_start: 0.8521 (t80) cc_final: 0.8189 (t80) REVERT: A 408 GLU cc_start: 0.7852 (tp30) cc_final: 0.7589 (tp30) REVERT: A 504 MET cc_start: 0.7578 (mtp) cc_final: 0.7280 (mtp) outliers start: 13 outliers final: 11 residues processed: 78 average time/residue: 0.1230 time to fit residues: 13.0987 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 : 0.433 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4030 r_free = 0.4030 target = 0.171720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.141124 restraints weight = 5453.170| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.37 r_work: 0.3571 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4471 Z= 0.223 Angle : 0.557 7.107 6099 Z= 0.283 Chirality : 0.039 0.196 675 Planarity : 0.004 0.045 741 Dihedral : 5.896 57.487 597 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.37 % Allowed : 18.28 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.80 (0.36), residues: 543 helix: 1.80 (0.25), residues: 405 sheet: None (None), residues: 0 loop : -0.61 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 166 HIS 0.003 0.001 HIS A 212 PHE 0.035 0.002 PHE A 232 TYR 0.018 0.001 TYR A 69 ARG 0.002 0.000 ARG A 177 ********************** 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 78 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.433 Fit side-chains REVERT: A 302 TYR cc_start: 0.8741 (m-80) cc_final: 0.8326 (m-80) REVERT: A 350 PHE cc_start: 0.8517 (t80) cc_final: 0.8169 (t80) REVERT: A 408 GLU cc_start: 0.7864 (tp30) cc_final: 0.7575 (tp30) outliers start: 11 outliers final: 11 residues processed: 76 average time/residue: 0.1286 time to fit residues: 13.2215 Evaluate side-chains 75 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.172324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.141630 restraints weight = 5547.899| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.39 r_work: 0.3580 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4471 Z= 0.211 Angle : 0.543 6.862 6099 Z= 0.280 Chirality : 0.038 0.191 675 Planarity : 0.005 0.045 741 Dihedral : 5.908 58.196 597 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.80 % Allowed : 18.71 % 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: 1.75 (0.35), residues: 543 helix: 1.78 (0.25), residues: 405 sheet: None (None), residues: 0 loop : -0.66 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 166 HIS 0.003 0.001 HIS A 212 PHE 0.037 0.002 PHE A 232 TYR 0.018 0.001 TYR A 69 ARG 0.001 0.000 ARG A 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2165.89 seconds wall clock time: 39 minutes 5.22 seconds (2345.22 seconds total)