Starting phenix.real_space_refine on Wed Jul 23 11:09:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cyh_30500/07_2025/7cyh_30500.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cyh_30500/07_2025/7cyh_30500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cyh_30500/07_2025/7cyh_30500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cyh_30500/07_2025/7cyh_30500.map" model { file = "/net/cci-nas-00/data/ceres_data/7cyh_30500/07_2025/7cyh_30500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cyh_30500/07_2025/7cyh_30500.cif" } resolution = 3.9 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= 0.210 sd= 1.412 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: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2057 2.51 5 N 551 2.21 5 O 619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3241 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "D" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 806 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 899 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 2.64, per 1000 atoms: 0.81 Number of scatterers: 3241 At special positions: 0 Unit cell: (72.45, 61.95, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 619 8.00 N 551 7.00 C 2057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 363.1 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 11 sheets defined 9.5% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.554A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.911A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.841A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.024A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 403 removed outlier: 3.650A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.885A pdb=" N CYS D 22 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 70 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 39 through 41 removed outlier: 4.021A pdb=" N VAL D 88 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.785A pdb=" N LYS E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 50 removed outlier: 6.383A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N MET E 34 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N CYS E 96 " --> pdb=" O TRP E 110 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TRP E 110 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG E 98 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 50 removed outlier: 6.383A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N MET E 34 " --> pdb=" O GLU E 50 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 156 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1045 1.34 - 1.46: 891 1.46 - 1.59: 1370 1.59 - 1.71: 0 1.71 - 1.83: 16 Bond restraints: 3322 Sorted by residual: bond pdb=" C PHE A 497 " pdb=" N GLN A 498 " ideal model delta sigma weight residual 1.329 1.256 0.073 1.86e-02 2.89e+03 1.53e+01 bond pdb=" CA VAL A 512 " pdb=" C VAL A 512 " ideal model delta sigma weight residual 1.525 1.503 0.022 9.00e-03 1.23e+04 6.10e+00 bond pdb=" C GLN A 498 " pdb=" N PRO A 499 " ideal model delta sigma weight residual 1.336 1.307 0.029 1.25e-02 6.40e+03 5.50e+00 bond pdb=" CB PHE A 429 " pdb=" CG PHE A 429 " ideal model delta sigma weight residual 1.502 1.449 0.053 2.30e-02 1.89e+03 5.27e+00 bond pdb=" CB PHE A 377 " pdb=" CG PHE A 377 " ideal model delta sigma weight residual 1.502 1.449 0.053 2.30e-02 1.89e+03 5.24e+00 ... (remaining 3317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 4410 3.27 - 6.55: 95 6.55 - 9.82: 9 9.82 - 13.09: 0 13.09 - 16.36: 1 Bond angle restraints: 4515 Sorted by residual: angle pdb=" C PHE A 497 " pdb=" N GLN A 498 " pdb=" CA GLN A 498 " ideal model delta sigma weight residual 121.48 105.12 16.36 2.04e+00 2.40e-01 6.44e+01 angle pdb=" N VAL A 512 " pdb=" CA VAL A 512 " pdb=" C VAL A 512 " ideal model delta sigma weight residual 108.53 99.98 8.55 1.22e+00 6.72e-01 4.91e+01 angle pdb=" N GLY E 105 " pdb=" CA GLY E 105 " pdb=" C GLY E 105 " ideal model delta sigma weight residual 111.42 103.58 7.84 1.51e+00 4.39e-01 2.69e+01 angle pdb=" C PHE D 35 " pdb=" N MET D 36 " pdb=" CA MET D 36 " ideal model delta sigma weight residual 121.53 131.27 -9.74 2.25e+00 1.98e-01 1.87e+01 angle pdb=" C ARG D 99 " pdb=" N ILE D 100 " pdb=" CA ILE D 100 " ideal model delta sigma weight residual 121.97 128.15 -6.18 1.80e+00 3.09e-01 1.18e+01 ... (remaining 4510 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.72: 1830 15.72 - 31.43: 108 31.43 - 47.14: 7 47.14 - 62.85: 1 62.85 - 78.56: 1 Dihedral angle restraints: 1947 sinusoidal: 738 harmonic: 1209 Sorted by residual: dihedral pdb=" CA THR E 63 " pdb=" C THR E 63 " pdb=" N VAL E 64 " pdb=" CA VAL E 64 " ideal model delta harmonic sigma weight residual 180.00 146.98 33.02 0 5.00e+00 4.00e-02 4.36e+01 dihedral pdb=" CA GLN D 92 " pdb=" C GLN D 92 " pdb=" N GLN D 93 " pdb=" CA GLN D 93 " ideal model delta harmonic sigma weight residual 180.00 149.00 31.00 0 5.00e+00 4.00e-02 3.84e+01 dihedral pdb=" CA SER A 383 " pdb=" C SER A 383 " pdb=" N PRO A 384 " pdb=" CA PRO A 384 " ideal model delta harmonic sigma weight residual 180.00 -149.34 -30.66 0 5.00e+00 4.00e-02 3.76e+01 ... (remaining 1944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 263 0.042 - 0.084: 136 0.084 - 0.127: 55 0.127 - 0.169: 27 0.169 - 0.211: 3 Chirality restraints: 484 Sorted by residual: chirality pdb=" CA HIS A 519 " pdb=" N HIS A 519 " pdb=" C HIS A 519 " pdb=" CB HIS A 519 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL A 511 " pdb=" CA VAL A 511 " pdb=" CG1 VAL A 511 " pdb=" CG2 VAL A 511 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CA THR E 58 " pdb=" N THR E 58 " pdb=" C THR E 58 " pdb=" CB THR E 58 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 481 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.056 5.00e-02 4.00e+02 8.50e-02 1.16e+01 pdb=" N PRO A 527 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 398 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.31e+00 pdb=" C ASP A 398 " 0.053 2.00e-02 2.50e+03 pdb=" O ASP A 398 " -0.020 2.00e-02 2.50e+03 pdb=" N SER A 399 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 60 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO E 61 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 61 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 61 " -0.030 5.00e-02 4.00e+02 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 107 2.65 - 3.21: 3284 3.21 - 3.77: 4889 3.77 - 4.34: 6489 4.34 - 4.90: 10557 Nonbonded interactions: 25326 Sorted by model distance: nonbonded pdb=" OG1 THR A 393 " pdb=" OE1 GLU A 516 " model vdw 2.087 3.040 nonbonded pdb=" O THR E 30 " pdb=" OG SER E 53 " model vdw 2.093 3.040 nonbonded pdb=" O SER E 52 " pdb=" NH1 ARG E 72 " model vdw 2.145 3.120 nonbonded pdb=" O LEU A 513 " pdb=" OG SER A 514 " model vdw 2.165 3.040 nonbonded pdb=" NH1 ARG A 457 " pdb=" OG SER A 459 " model vdw 2.169 3.120 ... (remaining 25321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.660 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 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 : 0.011 0.073 3327 Z= 0.494 Angle : 1.177 16.365 4525 Z= 0.656 Chirality : 0.062 0.211 484 Planarity : 0.008 0.085 589 Dihedral : 9.756 78.558 1170 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 28.64 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.83 % Favored : 89.69 % Rotamer: Outliers : 0.87 % Allowed : 0.87 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 4.76 % Twisted General : 0.75 % 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: -4.10 (0.33), residues: 417 helix: -4.58 (0.31), residues: 26 sheet: -2.91 (0.39), residues: 108 loop : -2.59 (0.31), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP A 353 HIS 0.000 0.000 HIS A 519 PHE 0.036 0.005 PHE A 497 TYR 0.032 0.004 TYR A 495 ARG 0.007 0.001 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.31241 ( 62) hydrogen bonds : angle 12.73712 ( 156) SS BOND : bond 0.00608 ( 5) SS BOND : angle 1.71565 ( 10) covalent geometry : bond 0.01073 ( 3322) covalent geometry : angle 1.17561 ( 4515) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8298 (m-80) cc_final: 0.8050 (m-80) REVERT: A 493 GLN cc_start: 0.7362 (tt0) cc_final: 0.7029 (tt0) outliers start: 3 outliers final: 3 residues processed: 112 average time/residue: 0.2126 time to fit residues: 27.3013 Evaluate side-chains 73 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 515 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN D 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.162262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.116799 restraints weight = 5336.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.119438 restraints weight = 3585.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.121393 restraints weight = 2764.528| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3327 Z= 0.172 Angle : 0.810 9.667 4525 Z= 0.421 Chirality : 0.052 0.164 484 Planarity : 0.006 0.050 589 Dihedral : 8.013 56.025 474 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.95 % Favored : 92.57 % Rotamer: Outliers : 2.91 % Allowed : 10.47 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -2.94 (0.37), residues: 417 helix: -4.16 (0.53), residues: 25 sheet: -2.36 (0.43), residues: 104 loop : -1.64 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 353 HIS 0.002 0.001 HIS A 519 PHE 0.027 0.003 PHE A 497 TYR 0.029 0.003 TYR A 495 ARG 0.005 0.001 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 62) hydrogen bonds : angle 9.46474 ( 156) SS BOND : bond 0.00551 ( 5) SS BOND : angle 1.04340 ( 10) covalent geometry : bond 0.00390 ( 3322) covalent geometry : angle 0.80919 ( 4515) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.7402 (tt0) cc_final: 0.6989 (tt0) REVERT: D 56 ASN cc_start: 0.7293 (m110) cc_final: 0.6964 (m110) REVERT: E 29 PHE cc_start: 0.8837 (t80) cc_final: 0.8438 (t80) REVERT: E 34 MET cc_start: 0.7645 (mmm) cc_final: 0.7283 (mmm) REVERT: E 80 TYR cc_start: 0.8771 (m-80) cc_final: 0.8097 (m-10) outliers start: 10 outliers final: 6 residues processed: 102 average time/residue: 0.1681 time to fit residues: 20.4631 Evaluate side-chains 82 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain E residue 96 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 4 optimal weight: 0.0470 chunk 38 optimal weight: 20.0000 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** 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 = 0.4324 r_free = 0.4324 target = 0.165457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.119562 restraints weight = 5277.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.122519 restraints weight = 3465.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.124757 restraints weight = 2613.501| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 3327 Z= 0.152 Angle : 0.826 14.042 4525 Z= 0.414 Chirality : 0.050 0.191 484 Planarity : 0.006 0.058 589 Dihedral : 7.364 59.086 473 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.71 % Favored : 92.81 % Rotamer: Outliers : 3.78 % Allowed : 14.24 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -2.42 (0.39), residues: 417 helix: -3.89 (0.62), residues: 25 sheet: -1.99 (0.45), residues: 112 loop : -1.22 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 47 HIS 0.003 0.002 HIS A 519 PHE 0.023 0.002 PHE D 101 TYR 0.023 0.002 TYR A 495 ARG 0.007 0.001 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 62) hydrogen bonds : angle 8.31819 ( 156) SS BOND : bond 0.00780 ( 5) SS BOND : angle 2.23450 ( 10) covalent geometry : bond 0.00358 ( 3322) covalent geometry : angle 0.82020 ( 4515) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7902 (ttt90) cc_final: 0.7629 (ttt90) REVERT: A 376 THR cc_start: 0.8718 (t) cc_final: 0.8491 (p) REVERT: A 406 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: E 29 PHE cc_start: 0.8844 (t80) cc_final: 0.8257 (t80) REVERT: E 34 MET cc_start: 0.7638 (mmm) cc_final: 0.7387 (mmm) REVERT: E 47 TRP cc_start: 0.8035 (t60) cc_final: 0.7583 (t60) outliers start: 13 outliers final: 8 residues processed: 98 average time/residue: 0.1573 time to fit residues: 18.5106 Evaluate side-chains 91 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 3 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN D 37 ASN ** D 45 GLN ** 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 = 0.4261 r_free = 0.4261 target = 0.159204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.112141 restraints weight = 5309.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.114318 restraints weight = 3710.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.115997 restraints weight = 2966.801| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 3327 Z= 0.237 Angle : 0.842 12.434 4525 Z= 0.433 Chirality : 0.052 0.242 484 Planarity : 0.006 0.062 589 Dihedral : 7.386 49.219 473 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.63 % Favored : 90.89 % Rotamer: Outliers : 4.65 % Allowed : 16.28 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -2.40 (0.40), residues: 417 helix: -3.84 (0.62), residues: 25 sheet: -2.01 (0.44), residues: 123 loop : -1.12 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.003 0.002 HIS A 519 PHE 0.022 0.003 PHE A 347 TYR 0.021 0.002 TYR A 495 ARG 0.003 0.001 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 62) hydrogen bonds : angle 8.26380 ( 156) SS BOND : bond 0.01078 ( 5) SS BOND : angle 2.05393 ( 10) covalent geometry : bond 0.00538 ( 3322) covalent geometry : angle 0.83762 ( 4515) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.8057 (ttt90) cc_final: 0.7702 (ttt90) REVERT: A 389 ASP cc_start: 0.7402 (t70) cc_final: 0.6845 (t0) REVERT: E 29 PHE cc_start: 0.8904 (t80) cc_final: 0.8332 (t80) outliers start: 16 outliers final: 13 residues processed: 91 average time/residue: 0.1714 time to fit residues: 18.6175 Evaluate side-chains 81 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** 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 = 0.4273 r_free = 0.4273 target = 0.160336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.113582 restraints weight = 5398.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.116434 restraints weight = 3738.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.117196 restraints weight = 2669.160| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3327 Z= 0.194 Angle : 0.802 10.345 4525 Z= 0.409 Chirality : 0.050 0.231 484 Planarity : 0.005 0.064 589 Dihedral : 6.946 34.010 473 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.15 % Favored : 91.37 % Rotamer: Outliers : 5.81 % Allowed : 15.99 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -2.24 (0.41), residues: 417 helix: -4.34 (0.40), residues: 19 sheet: -1.83 (0.45), residues: 123 loop : -1.08 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 47 HIS 0.002 0.001 HIS A 519 PHE 0.019 0.002 PHE A 429 TYR 0.024 0.002 TYR D 52 ARG 0.005 0.001 ARG D 48 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 62) hydrogen bonds : angle 7.81917 ( 156) SS BOND : bond 0.00931 ( 5) SS BOND : angle 1.99540 ( 10) covalent geometry : bond 0.00441 ( 3322) covalent geometry : angle 0.79744 ( 4515) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7958 (ttt90) cc_final: 0.7502 (ttt90) REVERT: A 376 THR cc_start: 0.8778 (t) cc_final: 0.8430 (p) REVERT: A 389 ASP cc_start: 0.7413 (t70) cc_final: 0.6844 (t0) outliers start: 20 outliers final: 16 residues processed: 96 average time/residue: 0.1535 time to fit residues: 17.7826 Evaluate side-chains 85 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.0030 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.161440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.114476 restraints weight = 5433.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.117074 restraints weight = 3581.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.118346 restraints weight = 2755.184| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3327 Z= 0.165 Angle : 0.777 9.076 4525 Z= 0.397 Chirality : 0.050 0.227 484 Planarity : 0.005 0.063 589 Dihedral : 6.410 27.927 471 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.63 % Favored : 90.65 % Rotamer: Outliers : 4.65 % Allowed : 19.19 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -2.14 (0.42), residues: 417 helix: -3.87 (0.61), residues: 25 sheet: -1.60 (0.48), residues: 114 loop : -1.09 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 47 HIS 0.002 0.001 HIS A 519 PHE 0.022 0.002 PHE A 515 TYR 0.017 0.002 TYR A 495 ARG 0.007 0.001 ARG D 48 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 62) hydrogen bonds : angle 7.27549 ( 156) SS BOND : bond 0.00853 ( 5) SS BOND : angle 1.95216 ( 10) covalent geometry : bond 0.00376 ( 3322) covalent geometry : angle 0.77240 ( 4515) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7955 (ttt90) cc_final: 0.7608 (ttt90) REVERT: A 376 THR cc_start: 0.8803 (t) cc_final: 0.8473 (p) REVERT: A 389 ASP cc_start: 0.7311 (t70) cc_final: 0.6770 (t0) REVERT: A 506 GLN cc_start: 0.5945 (mt0) cc_final: 0.5743 (mt0) REVERT: D 101 PHE cc_start: 0.8799 (m-80) cc_final: 0.8560 (m-10) REVERT: E 34 MET cc_start: 0.7697 (mmm) cc_final: 0.7364 (mmm) REVERT: E 76 LYS cc_start: 0.8496 (mttt) cc_final: 0.8295 (mttt) outliers start: 16 outliers final: 13 residues processed: 87 average time/residue: 0.1704 time to fit residues: 17.7089 Evaluate side-chains 78 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 10 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN D 40 GLN D 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.163321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.116858 restraints weight = 5334.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.119852 restraints weight = 3401.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.122022 restraints weight = 2572.196| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3327 Z= 0.149 Angle : 0.757 8.370 4525 Z= 0.385 Chirality : 0.049 0.207 484 Planarity : 0.006 0.066 589 Dihedral : 6.135 27.372 471 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.19 % Favored : 92.09 % Rotamer: Outliers : 5.23 % Allowed : 18.31 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -2.08 (0.41), residues: 417 helix: -3.85 (0.64), residues: 25 sheet: -1.51 (0.48), residues: 114 loop : -1.08 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 47 HIS 0.001 0.001 HIS A 519 PHE 0.016 0.002 PHE A 515 TYR 0.023 0.002 TYR D 52 ARG 0.010 0.001 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 62) hydrogen bonds : angle 6.95435 ( 156) SS BOND : bond 0.00847 ( 5) SS BOND : angle 1.85761 ( 10) covalent geometry : bond 0.00342 ( 3322) covalent geometry : angle 0.75294 ( 4515) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8281 (m) cc_final: 0.7783 (p) REVERT: A 355 ARG cc_start: 0.7891 (ttt90) cc_final: 0.7539 (ttt90) REVERT: A 376 THR cc_start: 0.8752 (t) cc_final: 0.8447 (p) REVERT: A 389 ASP cc_start: 0.7146 (t70) cc_final: 0.6606 (t0) REVERT: A 506 GLN cc_start: 0.5866 (mt0) cc_final: 0.5594 (mt0) REVERT: D 37 ASN cc_start: 0.6939 (m-40) cc_final: 0.6738 (m110) REVERT: E 34 MET cc_start: 0.7768 (mmm) cc_final: 0.7472 (mmm) REVERT: E 80 TYR cc_start: 0.8224 (m-10) cc_final: 0.7971 (m-10) outliers start: 18 outliers final: 14 residues processed: 83 average time/residue: 0.2059 time to fit residues: 21.0770 Evaluate side-chains 77 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 3 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN D 40 GLN ** D 45 GLN ** 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 = 0.4335 r_free = 0.4335 target = 0.166618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.122189 restraints weight = 5262.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.124830 restraints weight = 3569.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.126304 restraints weight = 2457.512| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3327 Z= 0.127 Angle : 0.738 8.260 4525 Z= 0.377 Chirality : 0.051 0.309 484 Planarity : 0.005 0.065 589 Dihedral : 5.676 22.212 471 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.24 % Favored : 93.05 % Rotamer: Outliers : 4.36 % Allowed : 20.64 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -1.88 (0.42), residues: 417 helix: -3.74 (0.65), residues: 25 sheet: -1.26 (0.49), residues: 114 loop : -0.99 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 47 HIS 0.001 0.001 HIS A 519 PHE 0.013 0.002 PHE A 429 TYR 0.019 0.002 TYR D 52 ARG 0.009 0.001 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.02886 ( 62) hydrogen bonds : angle 6.53918 ( 156) SS BOND : bond 0.00788 ( 5) SS BOND : angle 1.66787 ( 10) covalent geometry : bond 0.00289 ( 3322) covalent geometry : angle 0.73507 ( 4515) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8057 (m) cc_final: 0.7635 (p) REVERT: A 355 ARG cc_start: 0.7712 (ttt90) cc_final: 0.7431 (tpp80) REVERT: A 389 ASP cc_start: 0.7194 (t70) cc_final: 0.6665 (t0) REVERT: E 11 LEU cc_start: 0.7975 (tp) cc_final: 0.7192 (mp) REVERT: E 36 TRP cc_start: 0.8325 (m100) cc_final: 0.8103 (m100) REVERT: E 79 LEU cc_start: 0.8823 (tp) cc_final: 0.8553 (tt) outliers start: 15 outliers final: 12 residues processed: 88 average time/residue: 0.1908 time to fit residues: 20.1281 Evaluate side-chains 79 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN ** D 45 GLN ** 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 = 0.4341 r_free = 0.4341 target = 0.166861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.121790 restraints weight = 5207.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.124986 restraints weight = 3287.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.127320 restraints weight = 2441.574| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.6177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3327 Z= 0.127 Angle : 0.755 8.053 4525 Z= 0.384 Chirality : 0.049 0.269 484 Planarity : 0.005 0.064 589 Dihedral : 5.579 21.349 471 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.43 % Favored : 91.85 % Rotamer: Outliers : 3.78 % Allowed : 22.09 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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 (0.42), residues: 417 helix: -3.73 (0.65), residues: 25 sheet: -0.72 (0.52), residues: 106 loop : -1.06 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 47 HIS 0.003 0.002 HIS A 519 PHE 0.014 0.002 PHE A 515 TYR 0.017 0.001 TYR D 52 ARG 0.007 0.000 ARG D 48 Details of bonding type rmsd hydrogen bonds : bond 0.02934 ( 62) hydrogen bonds : angle 6.31543 ( 156) SS BOND : bond 0.00769 ( 5) SS BOND : angle 1.60243 ( 10) covalent geometry : bond 0.00290 ( 3322) covalent geometry : angle 0.75255 ( 4515) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8063 (m) cc_final: 0.7716 (p) REVERT: A 355 ARG cc_start: 0.7764 (ttt90) cc_final: 0.7527 (tpp80) REVERT: A 389 ASP cc_start: 0.7050 (t70) cc_final: 0.6538 (t0) REVERT: A 452 LEU cc_start: 0.8298 (tt) cc_final: 0.8006 (mt) REVERT: A 471 GLU cc_start: 0.7656 (pp20) cc_final: 0.6978 (pt0) REVERT: D 92 GLN cc_start: 0.7852 (tp40) cc_final: 0.7625 (tm-30) REVERT: E 11 LEU cc_start: 0.8006 (tp) cc_final: 0.7239 (mp) REVERT: E 79 LEU cc_start: 0.8773 (tp) cc_final: 0.8544 (tt) REVERT: E 96 CYS cc_start: 0.4513 (OUTLIER) cc_final: 0.4237 (p) outliers start: 13 outliers final: 10 residues processed: 80 average time/residue: 0.1655 time to fit residues: 15.7899 Evaluate side-chains 78 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 38 optimal weight: 20.0000 chunk 35 optimal weight: 0.0030 chunk 39 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN D 37 ASN ** D 45 GLN ** 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 = 0.4295 r_free = 0.4295 target = 0.162014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.115839 restraints weight = 5222.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.118406 restraints weight = 3507.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.120384 restraints weight = 2726.317| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.6170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3327 Z= 0.189 Angle : 0.818 8.950 4525 Z= 0.420 Chirality : 0.051 0.247 484 Planarity : 0.005 0.064 589 Dihedral : 5.853 21.905 469 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.83 % Favored : 89.21 % Rotamer: Outliers : 4.36 % Allowed : 21.80 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -1.73 (0.43), residues: 417 helix: -3.99 (0.47), residues: 25 sheet: -1.01 (0.53), residues: 107 loop : -0.93 (0.40), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP E 36 HIS 0.003 0.002 HIS A 519 PHE 0.018 0.002 PHE A 392 TYR 0.016 0.002 TYR A 451 ARG 0.009 0.001 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03000 ( 62) hydrogen bonds : angle 6.62729 ( 156) SS BOND : bond 0.00884 ( 5) SS BOND : angle 2.11589 ( 10) covalent geometry : bond 0.00442 ( 3322) covalent geometry : angle 0.81299 ( 4515) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8470 (m) cc_final: 0.8129 (p) REVERT: A 355 ARG cc_start: 0.7923 (ttt90) cc_final: 0.7671 (tpp80) REVERT: A 389 ASP cc_start: 0.7079 (t70) cc_final: 0.6468 (t0) REVERT: A 439 ASN cc_start: 0.7811 (m-40) cc_final: 0.6968 (m-40) REVERT: A 452 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8157 (mt) REVERT: E 11 LEU cc_start: 0.8045 (tp) cc_final: 0.7251 (mp) outliers start: 15 outliers final: 12 residues processed: 72 average time/residue: 0.1716 time to fit residues: 15.0091 Evaluate side-chains 74 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 36 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN ** D 45 GLN ** 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 = 0.4284 r_free = 0.4284 target = 0.160943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.115792 restraints weight = 5342.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.117683 restraints weight = 4136.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.118888 restraints weight = 3003.256| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.6126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3327 Z= 0.213 Angle : 0.838 8.542 4525 Z= 0.429 Chirality : 0.051 0.217 484 Planarity : 0.005 0.065 589 Dihedral : 6.032 22.644 469 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.96 % Allowed : 10.31 % Favored : 88.73 % Rotamer: Outliers : 4.36 % Allowed : 22.09 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -1.72 (0.43), residues: 417 helix: -4.27 (0.42), residues: 19 sheet: -1.04 (0.53), residues: 109 loop : -0.96 (0.40), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP E 36 HIS 0.002 0.002 HIS A 519 PHE 0.027 0.003 PHE A 392 TYR 0.018 0.002 TYR A 451 ARG 0.007 0.001 ARG D 48 Details of bonding type rmsd hydrogen bonds : bond 0.03082 ( 62) hydrogen bonds : angle 6.77342 ( 156) SS BOND : bond 0.00828 ( 5) SS BOND : angle 2.00200 ( 10) covalent geometry : bond 0.00491 ( 3322) covalent geometry : angle 0.83317 ( 4515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1632.48 seconds wall clock time: 29 minutes 16.29 seconds (1756.29 seconds total)