Starting phenix.real_space_refine on Wed Jul 23 16:31:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n9a_24253/07_2025/7n9a_24253.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n9a_24253/07_2025/7n9a_24253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n9a_24253/07_2025/7n9a_24253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n9a_24253/07_2025/7n9a_24253.map" model { file = "/net/cci-nas-00/data/ceres_data/7n9a_24253/07_2025/7n9a_24253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n9a_24253/07_2025/7n9a_24253.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1545 atoms to isotropic. 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 11 5.16 5 C 1540 2.51 5 N 420 2.21 5 O 460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 2431 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 886 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "E" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1545 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Time building chain proxies: 4.34, per 1000 atoms: 1.79 Number of scatterers: 2431 At special positions: 0 Unit cell: (79.68, 60.59, 79.68, 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 11 16.00 O 460 8.00 N 420 7.00 C 1540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 94 " distance=2.05 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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: 0.56 Conformation dependent library (CDL) restraints added in 296.5 milliseconds 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 5 sheets defined 13.5% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.524A pdb=" N THR A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.580A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 371 removed outlier: 4.099A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 390 removed outlier: 3.817A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 408 removed outlier: 4.382A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 405 through 408' Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.544A pdb=" N SER A 7 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 21 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 67 " --> pdb=" O GLN A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.786A pdb=" N VAL A 113 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 90 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 91 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG A 36 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 45 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.786A pdb=" N VAL A 113 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 90 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.597A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 66 hydrogen bonds defined for protein. 171 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: 0.57 Time building geometry restraints manager: 0.69 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: 796 1.34 - 1.47: 657 1.47 - 1.59: 1025 1.59 - 1.71: 0 1.71 - 1.84: 12 Bond restraints: 2490 Sorted by residual: bond pdb=" N PRO E 499 " pdb=" CD PRO E 499 " ideal model delta sigma weight residual 1.473 1.446 0.027 1.40e-02 5.10e+03 3.76e+00 bond pdb=" CB VAL A 2 " pdb=" CG1 VAL A 2 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.78e+00 bond pdb=" CA PRO E 499 " pdb=" CB PRO E 499 " ideal model delta sigma weight residual 1.534 1.558 -0.024 1.49e-02 4.50e+03 2.65e+00 bond pdb=" CG LEU E 518 " pdb=" CD1 LEU E 518 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" CB PHE A 45 " pdb=" CG PHE A 45 " ideal model delta sigma weight residual 1.502 1.467 0.035 2.30e-02 1.89e+03 2.36e+00 ... (remaining 2485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 3149 2.28 - 4.55: 185 4.55 - 6.83: 37 6.83 - 9.11: 5 9.11 - 11.39: 5 Bond angle restraints: 3381 Sorted by residual: angle pdb=" CA PRO E 499 " pdb=" N PRO E 499 " pdb=" CD PRO E 499 " ideal model delta sigma weight residual 112.00 102.71 9.29 1.40e+00 5.10e-01 4.40e+01 angle pdb=" N GLY E 482 " pdb=" CA GLY E 482 " pdb=" C GLY E 482 " ideal model delta sigma weight residual 114.90 122.64 -7.74 1.54e+00 4.22e-01 2.53e+01 angle pdb=" CA CYS A 22 " pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " ideal model delta sigma weight residual 114.40 125.79 -11.39 2.30e+00 1.89e-01 2.45e+01 angle pdb=" C GLN E 409 " pdb=" N ILE E 410 " pdb=" CA ILE E 410 " ideal model delta sigma weight residual 123.11 117.10 6.01 1.36e+00 5.41e-01 1.95e+01 angle pdb=" CA TYR E 495 " pdb=" CB TYR E 495 " pdb=" CG TYR E 495 " ideal model delta sigma weight residual 113.90 121.76 -7.86 1.80e+00 3.09e-01 1.91e+01 ... (remaining 3376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 1342 16.68 - 33.36: 93 33.36 - 50.04: 20 50.04 - 66.72: 5 66.72 - 83.40: 4 Dihedral angle restraints: 1464 sinusoidal: 569 harmonic: 895 Sorted by residual: dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 94 " pdb=" CB CYS A 94 " ideal model delta sinusoidal sigma weight residual 93.00 165.21 -72.21 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 145.12 -52.12 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" SG CYS E 391 " pdb=" CB CYS E 525 " pdb=" SG CYS E 525 " pdb=" CA CYS E 525 " ideal model delta sinusoidal sigma weight residual -73.00 -14.99 -58.01 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 1461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 202 0.045 - 0.090: 101 0.090 - 0.136: 39 0.136 - 0.181: 12 0.181 - 0.226: 4 Chirality restraints: 358 Sorted by residual: chirality pdb=" CA ASN E 481 " pdb=" N ASN E 481 " pdb=" C ASN E 481 " pdb=" CB ASN E 481 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA PHE E 497 " pdb=" N PHE E 497 " pdb=" C PHE E 497 " pdb=" CB PHE E 497 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CG LEU E 455 " pdb=" CB LEU E 455 " pdb=" CD1 LEU E 455 " pdb=" CD2 LEU E 455 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 355 not shown) Planarity restraints: 445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 498 " 0.067 5.00e-02 4.00e+02 9.57e-02 1.46e+01 pdb=" N PRO E 499 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO E 499 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 499 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 495 " -0.026 2.00e-02 2.50e+03 2.25e-02 1.01e+01 pdb=" CG TYR E 495 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR E 495 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR E 495 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 495 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR E 495 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR E 495 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 495 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 497 " 0.003 2.00e-02 2.50e+03 2.34e-02 9.60e+00 pdb=" CG PHE E 497 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE E 497 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE E 497 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE E 497 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 PHE E 497 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE E 497 " 0.000 2.00e-02 2.50e+03 ... (remaining 442 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 75 2.69 - 3.24: 2344 3.24 - 3.79: 3625 3.79 - 4.35: 4704 4.35 - 4.90: 7651 Nonbonded interactions: 18399 Sorted by model distance: nonbonded pdb=" O THR A 101 " pdb=" OH TYR E 489 " model vdw 2.135 3.040 nonbonded pdb=" OD1 ASN E 448 " pdb=" ND2 ASN E 450 " model vdw 2.182 3.120 nonbonded pdb=" O GLN E 414 " pdb=" NZ LYS E 424 " model vdw 2.246 3.120 nonbonded pdb=" O ASN A 72 " pdb=" ND2 ASN A 72 " model vdw 2.315 3.120 nonbonded pdb=" OD1 ASN E 388 " pdb=" N ASP E 389 " model vdw 2.316 3.120 ... (remaining 18394 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: 5.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.430 Find NCS groups from input model: 0.020 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: 21.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 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 0.055 2495 Z= 0.301 Angle : 1.287 13.720 3391 Z= 0.745 Chirality : 0.064 0.226 358 Planarity : 0.007 0.096 445 Dihedral : 12.630 83.395 885 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.45), residues: 308 helix: -2.13 (0.71), residues: 30 sheet: 1.69 (0.55), residues: 74 loop : -0.48 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP E 353 HIS 0.005 0.002 HIS A 30 PHE 0.042 0.004 PHE E 497 TYR 0.056 0.005 TYR E 495 ARG 0.006 0.001 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.29651 ( 62) hydrogen bonds : angle 10.02280 ( 171) SS BOND : bond 0.00864 ( 5) SS BOND : angle 5.13315 ( 10) covalent geometry : bond 0.00693 ( 2490) covalent geometry : angle 1.25857 ( 3381) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.252 Fit side-chains REVERT: A 42 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6715 (tm-30) REVERT: E 489 TYR cc_start: 0.6940 (m-80) cc_final: 0.6408 (m-80) REVERT: E 501 ASN cc_start: 0.7721 (m110) cc_final: 0.7519 (m110) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1106 time to fit residues: 9.9538 Evaluate side-chains 66 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.0980 chunk 22 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.0040 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.0570 chunk 8 optimal weight: 0.0470 overall best weight: 0.1008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.147785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.135675 restraints weight = 4374.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.139454 restraints weight = 2346.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.141971 restraints weight = 1390.372| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2495 Z= 0.134 Angle : 0.649 7.303 3391 Z= 0.353 Chirality : 0.047 0.136 358 Planarity : 0.004 0.039 445 Dihedral : 5.393 25.473 349 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.33 % Allowed : 10.47 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.45), residues: 308 helix: -1.90 (0.86), residues: 23 sheet: 1.47 (0.59), residues: 73 loop : -0.56 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 34 HIS 0.001 0.000 HIS A 30 PHE 0.016 0.002 PHE E 497 TYR 0.019 0.002 TYR A 106 ARG 0.003 0.001 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.04485 ( 62) hydrogen bonds : angle 7.54841 ( 171) SS BOND : bond 0.00268 ( 5) SS BOND : angle 1.57669 ( 10) covalent geometry : bond 0.00288 ( 2490) covalent geometry : angle 0.64441 ( 3381) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.200 Fit side-chains REVERT: A 42 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6746 (tm-30) REVERT: E 395 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7638 (t) REVERT: E 489 TYR cc_start: 0.7214 (m-80) cc_final: 0.6677 (m-80) outliers start: 6 outliers final: 4 residues processed: 63 average time/residue: 0.1214 time to fit residues: 9.5005 Evaluate side-chains 65 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 395 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 15 optimal weight: 0.0970 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 11 optimal weight: 0.0970 chunk 1 optimal weight: 0.0010 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 19 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 overall best weight: 0.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 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 = 0.3955 r_free = 0.3955 target = 0.146606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.134071 restraints weight = 4356.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.137915 restraints weight = 2363.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.140530 restraints weight = 1417.392| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2495 Z= 0.146 Angle : 0.599 6.620 3391 Z= 0.321 Chirality : 0.046 0.143 358 Planarity : 0.005 0.044 445 Dihedral : 5.143 17.798 349 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.49 % Allowed : 14.34 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.46), residues: 308 helix: -1.63 (0.93), residues: 21 sheet: 1.17 (0.55), residues: 79 loop : -0.41 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 34 HIS 0.002 0.001 HIS A 30 PHE 0.031 0.002 PHE E 497 TYR 0.014 0.002 TYR E 495 ARG 0.004 0.000 ARG A 97 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 62) hydrogen bonds : angle 7.11659 ( 171) SS BOND : bond 0.00248 ( 5) SS BOND : angle 1.10058 ( 10) covalent geometry : bond 0.00328 ( 2490) covalent geometry : angle 0.59726 ( 3381) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.255 Fit side-chains REVERT: A 42 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6828 (tm-30) outliers start: 9 outliers final: 6 residues processed: 65 average time/residue: 0.1215 time to fit residues: 9.6949 Evaluate side-chains 65 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 29 optimal weight: 0.1980 chunk 28 optimal weight: 0.4980 chunk 18 optimal weight: 0.0770 chunk 21 optimal weight: 0.4980 chunk 19 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 overall best weight: 0.2938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.143543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.130903 restraints weight = 4287.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.134782 restraints weight = 2329.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.137404 restraints weight = 1396.772| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2495 Z= 0.203 Angle : 0.638 9.062 3391 Z= 0.339 Chirality : 0.047 0.141 358 Planarity : 0.005 0.046 445 Dihedral : 5.396 18.179 349 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.43 % Allowed : 15.12 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.45), residues: 308 helix: -2.58 (0.77), residues: 29 sheet: 0.62 (0.54), residues: 81 loop : -0.47 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 107 HIS 0.004 0.001 HIS A 30 PHE 0.044 0.003 PHE E 497 TYR 0.018 0.002 TYR E 453 ARG 0.004 0.001 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 62) hydrogen bonds : angle 6.74508 ( 171) SS BOND : bond 0.00261 ( 5) SS BOND : angle 1.19110 ( 10) covalent geometry : bond 0.00456 ( 2490) covalent geometry : angle 0.63543 ( 3381) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.261 Fit side-chains REVERT: A 42 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6851 (tm-30) outliers start: 14 outliers final: 13 residues processed: 69 average time/residue: 0.1066 time to fit residues: 9.1827 Evaluate side-chains 79 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 501 ASN Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 0.0040 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 chunk 21 optimal weight: 0.0670 chunk 6 optimal weight: 0.0170 chunk 27 optimal weight: 0.0570 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 overall best weight: 0.0686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.147355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.134241 restraints weight = 4417.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.138262 restraints weight = 2382.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140961 restraints weight = 1424.983| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2495 Z= 0.105 Angle : 0.555 6.552 3391 Z= 0.293 Chirality : 0.044 0.142 358 Planarity : 0.005 0.050 445 Dihedral : 4.736 16.150 349 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.04 % Allowed : 18.22 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.44), residues: 308 helix: -1.73 (0.94), residues: 23 sheet: 0.37 (0.57), residues: 74 loop : -0.49 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 34 HIS 0.001 0.001 HIS E 519 PHE 0.027 0.002 PHE A 45 TYR 0.013 0.001 TYR A 106 ARG 0.002 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 62) hydrogen bonds : angle 6.48555 ( 171) SS BOND : bond 0.00351 ( 5) SS BOND : angle 0.96626 ( 10) covalent geometry : bond 0.00232 ( 2490) covalent geometry : angle 0.55363 ( 3381) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.256 Fit side-chains REVERT: A 42 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6828 (tm-30) REVERT: E 457 ARG cc_start: 0.8271 (ttt-90) cc_final: 0.7721 (ttt90) outliers start: 13 outliers final: 11 residues processed: 69 average time/residue: 0.1232 time to fit residues: 10.3207 Evaluate side-chains 76 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.0570 chunk 4 optimal weight: 0.6980 chunk 10 optimal weight: 0.0030 chunk 13 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 9 optimal weight: 0.0970 chunk 21 optimal weight: 0.3980 chunk 15 optimal weight: 0.0870 overall best weight: 0.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.146997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.133744 restraints weight = 4426.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.137712 restraints weight = 2352.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.140401 restraints weight = 1407.200| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2495 Z= 0.100 Angle : 0.541 6.549 3391 Z= 0.286 Chirality : 0.043 0.134 358 Planarity : 0.005 0.052 445 Dihedral : 4.554 14.807 349 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.04 % Allowed : 19.77 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.44), residues: 308 helix: -1.70 (0.96), residues: 23 sheet: 0.57 (0.58), residues: 74 loop : -0.49 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 107 HIS 0.005 0.002 HIS A 30 PHE 0.018 0.002 PHE E 497 TYR 0.010 0.001 TYR A 106 ARG 0.005 0.000 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 62) hydrogen bonds : angle 6.40337 ( 171) SS BOND : bond 0.00194 ( 5) SS BOND : angle 0.96533 ( 10) covalent geometry : bond 0.00217 ( 2490) covalent geometry : angle 0.53947 ( 3381) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.260 Fit side-chains REVERT: A 42 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6796 (tm-30) REVERT: E 457 ARG cc_start: 0.7986 (ttt-90) cc_final: 0.7752 (ttt90) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.1350 time to fit residues: 11.6772 Evaluate side-chains 77 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.0970 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 0.0670 chunk 25 optimal weight: 0.2980 chunk 23 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 11 optimal weight: 0.3980 overall best weight: 0.1716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.144850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131235 restraints weight = 4459.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.135294 restraints weight = 2402.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.138112 restraints weight = 1444.465| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2495 Z= 0.138 Angle : 0.563 6.705 3391 Z= 0.302 Chirality : 0.044 0.146 358 Planarity : 0.005 0.051 445 Dihedral : 4.665 14.651 349 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 6.20 % Allowed : 18.22 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.44), residues: 308 helix: -2.66 (0.77), residues: 31 sheet: 0.51 (0.56), residues: 74 loop : -0.50 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 107 HIS 0.002 0.001 HIS A 30 PHE 0.020 0.002 PHE E 497 TYR 0.011 0.001 TYR E 453 ARG 0.006 0.001 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 62) hydrogen bonds : angle 6.39006 ( 171) SS BOND : bond 0.00151 ( 5) SS BOND : angle 1.03768 ( 10) covalent geometry : bond 0.00314 ( 2490) covalent geometry : angle 0.56119 ( 3381) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.236 Fit side-chains REVERT: A 42 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6886 (tm-30) REVERT: A 68 ILE cc_start: 0.6838 (mm) cc_final: 0.6412 (mm) outliers start: 16 outliers final: 16 residues processed: 69 average time/residue: 0.1189 time to fit residues: 9.9522 Evaluate side-chains 81 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 501 ASN Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 12 optimal weight: 0.0980 chunk 29 optimal weight: 0.0970 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 0.0050 chunk 28 optimal weight: 0.0870 chunk 22 optimal weight: 0.5980 overall best weight: 0.1570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.145165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.131634 restraints weight = 4447.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.135737 restraints weight = 2393.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.138478 restraints weight = 1429.375| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2495 Z= 0.132 Angle : 0.568 6.745 3391 Z= 0.305 Chirality : 0.044 0.142 358 Planarity : 0.005 0.051 445 Dihedral : 4.729 15.108 349 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.04 % Allowed : 19.38 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.44), residues: 308 helix: -2.71 (0.76), residues: 31 sheet: 0.61 (0.54), residues: 80 loop : -0.60 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP E 353 HIS 0.002 0.001 HIS A 30 PHE 0.040 0.002 PHE E 497 TYR 0.015 0.001 TYR E 495 ARG 0.004 0.001 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 62) hydrogen bonds : angle 6.43886 ( 171) SS BOND : bond 0.00141 ( 5) SS BOND : angle 1.19476 ( 10) covalent geometry : bond 0.00299 ( 2490) covalent geometry : angle 0.56490 ( 3381) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.228 Fit side-chains REVERT: A 42 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6914 (tm-30) REVERT: A 68 ILE cc_start: 0.6926 (mm) cc_final: 0.6551 (mm) REVERT: E 457 ARG cc_start: 0.8111 (ttt90) cc_final: 0.7715 (ttt90) outliers start: 13 outliers final: 13 residues processed: 68 average time/residue: 0.1367 time to fit residues: 11.0789 Evaluate side-chains 77 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.0570 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.0970 chunk 12 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 0.0970 chunk 6 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 overall best weight: 0.1294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.145527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.132074 restraints weight = 4388.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.136214 restraints weight = 2359.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.138975 restraints weight = 1410.443| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2495 Z= 0.119 Angle : 0.553 6.978 3391 Z= 0.295 Chirality : 0.043 0.133 358 Planarity : 0.005 0.051 445 Dihedral : 4.604 15.244 349 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 6.98 % Allowed : 17.05 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.44), residues: 308 helix: -2.65 (0.77), residues: 31 sheet: 0.58 (0.54), residues: 80 loop : -0.67 (0.41), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 353 HIS 0.002 0.001 HIS A 30 PHE 0.036 0.002 PHE E 497 TYR 0.013 0.001 TYR E 495 ARG 0.004 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03196 ( 62) hydrogen bonds : angle 6.45588 ( 171) SS BOND : bond 0.00195 ( 5) SS BOND : angle 1.15573 ( 10) covalent geometry : bond 0.00269 ( 2490) covalent geometry : angle 0.55004 ( 3381) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.230 Fit side-chains REVERT: A 42 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6910 (tm-30) REVERT: A 68 ILE cc_start: 0.6892 (mm) cc_final: 0.6532 (mm) outliers start: 18 outliers final: 15 residues processed: 71 average time/residue: 0.1324 time to fit residues: 11.3307 Evaluate side-chains 78 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 501 ASN Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.0670 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.0770 chunk 16 optimal weight: 0.4980 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.142794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.129989 restraints weight = 4335.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.133860 restraints weight = 2376.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.136517 restraints weight = 1433.912| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 2495 Z= 0.203 Angle : 0.659 10.355 3391 Z= 0.348 Chirality : 0.047 0.154 358 Planarity : 0.006 0.049 445 Dihedral : 5.096 16.062 349 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 6.20 % Allowed : 17.83 % Favored : 75.97 % 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: -1.02 (0.45), residues: 308 helix: -2.68 (0.78), residues: 31 sheet: 0.22 (0.53), residues: 86 loop : -0.73 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP E 353 HIS 0.003 0.001 HIS A 30 PHE 0.039 0.002 PHE E 497 TYR 0.014 0.002 TYR E 495 ARG 0.004 0.001 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 62) hydrogen bonds : angle 6.69146 ( 171) SS BOND : bond 0.00314 ( 5) SS BOND : angle 1.60904 ( 10) covalent geometry : bond 0.00459 ( 2490) covalent geometry : angle 0.65396 ( 3381) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.260 Fit side-chains REVERT: A 42 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6980 (tm-30) REVERT: A 68 ILE cc_start: 0.7077 (mm) cc_final: 0.6736 (mm) outliers start: 16 outliers final: 15 residues processed: 70 average time/residue: 0.1288 time to fit residues: 11.0027 Evaluate side-chains 78 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 501 ASN Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.0470 chunk 11 optimal weight: 0.0060 chunk 17 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 27 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.1894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.144360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.131105 restraints weight = 4402.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.135060 restraints weight = 2412.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.137744 restraints weight = 1452.991| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2495 Z= 0.152 Angle : 0.628 9.982 3391 Z= 0.332 Chirality : 0.046 0.149 358 Planarity : 0.005 0.050 445 Dihedral : 4.885 15.797 349 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.43 % Allowed : 19.77 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.46), residues: 308 helix: -1.74 (0.99), residues: 23 sheet: 0.46 (0.55), residues: 81 loop : -0.88 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP E 353 HIS 0.002 0.001 HIS A 30 PHE 0.036 0.002 PHE E 497 TYR 0.012 0.002 TYR E 453 ARG 0.004 0.001 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 62) hydrogen bonds : angle 6.73434 ( 171) SS BOND : bond 0.00179 ( 5) SS BOND : angle 1.33151 ( 10) covalent geometry : bond 0.00349 ( 2490) covalent geometry : angle 0.62447 ( 3381) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2791.26 seconds wall clock time: 50 minutes 11.28 seconds (3011.28 seconds total)