Starting phenix.real_space_refine on Sat May 10 20:26:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ijz_60646/05_2025/9ijz_60646_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ijz_60646/05_2025/9ijz_60646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ijz_60646/05_2025/9ijz_60646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ijz_60646/05_2025/9ijz_60646.map" model { file = "/net/cci-nas-00/data/ceres_data/9ijz_60646/05_2025/9ijz_60646_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ijz_60646/05_2025/9ijz_60646_trim.cif" } resolution = 2.91 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= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 32 5.16 5 C 4474 2.51 5 N 1054 2.21 5 O 1090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6654 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3270 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 13, 'TRANS': 378} Chain breaks: 1 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'6PL': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 5.73, per 1000 atoms: 0.86 Number of scatterers: 6654 At special positions: 0 Unit cell: (69.9, 123.956, 77.356, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 4 15.00 O 1090 8.00 N 1054 7.00 C 4474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 796.9 milliseconds 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 77.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 230 through 257 Processing helix chain 'A' and resid 265 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 312 through 336 Processing helix chain 'A' and resid 345 through 361 removed outlier: 3.802A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 removed outlier: 3.591A pdb=" N PHE A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 403 Processing helix chain 'A' and resid 403 through 420 removed outlier: 3.757A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 470 Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 472 through 503 removed outlier: 4.130A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 532 removed outlier: 4.403A pdb=" N VAL A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 571 removed outlier: 4.104A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 583 removed outlier: 3.820A pdb=" N ILE A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 618 Proline residue: A 598 - end of helix removed outlier: 3.835A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 257 Processing helix chain 'B' and resid 265 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 312 through 336 Processing helix chain 'B' and resid 345 through 361 removed outlier: 3.802A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 removed outlier: 3.591A pdb=" N PHE B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.757A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 470 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 472 through 503 removed outlier: 4.130A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 502 " --> pdb=" O THR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 532 removed outlier: 4.403A pdb=" N VAL B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 571 removed outlier: 4.104A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 583 removed outlier: 3.820A pdb=" N ILE B 575 " --> pdb=" O PHE B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 618 Proline residue: B 598 - end of helix removed outlier: 3.835A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 946 1.31 - 1.43: 2116 1.43 - 1.56: 3756 1.56 - 1.68: 4 1.68 - 1.81: 44 Bond restraints: 6866 Sorted by residual: bond pdb=" C11 6PL A1002 " pdb=" O3 6PL A1002 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C11 6PL B1002 " pdb=" O3 6PL B1002 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C31 6PL B1002 " pdb=" O2 6PL B1002 " ideal model delta sigma weight residual 1.330 1.416 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C31 6PL A1002 " pdb=" O2 6PL A1002 " ideal model delta sigma weight residual 1.330 1.416 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" CA TYR B 524 " pdb=" C TYR B 524 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.29e-02 6.01e+03 1.69e+01 ... (remaining 6861 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.78: 9252 3.78 - 7.56: 58 7.56 - 11.34: 4 11.34 - 15.12: 0 15.12 - 18.90: 4 Bond angle restraints: 9318 Sorted by residual: angle pdb=" O1P 6PL A1002 " pdb=" P 6PL A1002 " pdb=" O2P 6PL A1002 " ideal model delta sigma weight residual 119.71 100.81 18.90 3.00e+00 1.11e-01 3.97e+01 angle pdb=" O1P 6PL B1002 " pdb=" P 6PL B1002 " pdb=" O2P 6PL B1002 " ideal model delta sigma weight residual 119.71 100.81 18.90 3.00e+00 1.11e-01 3.97e+01 angle pdb=" O3P 6PL A1002 " pdb=" P 6PL A1002 " pdb=" O4P 6PL A1002 " ideal model delta sigma weight residual 93.65 110.78 -17.13 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O3P 6PL B1002 " pdb=" P 6PL B1002 " pdb=" O4P 6PL B1002 " ideal model delta sigma weight residual 93.65 110.78 -17.13 3.00e+00 1.11e-01 3.26e+01 angle pdb=" CA GLU B 549 " pdb=" CB GLU B 549 " pdb=" CG GLU B 549 " ideal model delta sigma weight residual 114.10 121.53 -7.43 2.00e+00 2.50e-01 1.38e+01 ... (remaining 9313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.77: 3262 14.77 - 29.53: 444 29.53 - 44.30: 146 44.30 - 59.07: 64 59.07 - 73.83: 4 Dihedral angle restraints: 3920 sinusoidal: 1610 harmonic: 2310 Sorted by residual: dihedral pdb=" CA PRO B 475 " pdb=" C PRO B 475 " pdb=" N HIS B 476 " pdb=" CA HIS B 476 " ideal model delta harmonic sigma weight residual -180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA PRO A 475 " pdb=" C PRO A 475 " pdb=" N HIS A 476 " pdb=" CA HIS A 476 " ideal model delta harmonic sigma weight residual -180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA GLY A 621 " pdb=" C GLY A 621 " pdb=" N GLU A 622 " pdb=" CA GLU A 622 " ideal model delta harmonic sigma weight residual -180.00 -163.71 -16.29 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 3917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 708 0.037 - 0.074: 234 0.074 - 0.112: 54 0.112 - 0.149: 8 0.149 - 0.186: 2 Chirality restraints: 1006 Sorted by residual: chirality pdb=" C2 6PL A1002 " pdb=" C1 6PL A1002 " pdb=" C3 6PL A1002 " pdb=" O2 6PL A1002 " both_signs ideal model delta sigma weight residual False -2.33 -2.51 0.19 2.00e-01 2.50e+01 8.64e-01 chirality pdb=" C2 6PL B1002 " pdb=" C1 6PL B1002 " pdb=" C3 6PL B1002 " pdb=" O2 6PL B1002 " both_signs ideal model delta sigma weight residual False -2.33 -2.51 0.19 2.00e-01 2.50e+01 8.64e-01 chirality pdb=" CA GLU A 549 " pdb=" N GLU A 549 " pdb=" C GLU A 549 " pdb=" CB GLU A 549 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 1003 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 523 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C CYS B 523 " 0.042 2.00e-02 2.50e+03 pdb=" O CYS B 523 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR B 524 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 523 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C CYS A 523 " -0.042 2.00e-02 2.50e+03 pdb=" O CYS A 523 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR A 524 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 394 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C PHE B 394 " 0.035 2.00e-02 2.50e+03 pdb=" O PHE B 394 " -0.013 2.00e-02 2.50e+03 pdb=" N TRP B 395 " -0.012 2.00e-02 2.50e+03 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 78 2.61 - 3.18: 6004 3.18 - 3.75: 10815 3.75 - 4.33: 14931 4.33 - 4.90: 24260 Nonbonded interactions: 56088 Sorted by model distance: nonbonded pdb=" O PHE A 366 " pdb=" NH1 ARG A 371 " model vdw 2.034 3.120 nonbonded pdb=" O PHE B 366 " pdb=" NH1 ARG B 371 " model vdw 2.034 3.120 nonbonded pdb=" O LYS A 482 " pdb=" OG1 THR A 485 " model vdw 2.193 3.040 nonbonded pdb=" O LYS B 482 " pdb=" OG1 THR B 485 " model vdw 2.193 3.040 nonbonded pdb=" O ILE B 579 " pdb=" OG1 THR B 583 " model vdw 2.206 3.040 ... (remaining 56083 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.100 Find NCS groups from input model: 0.110 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:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 6868 Z= 0.286 Angle : 0.787 18.904 9322 Z= 0.363 Chirality : 0.040 0.186 1006 Planarity : 0.004 0.024 1122 Dihedral : 16.399 73.832 2426 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.29 % Allowed : 25.36 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.29), residues: 776 helix: 1.12 (0.20), residues: 554 sheet: None (None), residues: 0 loop : -1.53 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 373 HIS 0.002 0.001 HIS A 476 PHE 0.011 0.001 PHE A 610 TYR 0.014 0.001 TYR A 524 ARG 0.003 0.000 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.12370 ( 458) hydrogen bonds : angle 5.48158 ( 1374) SS BOND : bond 0.00029 ( 2) SS BOND : angle 0.02713 ( 4) covalent geometry : bond 0.00554 ( 6866) covalent geometry : angle 0.78755 ( 9318) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.734 Fit side-chains REVERT: A 511 PHE cc_start: 0.9074 (t80) cc_final: 0.8849 (t80) REVERT: B 511 PHE cc_start: 0.9073 (t80) cc_final: 0.8849 (t80) outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 0.7548 time to fit residues: 85.1096 Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9980 chunk 59 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.0770 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 452 GLN B 248 ASN B 452 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.183324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.147615 restraints weight = 8490.407| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.35 r_work: 0.3603 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6868 Z= 0.145 Angle : 0.552 5.601 9322 Z= 0.300 Chirality : 0.040 0.126 1006 Planarity : 0.004 0.027 1122 Dihedral : 10.451 79.782 960 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.59 % Allowed : 22.48 % Favored : 74.93 % 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: 1.10 (0.30), residues: 776 helix: 1.63 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -1.79 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 232 HIS 0.001 0.001 HIS A 476 PHE 0.017 0.002 PHE A 257 TYR 0.013 0.002 TYR B 352 ARG 0.005 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.05004 ( 458) hydrogen bonds : angle 4.38262 ( 1374) SS BOND : bond 0.00074 ( 2) SS BOND : angle 0.27124 ( 4) covalent geometry : bond 0.00310 ( 6866) covalent geometry : angle 0.55218 ( 9318) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.670 Fit side-chains REVERT: A 448 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7195 (ttp-110) REVERT: A 511 PHE cc_start: 0.9085 (t80) cc_final: 0.8824 (t80) REVERT: B 448 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7209 (ttp-110) REVERT: B 511 PHE cc_start: 0.9086 (t80) cc_final: 0.8826 (t80) outliers start: 18 outliers final: 8 residues processed: 116 average time/residue: 0.7521 time to fit residues: 94.3890 Evaluate side-chains 110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 448 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 0.0040 chunk 2 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 chunk 14 optimal weight: 0.9990 chunk 65 optimal weight: 0.0870 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.3528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.184688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.148966 restraints weight = 8634.921| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.35 r_work: 0.3612 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6868 Z= 0.128 Angle : 0.513 5.492 9322 Z= 0.279 Chirality : 0.039 0.141 1006 Planarity : 0.004 0.056 1122 Dihedral : 9.985 72.628 960 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.46 % Allowed : 20.46 % Favored : 76.08 % 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: 1.31 (0.30), residues: 776 helix: 1.79 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -1.78 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 327 HIS 0.001 0.000 HIS A 313 PHE 0.014 0.001 PHE A 391 TYR 0.011 0.001 TYR A 352 ARG 0.003 0.000 ARG B 448 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 458) hydrogen bonds : angle 4.27990 ( 1374) SS BOND : bond 0.00056 ( 2) SS BOND : angle 0.09575 ( 4) covalent geometry : bond 0.00272 ( 6866) covalent geometry : angle 0.51335 ( 9318) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.659 Fit side-chains REVERT: A 448 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7242 (ttm110) REVERT: A 477 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8173 (mm) REVERT: A 511 PHE cc_start: 0.9091 (t80) cc_final: 0.8861 (t80) REVERT: B 448 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7248 (ttm110) REVERT: B 477 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8180 (mm) REVERT: B 511 PHE cc_start: 0.9090 (t80) cc_final: 0.8861 (t80) outliers start: 24 outliers final: 14 residues processed: 130 average time/residue: 0.7638 time to fit residues: 107.2195 Evaluate side-chains 122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 477 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.180078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.143832 restraints weight = 8618.391| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.41 r_work: 0.3563 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6868 Z= 0.178 Angle : 0.576 5.619 9322 Z= 0.313 Chirality : 0.041 0.131 1006 Planarity : 0.004 0.040 1122 Dihedral : 10.143 73.046 960 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.32 % Allowed : 20.75 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.30), residues: 776 helix: 1.68 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -1.78 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 232 HIS 0.003 0.001 HIS B 313 PHE 0.018 0.002 PHE B 391 TYR 0.011 0.002 TYR A 352 ARG 0.003 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.04944 ( 458) hydrogen bonds : angle 4.38709 ( 1374) SS BOND : bond 0.00116 ( 2) SS BOND : angle 0.35481 ( 4) covalent geometry : bond 0.00404 ( 6866) covalent geometry : angle 0.57654 ( 9318) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.669 Fit side-chains REVERT: A 448 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7256 (ttm110) REVERT: A 511 PHE cc_start: 0.9076 (t80) cc_final: 0.8854 (t80) REVERT: A 549 GLU cc_start: 0.7769 (pp20) cc_final: 0.7515 (pp20) REVERT: B 448 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7262 (ttm110) REVERT: B 511 PHE cc_start: 0.9076 (t80) cc_final: 0.8854 (t80) REVERT: B 549 GLU cc_start: 0.7783 (pp20) cc_final: 0.7524 (pp20) outliers start: 30 outliers final: 10 residues processed: 126 average time/residue: 0.8202 time to fit residues: 111.1111 Evaluate side-chains 114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 448 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 0.0770 chunk 24 optimal weight: 0.5980 chunk 58 optimal weight: 0.0060 chunk 23 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.4354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.182606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.146999 restraints weight = 8623.847| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.36 r_work: 0.3599 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6868 Z= 0.134 Angle : 0.538 5.484 9322 Z= 0.294 Chirality : 0.040 0.143 1006 Planarity : 0.004 0.035 1122 Dihedral : 9.913 68.798 960 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.88 % Allowed : 21.61 % Favored : 75.50 % 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: 1.29 (0.30), residues: 776 helix: 1.78 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -1.77 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 327 HIS 0.002 0.000 HIS A 476 PHE 0.018 0.001 PHE A 391 TYR 0.012 0.001 TYR A 352 ARG 0.003 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.04616 ( 458) hydrogen bonds : angle 4.27146 ( 1374) SS BOND : bond 0.00089 ( 2) SS BOND : angle 0.23355 ( 4) covalent geometry : bond 0.00291 ( 6866) covalent geometry : angle 0.53814 ( 9318) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.7906 (t) REVERT: A 377 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6400 (tp) REVERT: A 511 PHE cc_start: 0.9083 (t80) cc_final: 0.8839 (t80) REVERT: A 549 GLU cc_start: 0.7782 (pp20) cc_final: 0.7506 (pp20) REVERT: B 261 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.7904 (t) REVERT: B 377 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6387 (tp) REVERT: B 511 PHE cc_start: 0.9085 (t80) cc_final: 0.8842 (t80) REVERT: B 549 GLU cc_start: 0.7783 (pp20) cc_final: 0.7505 (pp20) outliers start: 20 outliers final: 12 residues processed: 126 average time/residue: 0.7567 time to fit residues: 103.1509 Evaluate side-chains 118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 448 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 294 GLN B 248 ASN B 294 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.180473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.144131 restraints weight = 8471.933| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.40 r_work: 0.3572 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6868 Z= 0.163 Angle : 0.573 7.289 9322 Z= 0.309 Chirality : 0.041 0.139 1006 Planarity : 0.004 0.033 1122 Dihedral : 9.860 67.764 960 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 5.19 % Allowed : 19.31 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.29), residues: 776 helix: 1.67 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -1.71 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 327 HIS 0.002 0.001 HIS A 313 PHE 0.041 0.002 PHE A 391 TYR 0.012 0.002 TYR A 352 ARG 0.003 0.000 ARG B 448 Details of bonding type rmsd hydrogen bonds : bond 0.04838 ( 458) hydrogen bonds : angle 4.36094 ( 1374) SS BOND : bond 0.00129 ( 2) SS BOND : angle 0.43679 ( 4) covalent geometry : bond 0.00373 ( 6866) covalent geometry : angle 0.57277 ( 9318) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.7940 (t) REVERT: A 377 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6468 (tp) REVERT: A 477 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8204 (mm) REVERT: A 499 HIS cc_start: 0.8260 (OUTLIER) cc_final: 0.7862 (m-70) REVERT: A 549 GLU cc_start: 0.7780 (pp20) cc_final: 0.7506 (pp20) REVERT: B 261 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.7942 (t) REVERT: B 377 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6450 (tp) REVERT: B 477 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8221 (mm) REVERT: B 499 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.7870 (m-70) REVERT: B 549 GLU cc_start: 0.7780 (pp20) cc_final: 0.7508 (pp20) outliers start: 36 outliers final: 14 residues processed: 126 average time/residue: 0.7754 time to fit residues: 105.3090 Evaluate side-chains 122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 499 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 0.0010 chunk 52 optimal weight: 0.8980 chunk 3 optimal weight: 0.0770 chunk 64 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 overall best weight: 0.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.183080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.147482 restraints weight = 8616.147| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.32 r_work: 0.3608 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6868 Z= 0.135 Angle : 0.548 6.717 9322 Z= 0.296 Chirality : 0.040 0.138 1006 Planarity : 0.004 0.032 1122 Dihedral : 9.297 62.566 960 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.17 % Allowed : 21.90 % Favored : 74.93 % 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: 1.27 (0.29), residues: 776 helix: 1.72 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -1.66 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 327 HIS 0.001 0.000 HIS A 313 PHE 0.037 0.002 PHE B 391 TYR 0.014 0.001 TYR B 352 ARG 0.005 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.04580 ( 458) hydrogen bonds : angle 4.27181 ( 1374) SS BOND : bond 0.00125 ( 2) SS BOND : angle 0.34388 ( 4) covalent geometry : bond 0.00300 ( 6866) covalent geometry : angle 0.54769 ( 9318) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.7920 (t) REVERT: A 377 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6484 (tp) REVERT: A 477 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8098 (mm) REVERT: B 261 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.7921 (t) REVERT: B 377 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6485 (tp) REVERT: B 477 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8099 (mm) outliers start: 22 outliers final: 10 residues processed: 120 average time/residue: 0.6667 time to fit residues: 87.1315 Evaluate side-chains 110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 477 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 0.0980 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.181991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.146008 restraints weight = 8762.683| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.39 r_work: 0.3584 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6868 Z= 0.150 Angle : 0.572 6.509 9322 Z= 0.309 Chirality : 0.041 0.129 1006 Planarity : 0.004 0.033 1122 Dihedral : 9.024 59.622 960 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.17 % Allowed : 21.33 % Favored : 75.50 % 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: 1.24 (0.29), residues: 776 helix: 1.68 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -1.62 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 327 HIS 0.002 0.001 HIS B 313 PHE 0.036 0.002 PHE A 391 TYR 0.013 0.002 TYR B 352 ARG 0.004 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.04696 ( 458) hydrogen bonds : angle 4.31685 ( 1374) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.36906 ( 4) covalent geometry : bond 0.00341 ( 6866) covalent geometry : angle 0.57208 ( 9318) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.7914 (t) REVERT: A 477 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8086 (mm) REVERT: A 590 ASP cc_start: 0.7852 (m-30) cc_final: 0.7631 (m-30) REVERT: B 261 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.7914 (t) REVERT: B 472 ARG cc_start: 0.6811 (ttm110) cc_final: 0.6610 (ttm-80) REVERT: B 477 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8093 (mm) REVERT: B 590 ASP cc_start: 0.7860 (m-30) cc_final: 0.7638 (m-30) outliers start: 22 outliers final: 12 residues processed: 106 average time/residue: 0.7418 time to fit residues: 85.2749 Evaluate side-chains 108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 477 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN B 294 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.182224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.146397 restraints weight = 8707.374| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.38 r_work: 0.3586 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6868 Z= 0.147 Angle : 0.564 6.354 9322 Z= 0.306 Chirality : 0.041 0.130 1006 Planarity : 0.004 0.033 1122 Dihedral : 8.812 56.887 960 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.88 % Allowed : 21.47 % Favored : 75.65 % 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: 1.26 (0.29), residues: 776 helix: 1.71 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -1.60 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.002 0.001 HIS A 476 PHE 0.035 0.002 PHE A 391 TYR 0.014 0.002 TYR B 352 ARG 0.004 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 458) hydrogen bonds : angle 4.31316 ( 1374) SS BOND : bond 0.00124 ( 2) SS BOND : angle 0.40172 ( 4) covalent geometry : bond 0.00333 ( 6866) covalent geometry : angle 0.56393 ( 9318) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7898 (t) REVERT: A 377 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6439 (tp) REVERT: A 477 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8077 (mm) REVERT: A 499 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.7855 (m-70) REVERT: B 261 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.7897 (t) REVERT: B 377 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6431 (tp) REVERT: B 477 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8069 (mm) REVERT: B 499 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.7870 (m-70) outliers start: 20 outliers final: 12 residues processed: 108 average time/residue: 0.6610 time to fit residues: 78.1024 Evaluate side-chains 111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 499 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 30 optimal weight: 0.0570 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN B 294 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.181244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.145045 restraints weight = 8834.269| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.40 r_work: 0.3580 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6868 Z= 0.162 Angle : 0.586 6.463 9322 Z= 0.317 Chirality : 0.042 0.146 1006 Planarity : 0.004 0.034 1122 Dihedral : 8.528 48.894 960 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.17 % Allowed : 22.05 % Favored : 74.78 % 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: 1.10 (0.29), residues: 776 helix: 1.57 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -1.60 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 327 HIS 0.002 0.001 HIS B 616 PHE 0.051 0.002 PHE B 391 TYR 0.014 0.002 TYR A 352 ARG 0.003 0.000 ARG B 380 Details of bonding type rmsd hydrogen bonds : bond 0.04719 ( 458) hydrogen bonds : angle 4.35407 ( 1374) SS BOND : bond 0.00146 ( 2) SS BOND : angle 0.43301 ( 4) covalent geometry : bond 0.00375 ( 6866) covalent geometry : angle 0.58581 ( 9318) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.7897 (t) REVERT: A 377 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6485 (tp) REVERT: A 477 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8081 (mm) REVERT: A 499 HIS cc_start: 0.8271 (OUTLIER) cc_final: 0.7862 (m-70) REVERT: B 261 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.7899 (t) REVERT: B 377 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6482 (tp) REVERT: B 477 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8127 (mm) REVERT: B 499 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7878 (m-70) outliers start: 22 outliers final: 12 residues processed: 113 average time/residue: 0.7002 time to fit residues: 86.1843 Evaluate side-chains 118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 499 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN B 294 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.181185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.144654 restraints weight = 8697.243| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.44 r_work: 0.3559 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6868 Z= 0.172 Angle : 0.599 6.717 9322 Z= 0.324 Chirality : 0.042 0.149 1006 Planarity : 0.004 0.034 1122 Dihedral : 8.344 46.829 960 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.88 % Allowed : 22.33 % Favored : 74.78 % 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: 1.04 (0.29), residues: 776 helix: 1.53 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -1.63 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 327 HIS 0.002 0.001 HIS A 476 PHE 0.054 0.002 PHE B 391 TYR 0.014 0.002 TYR B 352 ARG 0.003 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.04823 ( 458) hydrogen bonds : angle 4.38576 ( 1374) SS BOND : bond 0.00145 ( 2) SS BOND : angle 0.49841 ( 4) covalent geometry : bond 0.00400 ( 6866) covalent geometry : angle 0.59858 ( 9318) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3977.45 seconds wall clock time: 69 minutes 29.46 seconds (4169.46 seconds total)