Starting phenix.real_space_refine on Wed Jun 11 16:00:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvj_47208/06_2025/9dvj_47208_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvj_47208/06_2025/9dvj_47208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dvj_47208/06_2025/9dvj_47208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvj_47208/06_2025/9dvj_47208.map" model { file = "/net/cci-nas-00/data/ceres_data/9dvj_47208/06_2025/9dvj_47208_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvj_47208/06_2025/9dvj_47208_trim.cif" } resolution = 2.52 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= 0.023 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 32 5.16 5 C 4370 2.51 5 N 1004 2.21 5 O 1042 1.98 5 H 6258 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12710 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 6270 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 13, 'TRANS': 363} Chain breaks: 2 Chain: "B" Number of atoms: 6270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 6270 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 13, 'TRANS': 363} Chain breaks: 2 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'CLR': 1, 'CPL': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'CLR': 1, 'CPL': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.69, per 1000 atoms: 0.61 Number of scatterers: 12710 At special positions: 0 Unit cell: (75.946, 78.4225, 127.127, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 4 15.00 O 1042 8.00 N 1004 7.00 C 4370 6.00 H 6258 1.00 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: 3.30 Conformation dependent library (CDL) restraints added in 947.8 milliseconds 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 0 sheets defined 81.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 230 through 257 Processing helix chain 'A' and resid 267 through 296 removed outlier: 4.327A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 312 through 337 Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 390 through 403 Processing helix chain 'A' and resid 403 through 419 removed outlier: 4.089A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 453 through 471 Processing helix chain 'A' and resid 472 through 502 removed outlier: 4.097A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASN A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 Processing helix chain 'A' and resid 555 through 582 removed outlier: 4.027A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 618 Proline residue: A 598 - end of helix Processing helix chain 'B' and resid 230 through 257 Processing helix chain 'B' and resid 267 through 296 removed outlier: 4.211A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 312 through 337 Processing helix chain 'B' and resid 345 through 360 Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.038A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 445 through 471 removed outlier: 3.545A pdb=" N ALA B 449 " --> pdb=" O TYR B 445 " (cutoff:3.500A) Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 472 through 502 removed outlier: 3.955A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 Processing helix chain 'B' and resid 555 through 582 removed outlier: 3.951A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 618 removed outlier: 4.640A pdb=" N ASP B 590 " --> pdb=" O PRO B 586 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) Proline residue: B 598 - end of helix 466 hydrogen bonds defined for protein. 1398 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: 4.29 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6242 1.03 - 1.23: 23 1.23 - 1.42: 2945 1.42 - 1.62: 3666 1.62 - 1.81: 48 Bond restraints: 12924 Sorted by residual: bond pdb=" O3P CPL B 803 " pdb=" P CPL B 803 " ideal model delta sigma weight residual 1.633 1.740 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" O3P CPL A 803 " pdb=" P CPL A 803 " ideal model delta sigma weight residual 1.633 1.740 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" O4P CPL A 803 " pdb=" P CPL A 803 " ideal model delta sigma weight residual 1.648 1.714 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" O4P CPL B 803 " pdb=" P CPL B 803 " ideal model delta sigma weight residual 1.648 1.713 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" N TRP B 534 " pdb=" H TRP B 534 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.18e+00 ... (remaining 12919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 23083 3.05 - 6.10: 64 6.10 - 9.14: 9 9.14 - 12.19: 2 12.19 - 15.24: 2 Bond angle restraints: 23160 Sorted by residual: angle pdb=" O1P CPL A 803 " pdb=" P CPL A 803 " pdb=" O2P CPL A 803 " ideal model delta sigma weight residual 119.55 134.79 -15.24 3.00e+00 1.11e-01 2.58e+01 angle pdb=" O1P CPL B 803 " pdb=" P CPL B 803 " pdb=" O2P CPL B 803 " ideal model delta sigma weight residual 119.55 134.72 -15.17 3.00e+00 1.11e-01 2.56e+01 angle pdb=" CA PHE B 366 " pdb=" C PHE B 366 " pdb=" O PHE B 366 " ideal model delta sigma weight residual 120.85 115.50 5.35 1.67e+00 3.59e-01 1.03e+01 angle pdb=" N CPL B 803 " pdb=" C5 CPL B 803 " pdb=" C4 CPL B 803 " ideal model delta sigma weight residual 117.50 108.06 9.44 3.00e+00 1.11e-01 9.90e+00 angle pdb=" N CPL A 803 " pdb=" C5 CPL A 803 " pdb=" C4 CPL A 803 " ideal model delta sigma weight residual 117.50 108.12 9.38 3.00e+00 1.11e-01 9.77e+00 ... (remaining 23155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.48: 5932 27.48 - 54.96: 281 54.96 - 82.44: 38 82.44 - 109.92: 2 109.92 - 137.40: 5 Dihedral angle restraints: 6258 sinusoidal: 3264 harmonic: 2994 Sorted by residual: dihedral pdb=" C3 CPL A 803 " pdb=" C1 CPL A 803 " pdb=" C2 CPL A 803 " pdb=" O3P CPL A 803 " ideal model delta sinusoidal sigma weight residual 72.09 -65.31 137.40 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" O2 CPL A 803 " pdb=" C1 CPL A 803 " pdb=" C2 CPL A 803 " pdb=" O3P CPL A 803 " ideal model delta sinusoidal sigma weight residual 309.18 174.01 135.17 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" C33 CPL B 803 " pdb=" C31 CPL B 803 " pdb=" C32 CPL B 803 " pdb=" O2 CPL B 803 " ideal model delta sinusoidal sigma weight residual 171.65 47.74 123.91 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 6255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 898 0.073 - 0.147: 77 0.147 - 0.220: 1 0.220 - 0.293: 2 0.293 - 0.367: 8 Chirality restraints: 986 Sorted by residual: chirality pdb=" C17 CLR A 802 " pdb=" C13 CLR A 802 " pdb=" C16 CLR A 802 " pdb=" C20 CLR A 802 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" C17 CLR B 802 " pdb=" C13 CLR B 802 " pdb=" C16 CLR B 802 " pdb=" C20 CLR B 802 " both_signs ideal model delta sigma weight residual False 2.55 2.91 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C13 CLR A 802 " pdb=" C12 CLR A 802 " pdb=" C14 CLR A 802 " pdb=" C17 CLR A 802 " both_signs ideal model delta sigma weight residual False -2.93 -3.27 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 983 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 366 " -0.021 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" N TYR B 367 " 0.068 2.00e-02 2.50e+03 pdb=" CA TYR B 367 " -0.018 2.00e-02 2.50e+03 pdb=" H TYR B 367 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 366 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.15e+00 pdb=" C PHE B 366 " 0.049 2.00e-02 2.50e+03 pdb=" O PHE B 366 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR B 367 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 534 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.79e+00 pdb=" C TRP B 534 " -0.034 2.00e-02 2.50e+03 pdb=" O TRP B 534 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY B 535 " 0.012 2.00e-02 2.50e+03 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 921 2.22 - 2.81: 26631 2.81 - 3.41: 37281 3.41 - 4.00: 47682 4.00 - 4.60: 73473 Nonbonded interactions: 185988 Sorted by model distance: nonbonded pdb=" O ILE B 271 " pdb=" HH TYR B 352 " model vdw 1.620 2.450 nonbonded pdb=" O LYS B 482 " pdb=" HG1 THR B 485 " model vdw 1.629 2.450 nonbonded pdb=" O LYS A 482 " pdb=" HG1 THR A 485 " model vdw 1.647 2.450 nonbonded pdb=" O ILE A 271 " pdb=" HH TYR A 352 " model vdw 1.649 2.450 nonbonded pdb="HH12 ARG B 466 " pdb=" O GLY B 621 " model vdw 1.657 2.450 ... (remaining 185983 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: 0.01 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: 3.350 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: 0.220 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.090 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 : 0.004 0.107 6668 Z= 0.224 Angle : 0.651 15.241 9066 Z= 0.288 Chirality : 0.048 0.367 986 Planarity : 0.003 0.039 1080 Dihedral : 17.140 137.402 2442 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.75 % Allowed : 15.62 % Favored : 83.63 % 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: 3.78 (0.30), residues: 742 helix: 3.53 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -1.47 (0.41), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 327 HIS 0.002 0.000 HIS B 499 PHE 0.013 0.001 PHE A 610 TYR 0.009 0.001 TYR A 496 ARG 0.006 0.000 ARG B 380 Details of bonding type rmsd hydrogen bonds : bond 0.08683 ( 466) hydrogen bonds : angle 4.37064 ( 1398) SS BOND : bond 0.00180 ( 2) SS BOND : angle 0.48527 ( 4) covalent geometry : bond 0.00437 ( 6666) covalent geometry : angle 0.65066 ( 9062) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 PHE cc_start: 0.7300 (m-80) cc_final: 0.7046 (m-10) REVERT: A 366 PHE cc_start: 0.8448 (m-80) cc_final: 0.8246 (m-80) REVERT: A 487 PHE cc_start: 0.6648 (m-10) cc_final: 0.5803 (m-80) REVERT: A 539 LYS cc_start: 0.8010 (pttt) cc_final: 0.7335 (mmtm) REVERT: A 550 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6943 (mt-10) REVERT: B 550 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6925 (tt0) outliers start: 5 outliers final: 3 residues processed: 107 average time/residue: 1.6818 time to fit residues: 193.8701 Evaluate side-chains 62 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 609 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.0670 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 HIS B 576 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.144041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.114881 restraints weight = 22771.039| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.33 r_work: 0.3429 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6668 Z= 0.140 Angle : 0.476 5.129 9066 Z= 0.256 Chirality : 0.036 0.125 986 Planarity : 0.004 0.041 1080 Dihedral : 12.227 116.413 1052 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.35 % Allowed : 16.07 % Favored : 82.58 % 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: 3.47 (0.30), residues: 742 helix: 3.17 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -1.66 (0.44), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 327 HIS 0.006 0.001 HIS B 499 PHE 0.018 0.001 PHE A 605 TYR 0.011 0.001 TYR A 352 ARG 0.005 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.04934 ( 466) hydrogen bonds : angle 4.12504 ( 1398) SS BOND : bond 0.00272 ( 2) SS BOND : angle 1.03211 ( 4) covalent geometry : bond 0.00300 ( 6666) covalent geometry : angle 0.47590 ( 9062) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 PHE cc_start: 0.7351 (m-80) cc_final: 0.7003 (m-10) REVERT: A 386 PHE cc_start: 0.8097 (m-10) cc_final: 0.7880 (m-10) REVERT: A 539 LYS cc_start: 0.7975 (pttt) cc_final: 0.7210 (mmtm) REVERT: A 550 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6941 (mt-10) REVERT: B 411 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7760 (tm-30) REVERT: B 472 ARG cc_start: 0.6709 (mtt180) cc_final: 0.6230 (mtp85) REVERT: B 510 PHE cc_start: 0.7331 (m-10) cc_final: 0.7102 (m-80) REVERT: B 550 GLU cc_start: 0.7697 (mm-30) cc_final: 0.6998 (tt0) outliers start: 9 outliers final: 3 residues processed: 74 average time/residue: 1.8182 time to fit residues: 146.0227 Evaluate side-chains 62 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain B residue 609 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.130819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.101416 restraints weight = 23560.935| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.34 r_work: 0.3243 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6668 Z= 0.190 Angle : 0.539 7.264 9066 Z= 0.297 Chirality : 0.038 0.131 986 Planarity : 0.005 0.059 1080 Dihedral : 11.784 113.516 1050 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.40 % Allowed : 14.86 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.30), residues: 742 helix: 2.62 (0.20), residues: 594 sheet: None (None), residues: 0 loop : -1.91 (0.44), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 327 HIS 0.005 0.001 HIS B 499 PHE 0.033 0.002 PHE A 605 TYR 0.014 0.002 TYR B 417 ARG 0.005 0.001 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.06543 ( 466) hydrogen bonds : angle 4.31933 ( 1398) SS BOND : bond 0.00476 ( 2) SS BOND : angle 1.27075 ( 4) covalent geometry : bond 0.00422 ( 6666) covalent geometry : angle 0.53867 ( 9062) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 357 PHE cc_start: 0.7429 (m-80) cc_final: 0.7021 (m-10) REVERT: A 472 ARG cc_start: 0.7442 (mtt-85) cc_final: 0.7166 (ttm-80) REVERT: A 507 THR cc_start: 0.6564 (OUTLIER) cc_final: 0.6353 (m) REVERT: A 613 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8440 (tt0) REVERT: B 306 ASN cc_start: 0.7016 (t0) cc_final: 0.6670 (t0) REVERT: B 411 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7773 (tm-30) REVERT: B 469 ASP cc_start: 0.7738 (m-30) cc_final: 0.7528 (m-30) REVERT: B 472 ARG cc_start: 0.6986 (mtt180) cc_final: 0.6532 (mtp85) REVERT: B 529 ASP cc_start: 0.7744 (m-30) cc_final: 0.7528 (m-30) REVERT: B 550 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7071 (tt0) REVERT: B 613 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8565 (tm-30) outliers start: 16 outliers final: 2 residues processed: 83 average time/residue: 1.7525 time to fit residues: 156.4280 Evaluate side-chains 58 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 20 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN B 441 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.131886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102196 restraints weight = 22913.577| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.29 r_work: 0.3271 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6668 Z= 0.140 Angle : 0.468 5.227 9066 Z= 0.260 Chirality : 0.036 0.165 986 Planarity : 0.004 0.048 1080 Dihedral : 11.233 109.283 1046 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.50 % Allowed : 16.82 % Favored : 81.68 % 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: 2.87 (0.30), residues: 742 helix: 2.75 (0.20), residues: 594 sheet: None (None), residues: 0 loop : -1.91 (0.44), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 327 HIS 0.006 0.001 HIS B 441 PHE 0.025 0.001 PHE A 605 TYR 0.014 0.001 TYR B 368 ARG 0.003 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.05695 ( 466) hydrogen bonds : angle 4.15936 ( 1398) SS BOND : bond 0.00489 ( 2) SS BOND : angle 1.50164 ( 4) covalent geometry : bond 0.00298 ( 6666) covalent geometry : angle 0.46675 ( 9062) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 357 PHE cc_start: 0.7517 (m-80) cc_final: 0.7127 (m-10) REVERT: A 386 PHE cc_start: 0.8253 (m-10) cc_final: 0.8041 (m-10) REVERT: A 472 ARG cc_start: 0.7471 (mtt-85) cc_final: 0.7121 (ttm-80) REVERT: A 504 HIS cc_start: 0.6032 (m-70) cc_final: 0.5646 (m-70) REVERT: B 306 ASN cc_start: 0.7218 (t0) cc_final: 0.6850 (t0) REVERT: B 357 PHE cc_start: 0.6787 (m-10) cc_final: 0.5611 (t80) REVERT: B 472 ARG cc_start: 0.7075 (mtt180) cc_final: 0.6636 (mtp85) REVERT: B 550 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7074 (tt0) outliers start: 10 outliers final: 4 residues processed: 69 average time/residue: 2.1453 time to fit residues: 158.0540 Evaluate side-chains 59 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 55 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN B 441 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.130668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.100707 restraints weight = 23152.326| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.34 r_work: 0.3241 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6668 Z= 0.157 Angle : 0.477 5.211 9066 Z= 0.264 Chirality : 0.036 0.126 986 Planarity : 0.004 0.053 1080 Dihedral : 10.776 98.234 1046 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.80 % Allowed : 16.22 % Favored : 81.98 % 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: 2.82 (0.30), residues: 742 helix: 2.70 (0.20), residues: 594 sheet: None (None), residues: 0 loop : -1.91 (0.44), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 327 HIS 0.003 0.001 HIS B 476 PHE 0.025 0.002 PHE A 605 TYR 0.015 0.001 TYR B 417 ARG 0.004 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.05791 ( 466) hydrogen bonds : angle 4.14107 ( 1398) SS BOND : bond 0.00470 ( 2) SS BOND : angle 1.39018 ( 4) covalent geometry : bond 0.00346 ( 6666) covalent geometry : angle 0.47598 ( 9062) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 357 PHE cc_start: 0.7417 (m-80) cc_final: 0.7039 (m-10) REVERT: A 386 PHE cc_start: 0.8337 (m-10) cc_final: 0.8137 (m-10) REVERT: A 472 ARG cc_start: 0.7444 (mtt-85) cc_final: 0.7073 (ttm-80) REVERT: A 504 HIS cc_start: 0.5904 (m-70) cc_final: 0.5522 (m-70) REVERT: B 306 ASN cc_start: 0.7247 (t0) cc_final: 0.7006 (t0) REVERT: B 357 PHE cc_start: 0.6715 (m-10) cc_final: 0.5541 (t80) REVERT: B 411 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7532 (tm-30) REVERT: B 472 ARG cc_start: 0.7043 (mtt180) cc_final: 0.6588 (mtp85) REVERT: B 550 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7069 (tt0) outliers start: 12 outliers final: 6 residues processed: 71 average time/residue: 2.1655 time to fit residues: 163.6411 Evaluate side-chains 59 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN B 441 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.131486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.101276 restraints weight = 23204.729| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.35 r_work: 0.3250 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6668 Z= 0.137 Angle : 0.471 5.886 9066 Z= 0.259 Chirality : 0.035 0.151 986 Planarity : 0.004 0.037 1080 Dihedral : 10.516 93.860 1046 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.80 % Allowed : 16.67 % Favored : 81.53 % 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: 2.91 (0.30), residues: 742 helix: 2.78 (0.20), residues: 594 sheet: None (None), residues: 0 loop : -1.89 (0.44), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 327 HIS 0.021 0.001 HIS B 504 PHE 0.023 0.001 PHE A 605 TYR 0.010 0.001 TYR A 352 ARG 0.004 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.05532 ( 466) hydrogen bonds : angle 4.07828 ( 1398) SS BOND : bond 0.00422 ( 2) SS BOND : angle 1.38004 ( 4) covalent geometry : bond 0.00293 ( 6666) covalent geometry : angle 0.47053 ( 9062) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 PHE cc_start: 0.7402 (m-80) cc_final: 0.7012 (m-10) REVERT: A 472 ARG cc_start: 0.7486 (mtt-85) cc_final: 0.7140 (ttm-80) REVERT: A 504 HIS cc_start: 0.5911 (m-70) cc_final: 0.5546 (m-70) REVERT: B 306 ASN cc_start: 0.7238 (t0) cc_final: 0.7012 (t0) REVERT: B 357 PHE cc_start: 0.6737 (m-10) cc_final: 0.5557 (t80) REVERT: B 411 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7581 (tm-30) REVERT: B 472 ARG cc_start: 0.7060 (mtt180) cc_final: 0.6618 (mtp85) REVERT: B 550 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7141 (tt0) outliers start: 12 outliers final: 6 residues processed: 65 average time/residue: 2.0471 time to fit residues: 142.3267 Evaluate side-chains 60 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain B residue 518 TYR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A 608 ASN B 387 HIS B 441 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.127325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.097681 restraints weight = 23163.778| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.31 r_work: 0.3201 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6668 Z= 0.197 Angle : 0.516 5.796 9066 Z= 0.287 Chirality : 0.037 0.132 986 Planarity : 0.004 0.038 1080 Dihedral : 10.371 87.589 1046 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.65 % Allowed : 16.67 % Favored : 81.68 % 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: 2.57 (0.30), residues: 742 helix: 2.50 (0.20), residues: 596 sheet: None (None), residues: 0 loop : -1.90 (0.45), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 514 HIS 0.020 0.002 HIS B 504 PHE 0.030 0.002 PHE A 605 TYR 0.018 0.002 TYR B 417 ARG 0.003 0.001 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.06331 ( 466) hydrogen bonds : angle 4.27158 ( 1398) SS BOND : bond 0.00559 ( 2) SS BOND : angle 1.49118 ( 4) covalent geometry : bond 0.00444 ( 6666) covalent geometry : angle 0.51478 ( 9062) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 357 PHE cc_start: 0.7456 (m-80) cc_final: 0.7046 (m-10) REVERT: A 504 HIS cc_start: 0.5946 (m-70) cc_final: 0.5595 (m-70) REVERT: B 357 PHE cc_start: 0.6779 (m-10) cc_final: 0.5615 (t80) REVERT: B 472 ARG cc_start: 0.7169 (mtt180) cc_final: 0.6699 (mtp85) REVERT: B 538 ASP cc_start: 0.7234 (t0) cc_final: 0.6946 (t0) REVERT: B 550 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7142 (tt0) outliers start: 11 outliers final: 6 residues processed: 69 average time/residue: 1.9528 time to fit residues: 144.3349 Evaluate side-chains 59 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 608 ASN B 441 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.129022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.099033 restraints weight = 23317.832| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.35 r_work: 0.3220 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6668 Z= 0.149 Angle : 0.475 5.721 9066 Z= 0.264 Chirality : 0.036 0.125 986 Planarity : 0.004 0.037 1080 Dihedral : 10.070 85.297 1046 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.65 % Allowed : 17.12 % Favored : 81.23 % 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: 2.69 (0.30), residues: 742 helix: 2.59 (0.20), residues: 596 sheet: None (None), residues: 0 loop : -1.87 (0.45), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 514 HIS 0.003 0.001 HIS B 387 PHE 0.025 0.001 PHE A 605 TYR 0.010 0.001 TYR A 352 ARG 0.003 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.05838 ( 466) hydrogen bonds : angle 4.16111 ( 1398) SS BOND : bond 0.00484 ( 2) SS BOND : angle 1.45577 ( 4) covalent geometry : bond 0.00323 ( 6666) covalent geometry : angle 0.47453 ( 9062) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 357 PHE cc_start: 0.7434 (m-80) cc_final: 0.7028 (m-10) REVERT: A 472 ARG cc_start: 0.7606 (ttm-80) cc_final: 0.7346 (ttm-80) REVERT: A 504 HIS cc_start: 0.5954 (m-70) cc_final: 0.5609 (m-70) REVERT: B 357 PHE cc_start: 0.6757 (m-10) cc_final: 0.5599 (t80) REVERT: B 472 ARG cc_start: 0.7197 (mtt180) cc_final: 0.6741 (mtp85) REVERT: B 538 ASP cc_start: 0.7261 (t0) cc_final: 0.6964 (t0) REVERT: B 550 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7165 (tt0) outliers start: 11 outliers final: 6 residues processed: 63 average time/residue: 1.9435 time to fit residues: 131.3162 Evaluate side-chains 58 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 608 ASN B 441 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.129956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.100101 restraints weight = 23092.706| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.34 r_work: 0.3234 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6668 Z= 0.135 Angle : 0.462 5.618 9066 Z= 0.255 Chirality : 0.035 0.123 986 Planarity : 0.004 0.037 1080 Dihedral : 9.823 83.994 1046 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.20 % Allowed : 17.12 % Favored : 81.68 % 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: 2.83 (0.30), residues: 742 helix: 2.70 (0.20), residues: 594 sheet: None (None), residues: 0 loop : -1.85 (0.45), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 514 HIS 0.002 0.001 HIS B 299 PHE 0.022 0.001 PHE A 605 TYR 0.021 0.001 TYR B 417 ARG 0.003 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.05546 ( 466) hydrogen bonds : angle 4.07672 ( 1398) SS BOND : bond 0.00420 ( 2) SS BOND : angle 1.37240 ( 4) covalent geometry : bond 0.00289 ( 6666) covalent geometry : angle 0.46103 ( 9062) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 349 LEU cc_start: 0.8328 (tp) cc_final: 0.8052 (mm) REVERT: A 357 PHE cc_start: 0.7440 (m-80) cc_final: 0.7052 (m-10) REVERT: A 472 ARG cc_start: 0.7660 (ttm-80) cc_final: 0.7436 (ttm-80) REVERT: A 504 HIS cc_start: 0.5937 (m-70) cc_final: 0.5600 (m-70) REVERT: B 357 PHE cc_start: 0.6727 (m-10) cc_final: 0.5542 (t80) REVERT: B 472 ARG cc_start: 0.7184 (mtt180) cc_final: 0.6734 (mtp85) REVERT: B 538 ASP cc_start: 0.7323 (t0) cc_final: 0.7020 (t0) REVERT: B 550 GLU cc_start: 0.7940 (mm-30) cc_final: 0.6961 (tt0) outliers start: 8 outliers final: 7 residues processed: 64 average time/residue: 2.0628 time to fit residues: 141.6106 Evaluate side-chains 61 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 504 HIS Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 10 optimal weight: 0.0030 chunk 55 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 59 optimal weight: 0.0170 overall best weight: 0.3428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN B 441 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.132248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102241 restraints weight = 22966.704| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.36 r_work: 0.3264 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6668 Z= 0.111 Angle : 0.442 5.737 9066 Z= 0.244 Chirality : 0.035 0.130 986 Planarity : 0.003 0.035 1080 Dihedral : 9.473 81.714 1046 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.35 % Allowed : 17.27 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.30), residues: 742 helix: 2.86 (0.20), residues: 594 sheet: None (None), residues: 0 loop : -1.85 (0.44), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 514 HIS 0.002 0.001 HIS A 315 PHE 0.018 0.001 PHE A 605 TYR 0.011 0.001 TYR B 518 ARG 0.003 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.05043 ( 466) hydrogen bonds : angle 3.96610 ( 1398) SS BOND : bond 0.00395 ( 2) SS BOND : angle 1.35409 ( 4) covalent geometry : bond 0.00222 ( 6666) covalent geometry : angle 0.44106 ( 9062) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 349 LEU cc_start: 0.8344 (tp) cc_final: 0.8111 (mm) REVERT: A 357 PHE cc_start: 0.7412 (m-80) cc_final: 0.7031 (m-10) REVERT: A 472 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.7401 (ttm-80) REVERT: A 504 HIS cc_start: 0.5936 (m-70) cc_final: 0.5605 (m-70) REVERT: B 357 PHE cc_start: 0.6706 (m-10) cc_final: 0.5530 (t80) REVERT: B 472 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6733 (mtp85) REVERT: B 538 ASP cc_start: 0.7332 (t0) cc_final: 0.7013 (t0) REVERT: B 550 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7109 (tt0) REVERT: B 579 ILE cc_start: 0.7336 (mp) cc_final: 0.7034 (pp) outliers start: 9 outliers final: 4 residues processed: 64 average time/residue: 2.0878 time to fit residues: 143.9097 Evaluate side-chains 59 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN B 441 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.130002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099855 restraints weight = 23126.741| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.37 r_work: 0.3232 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6668 Z= 0.150 Angle : 0.468 6.005 9066 Z= 0.258 Chirality : 0.036 0.127 986 Planarity : 0.004 0.060 1080 Dihedral : 9.702 81.323 1046 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.20 % Allowed : 17.42 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.30), residues: 742 helix: 2.78 (0.20), residues: 594 sheet: None (None), residues: 0 loop : -1.86 (0.44), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 514 HIS 0.003 0.001 HIS B 299 PHE 0.024 0.001 PHE A 605 TYR 0.021 0.001 TYR B 417 ARG 0.009 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.05537 ( 466) hydrogen bonds : angle 4.04525 ( 1398) SS BOND : bond 0.00458 ( 2) SS BOND : angle 1.36843 ( 4) covalent geometry : bond 0.00330 ( 6666) covalent geometry : angle 0.46733 ( 9062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8965.62 seconds wall clock time: 155 minutes 46.81 seconds (9346.81 seconds total)