Starting phenix.real_space_refine on Sat May 10 03:16:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k5g_36905/05_2025/8k5g_36905.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k5g_36905/05_2025/8k5g_36905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k5g_36905/05_2025/8k5g_36905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k5g_36905/05_2025/8k5g_36905.map" model { file = "/net/cci-nas-00/data/ceres_data/8k5g_36905/05_2025/8k5g_36905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k5g_36905/05_2025/8k5g_36905.cif" } resolution = 3.41 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1744 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2152 2.51 5 N 574 2.21 5 O 637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 948 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "A" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1617 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 13, 'TRANS': 187} Time building chain proxies: 2.78, per 1000 atoms: 0.82 Number of scatterers: 3381 At special positions: 0 Unit cell: (60.3, 113.9, 75.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 637 8.00 N 574 7.00 C 2152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 105 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.02 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.04 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " 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: 0.78 Conformation dependent library (CDL) restraints added in 420.5 milliseconds 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 6.3% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.024A pdb=" N THR H 91 " --> pdb=" O PHE H 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.802A pdb=" N TRP A 350 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.524A pdb=" N LEU A 365 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.918A pdb=" N ALA A 408 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 3.995A pdb=" N TYR A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.731A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.562A pdb=" N PHE L 72 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.689A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.637A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 521 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.637A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASN A 391 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU A 513 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 401 " --> pdb=" O GLN A 503 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN A 503 " --> pdb=" O GLY A 401 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451 94 hydrogen bonds defined for protein. 216 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1084 1.35 - 1.46: 908 1.46 - 1.58: 1456 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 3470 Sorted by residual: bond pdb=" N VAL A 442 " pdb=" CA VAL A 442 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.25e-02 6.40e+03 1.05e+00 bond pdb=" CA SER A 443 " pdb=" C SER A 443 " ideal model delta sigma weight residual 1.519 1.513 0.005 5.30e-03 3.56e+04 9.61e-01 bond pdb=" CA CYS A 333 " pdb=" CB CYS A 333 " ideal model delta sigma weight residual 1.536 1.524 0.012 1.25e-02 6.40e+03 8.56e-01 bond pdb=" CB CYS A 358 " pdb=" SG CYS A 358 " ideal model delta sigma weight residual 1.808 1.778 0.030 3.30e-02 9.18e+02 8.12e-01 bond pdb=" CG PRO L 96 " pdb=" CD PRO L 96 " ideal model delta sigma weight residual 1.512 1.488 0.024 2.70e-02 1.37e+03 7.86e-01 ... (remaining 3465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 4613 2.00 - 4.00: 91 4.00 - 6.00: 5 6.00 - 8.00: 2 8.00 - 10.01: 2 Bond angle restraints: 4713 Sorted by residual: angle pdb=" C LYS A 441 " pdb=" N VAL A 442 " pdb=" CA VAL A 442 " ideal model delta sigma weight residual 121.97 131.98 -10.01 1.80e+00 3.09e-01 3.09e+01 angle pdb=" CA SER A 443 " pdb=" C SER A 443 " pdb=" N GLY A 444 " ideal model delta sigma weight residual 119.56 116.68 2.88 5.80e-01 2.97e+00 2.46e+01 angle pdb=" N VAL A 442 " pdb=" CA VAL A 442 " pdb=" CB VAL A 442 " ideal model delta sigma weight residual 111.23 116.46 -5.23 1.65e+00 3.67e-01 1.01e+01 angle pdb=" N SER A 443 " pdb=" CA SER A 443 " pdb=" C SER A 443 " ideal model delta sigma weight residual 108.12 112.89 -4.77 1.59e+00 3.96e-01 9.00e+00 angle pdb=" N PHE A 335 " pdb=" CA PHE A 335 " pdb=" C PHE A 335 " ideal model delta sigma weight residual 112.88 109.15 3.73 1.29e+00 6.01e-01 8.38e+00 ... (remaining 4708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 1843 17.57 - 35.15: 173 35.15 - 52.72: 31 52.72 - 70.29: 5 70.29 - 87.87: 3 Dihedral angle restraints: 2055 sinusoidal: 809 harmonic: 1246 Sorted by residual: dihedral pdb=" CB CYS A 477 " pdb=" SG CYS A 477 " pdb=" SG CYS A 485 " pdb=" CB CYS A 485 " ideal model delta sinusoidal sigma weight residual 93.00 -179.13 -87.87 1 1.00e+01 1.00e-02 9.24e+01 dihedral pdb=" CA CYS A 358 " pdb=" C CYS A 358 " pdb=" N VAL A 359 " pdb=" CA VAL A 359 " ideal model delta harmonic sigma weight residual 180.00 153.20 26.80 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA PRO A 334 " pdb=" C PRO A 334 " pdb=" N PHE A 335 " pdb=" CA PHE A 335 " ideal model delta harmonic sigma weight residual 180.00 158.40 21.60 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 2052 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.027: 259 0.027 - 0.054: 145 0.054 - 0.081: 51 0.081 - 0.107: 26 0.107 - 0.134: 20 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA PRO A 334 " pdb=" N PRO A 334 " pdb=" C PRO A 334 " pdb=" CB PRO A 334 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ASN A 391 " pdb=" N ASN A 391 " pdb=" C ASN A 391 " pdb=" CB ASN A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA VAL A 508 " pdb=" N VAL A 508 " pdb=" C VAL A 508 " pdb=" CB VAL A 508 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 498 not shown) Planarity restraints: 611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 441 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C LYS A 441 " 0.032 2.00e-02 2.50e+03 pdb=" O LYS A 441 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL A 442 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 369 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 370 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 517 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 518 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " 0.023 5.00e-02 4.00e+02 ... (remaining 608 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 553 2.77 - 3.30: 2862 3.30 - 3.83: 4873 3.83 - 4.37: 5694 4.37 - 4.90: 10813 Nonbonded interactions: 24795 Sorted by model distance: nonbonded pdb=" O SER A 443 " pdb=" NH1 ARG A 495 " model vdw 2.235 3.120 nonbonded pdb=" NH1 ARG A 454 " pdb=" OD2 ASP A 464 " model vdw 2.309 3.120 nonbonded pdb=" NE2 GLN L 39 " pdb=" O GLN L 43 " model vdw 2.348 3.120 nonbonded pdb=" NH2 ARG A 451 " pdb=" O SER A 466 " model vdw 2.367 3.120 nonbonded pdb=" OG SER H 106 " pdb=" OD2 ASP H 110 " model vdw 2.380 3.040 ... (remaining 24790 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.870 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 : 0.003 0.030 3477 Z= 0.137 Angle : 0.656 10.006 4727 Z= 0.354 Chirality : 0.045 0.134 501 Planarity : 0.004 0.043 611 Dihedral : 13.665 78.415 1242 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.00 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -2.07 (0.40), residues: 425 helix: -5.08 (0.53), residues: 8 sheet: -0.52 (0.46), residues: 150 loop : -1.85 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 350 HIS 0.002 0.001 HIS A 516 PHE 0.005 0.001 PHE L 99 TYR 0.007 0.001 TYR L 92 ARG 0.005 0.000 ARG A 506 Details of bonding type rmsd hydrogen bonds : bond 0.18109 ( 83) hydrogen bonds : angle 8.37344 ( 216) SS BOND : bond 0.00392 ( 7) SS BOND : angle 1.15166 ( 14) covalent geometry : bond 0.00298 ( 3470) covalent geometry : angle 0.65364 ( 4713) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.390 Fit side-chains REVERT: H 46 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7070 (mt-10) REVERT: H 73 ASP cc_start: 0.8043 (t70) cc_final: 0.7605 (t0) REVERT: H 87 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7756 (mtm180) REVERT: L 5 THR cc_start: 0.9000 (m) cc_final: 0.8764 (p) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1951 time to fit residues: 18.8019 Evaluate side-chains 64 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0980 chunk 31 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.085438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.065988 restraints weight = 7560.063| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.69 r_work: 0.2684 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3477 Z= 0.227 Angle : 0.706 11.510 4727 Z= 0.364 Chirality : 0.046 0.159 501 Planarity : 0.005 0.045 611 Dihedral : 5.236 28.879 478 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.88 % Favored : 89.88 % Rotamer: Outliers : 1.36 % Allowed : 9.81 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -2.14 (0.40), residues: 425 helix: -5.28 (0.33), residues: 14 sheet: -0.31 (0.47), residues: 146 loop : -1.95 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 433 HIS 0.002 0.001 HIS A 516 PHE 0.009 0.001 PHE L 99 TYR 0.016 0.002 TYR L 50 ARG 0.004 0.001 ARG L 46 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 83) hydrogen bonds : angle 6.36595 ( 216) SS BOND : bond 0.00513 ( 7) SS BOND : angle 1.55671 ( 14) covalent geometry : bond 0.00543 ( 3470) covalent geometry : angle 0.70227 ( 4713) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.366 Fit side-chains REVERT: H 73 ASP cc_start: 0.8310 (t70) cc_final: 0.7616 (t0) REVERT: H 100 TYR cc_start: 0.8970 (t80) cc_final: 0.8752 (t80) REVERT: L 5 THR cc_start: 0.9054 (m) cc_final: 0.8668 (p) REVERT: A 337 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8208 (tm-30) REVERT: A 386 ASP cc_start: 0.8726 (t0) cc_final: 0.8450 (t0) REVERT: A 417 ASP cc_start: 0.8790 (m-30) cc_final: 0.8579 (m-30) REVERT: A 430 VAL cc_start: 0.9418 (OUTLIER) cc_final: 0.9162 (t) outliers start: 5 outliers final: 3 residues processed: 69 average time/residue: 0.1984 time to fit residues: 16.0503 Evaluate side-chains 69 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain A residue 430 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN H 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.086634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.067946 restraints weight = 7337.358| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.52 r_work: 0.2733 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3477 Z= 0.133 Angle : 0.630 12.004 4727 Z= 0.317 Chirality : 0.044 0.126 501 Planarity : 0.004 0.044 611 Dihedral : 4.914 27.893 478 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.29 % Favored : 92.47 % Rotamer: Outliers : 1.91 % Allowed : 11.99 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -2.12 (0.40), residues: 425 helix: -5.33 (0.24), residues: 20 sheet: -0.08 (0.48), residues: 141 loop : -1.94 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 350 HIS 0.001 0.001 HIS A 516 PHE 0.006 0.001 PHE A 397 TYR 0.009 0.001 TYR A 505 ARG 0.004 0.001 ARG L 46 Details of bonding type rmsd hydrogen bonds : bond 0.02833 ( 83) hydrogen bonds : angle 5.88108 ( 216) SS BOND : bond 0.00346 ( 7) SS BOND : angle 1.09081 ( 14) covalent geometry : bond 0.00309 ( 3470) covalent geometry : angle 0.62854 ( 4713) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.401 Fit side-chains REVERT: H 62 GLN cc_start: 0.9096 (tp40) cc_final: 0.8888 (tp-100) REVERT: H 73 ASP cc_start: 0.8287 (t70) cc_final: 0.7585 (t0) REVERT: H 87 ARG cc_start: 0.8232 (mtm110) cc_final: 0.7673 (mtm110) REVERT: H 91 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8118 (t) REVERT: H 100 TYR cc_start: 0.8723 (t80) cc_final: 0.8513 (t80) REVERT: L 5 THR cc_start: 0.9048 (m) cc_final: 0.8676 (p) REVERT: A 337 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8093 (tm-30) REVERT: A 386 ASP cc_start: 0.8710 (t0) cc_final: 0.8368 (t0) REVERT: A 417 ASP cc_start: 0.8716 (m-30) cc_final: 0.8474 (m-30) REVERT: A 430 VAL cc_start: 0.9359 (OUTLIER) cc_final: 0.9116 (t) outliers start: 7 outliers final: 4 residues processed: 73 average time/residue: 0.1842 time to fit residues: 16.1588 Evaluate side-chains 69 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 41 optimal weight: 0.0970 chunk 25 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 34 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.088006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.068529 restraints weight = 7469.779| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.67 r_work: 0.2754 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3477 Z= 0.113 Angle : 0.611 12.148 4727 Z= 0.305 Chirality : 0.043 0.133 501 Planarity : 0.004 0.048 611 Dihedral : 4.640 26.232 478 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.76 % Favored : 92.00 % Rotamer: Outliers : 3.00 % Allowed : 14.17 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -2.02 (0.40), residues: 425 helix: -5.30 (0.24), residues: 20 sheet: -0.06 (0.48), residues: 141 loop : -1.84 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 350 HIS 0.001 0.000 HIS A 516 PHE 0.005 0.001 PHE A 397 TYR 0.009 0.001 TYR A 505 ARG 0.004 0.000 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.02569 ( 83) hydrogen bonds : angle 5.62285 ( 216) SS BOND : bond 0.00330 ( 7) SS BOND : angle 0.90795 ( 14) covalent geometry : bond 0.00260 ( 3470) covalent geometry : angle 0.60977 ( 4713) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.357 Fit side-chains REVERT: H 73 ASP cc_start: 0.8348 (t70) cc_final: 0.7582 (t0) REVERT: H 87 ARG cc_start: 0.8235 (mtm110) cc_final: 0.7659 (mtm110) REVERT: H 91 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.7808 (t) REVERT: H 100 TYR cc_start: 0.8645 (t80) cc_final: 0.8442 (t80) REVERT: L 5 THR cc_start: 0.9005 (m) cc_final: 0.8614 (p) REVERT: A 337 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8088 (tm-30) REVERT: A 386 ASP cc_start: 0.8718 (t0) cc_final: 0.8430 (t0) REVERT: A 417 ASP cc_start: 0.8742 (m-30) cc_final: 0.8487 (m-30) outliers start: 11 outliers final: 6 residues processed: 76 average time/residue: 0.1882 time to fit residues: 17.0777 Evaluate side-chains 71 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 0.0370 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 0.0050 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.5272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.087612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.068253 restraints weight = 7362.736| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.62 r_work: 0.2753 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3477 Z= 0.119 Angle : 0.621 11.885 4727 Z= 0.311 Chirality : 0.043 0.141 501 Planarity : 0.004 0.050 611 Dihedral : 4.553 25.819 478 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.76 % Favored : 92.00 % Rotamer: Outliers : 3.00 % Allowed : 14.99 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.95 (0.40), residues: 425 helix: -5.29 (0.25), residues: 20 sheet: -0.01 (0.48), residues: 141 loop : -1.79 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 350 HIS 0.001 0.001 HIS A 516 PHE 0.005 0.001 PHE L 99 TYR 0.008 0.001 TYR A 505 ARG 0.005 0.000 ARG L 46 Details of bonding type rmsd hydrogen bonds : bond 0.02545 ( 83) hydrogen bonds : angle 5.50617 ( 216) SS BOND : bond 0.00321 ( 7) SS BOND : angle 0.94684 ( 14) covalent geometry : bond 0.00278 ( 3470) covalent geometry : angle 0.62019 ( 4713) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.395 Fit side-chains REVERT: H 73 ASP cc_start: 0.8363 (t70) cc_final: 0.7596 (t0) REVERT: H 91 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.7763 (t) REVERT: L 5 THR cc_start: 0.9032 (m) cc_final: 0.8701 (p) REVERT: A 337 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8106 (tm-30) REVERT: A 386 ASP cc_start: 0.8727 (t0) cc_final: 0.8438 (t0) REVERT: A 417 ASP cc_start: 0.8773 (m-30) cc_final: 0.8494 (m-30) outliers start: 11 outliers final: 8 residues processed: 72 average time/residue: 0.1814 time to fit residues: 15.5984 Evaluate side-chains 71 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 0.0060 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.0070 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 0.0470 chunk 1 optimal weight: 0.0040 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.091024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.071394 restraints weight = 7550.770| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.69 r_work: 0.2817 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3477 Z= 0.101 Angle : 0.604 11.362 4727 Z= 0.298 Chirality : 0.042 0.136 501 Planarity : 0.004 0.048 611 Dihedral : 4.228 23.769 478 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.12 % Favored : 93.65 % Rotamer: Outliers : 3.00 % Allowed : 16.89 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.67 (0.40), residues: 425 helix: -5.27 (0.32), residues: 14 sheet: 0.26 (0.48), residues: 138 loop : -1.71 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 350 HIS 0.000 0.000 HIS A 516 PHE 0.009 0.001 PHE A 389 TYR 0.010 0.001 TYR A 505 ARG 0.005 0.000 ARG L 46 Details of bonding type rmsd hydrogen bonds : bond 0.02323 ( 83) hydrogen bonds : angle 5.19722 ( 216) SS BOND : bond 0.00258 ( 7) SS BOND : angle 0.72913 ( 14) covalent geometry : bond 0.00226 ( 3470) covalent geometry : angle 0.60365 ( 4713) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.364 Fit side-chains REVERT: H 23 LYS cc_start: 0.8631 (ttmm) cc_final: 0.8105 (ttmm) REVERT: H 46 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8349 (mt-10) REVERT: H 73 ASP cc_start: 0.8297 (t70) cc_final: 0.7517 (t0) REVERT: H 91 THR cc_start: 0.7805 (OUTLIER) cc_final: 0.7395 (t) REVERT: H 107 ASP cc_start: 0.8897 (t0) cc_final: 0.8525 (t0) REVERT: L 5 THR cc_start: 0.8963 (m) cc_final: 0.8585 (p) REVERT: L 80 GLU cc_start: 0.7022 (mp0) cc_final: 0.6810 (mp0) REVERT: A 337 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8096 (tm-30) REVERT: A 386 ASP cc_start: 0.8682 (t0) cc_final: 0.8409 (t0) REVERT: A 389 PHE cc_start: 0.8670 (m-80) cc_final: 0.8253 (m-80) REVERT: A 417 ASP cc_start: 0.8653 (m-30) cc_final: 0.8417 (m-30) REVERT: A 464 ASP cc_start: 0.8591 (t70) cc_final: 0.8390 (t0) outliers start: 11 outliers final: 7 residues processed: 77 average time/residue: 0.1737 time to fit residues: 16.0359 Evaluate side-chains 72 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.0670 chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.087912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.068187 restraints weight = 7499.304| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.70 r_work: 0.2747 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3477 Z= 0.139 Angle : 0.611 11.513 4727 Z= 0.308 Chirality : 0.043 0.128 501 Planarity : 0.004 0.051 611 Dihedral : 4.410 24.493 478 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.71 % Favored : 91.06 % Rotamer: Outliers : 3.54 % Allowed : 17.71 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.40), residues: 425 helix: -5.27 (0.26), residues: 20 sheet: 0.27 (0.47), residues: 138 loop : -1.72 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.002 0.001 HIS A 516 PHE 0.010 0.001 PHE A 389 TYR 0.016 0.001 TYR H 100 ARG 0.005 0.000 ARG L 46 Details of bonding type rmsd hydrogen bonds : bond 0.02648 ( 83) hydrogen bonds : angle 5.35523 ( 216) SS BOND : bond 0.00339 ( 7) SS BOND : angle 1.00017 ( 14) covalent geometry : bond 0.00330 ( 3470) covalent geometry : angle 0.60926 ( 4713) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.361 Fit side-chains REVERT: H 23 LYS cc_start: 0.8631 (ttmm) cc_final: 0.8132 (ttmm) REVERT: H 46 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8308 (mt-10) REVERT: H 73 ASP cc_start: 0.8348 (t70) cc_final: 0.7576 (t0) REVERT: H 91 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.7821 (t) REVERT: H 107 ASP cc_start: 0.8936 (t0) cc_final: 0.8551 (t0) REVERT: L 5 THR cc_start: 0.9024 (m) cc_final: 0.8687 (p) REVERT: L 61 ASP cc_start: 0.8778 (p0) cc_final: 0.8451 (t70) REVERT: A 337 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8138 (tm-30) REVERT: A 386 ASP cc_start: 0.8741 (t0) cc_final: 0.8437 (t0) REVERT: A 417 ASP cc_start: 0.8755 (m-30) cc_final: 0.8430 (m-30) outliers start: 13 outliers final: 11 residues processed: 70 average time/residue: 0.1650 time to fit residues: 13.9801 Evaluate side-chains 73 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 25 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.088238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.068670 restraints weight = 7420.667| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.66 r_work: 0.2762 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3477 Z= 0.118 Angle : 0.611 11.698 4727 Z= 0.306 Chirality : 0.043 0.129 501 Planarity : 0.004 0.048 611 Dihedral : 4.395 25.097 478 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.29 % Favored : 92.47 % Rotamer: Outliers : 4.09 % Allowed : 17.17 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.40), residues: 425 helix: -5.28 (0.25), residues: 20 sheet: 0.07 (0.46), residues: 143 loop : -1.59 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 350 HIS 0.001 0.000 HIS A 516 PHE 0.014 0.001 PHE A 389 TYR 0.016 0.001 TYR H 100 ARG 0.005 0.000 ARG L 46 Details of bonding type rmsd hydrogen bonds : bond 0.02460 ( 83) hydrogen bonds : angle 5.25062 ( 216) SS BOND : bond 0.00288 ( 7) SS BOND : angle 0.90934 ( 14) covalent geometry : bond 0.00278 ( 3470) covalent geometry : angle 0.60953 ( 4713) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.353 Fit side-chains REVERT: H 23 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8120 (ttmm) REVERT: H 46 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8336 (mt-10) REVERT: H 73 ASP cc_start: 0.8319 (t70) cc_final: 0.7542 (t0) REVERT: H 91 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7723 (t) REVERT: H 107 ASP cc_start: 0.8902 (t0) cc_final: 0.8535 (t0) REVERT: L 5 THR cc_start: 0.8995 (m) cc_final: 0.8667 (p) REVERT: L 61 ASP cc_start: 0.8817 (p0) cc_final: 0.8473 (t70) REVERT: A 337 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8130 (tm-30) REVERT: A 386 ASP cc_start: 0.8734 (t0) cc_final: 0.8425 (t0) REVERT: A 417 ASP cc_start: 0.8728 (m-30) cc_final: 0.8405 (m-30) outliers start: 15 outliers final: 10 residues processed: 72 average time/residue: 0.1637 time to fit residues: 14.4090 Evaluate side-chains 72 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 6 optimal weight: 3.9990 chunk 39 optimal weight: 0.0370 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.088400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.069198 restraints weight = 7306.871| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.58 r_work: 0.2774 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3477 Z= 0.114 Angle : 0.606 11.536 4727 Z= 0.304 Chirality : 0.042 0.128 501 Planarity : 0.004 0.050 611 Dihedral : 4.358 24.068 478 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.76 % Favored : 92.00 % Rotamer: Outliers : 3.54 % Allowed : 17.98 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.40), residues: 425 helix: -5.24 (0.34), residues: 14 sheet: 0.10 (0.46), residues: 143 loop : -1.61 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 350 HIS 0.001 0.000 HIS A 516 PHE 0.014 0.001 PHE A 389 TYR 0.017 0.001 TYR H 100 ARG 0.005 0.000 ARG L 46 Details of bonding type rmsd hydrogen bonds : bond 0.02414 ( 83) hydrogen bonds : angle 5.20322 ( 216) SS BOND : bond 0.00274 ( 7) SS BOND : angle 0.87664 ( 14) covalent geometry : bond 0.00267 ( 3470) covalent geometry : angle 0.60534 ( 4713) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.386 Fit side-chains REVERT: H 46 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8323 (mt-10) REVERT: H 73 ASP cc_start: 0.8324 (t70) cc_final: 0.7545 (t0) REVERT: H 91 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7706 (t) REVERT: H 107 ASP cc_start: 0.8878 (t0) cc_final: 0.8528 (t0) REVERT: L 5 THR cc_start: 0.9005 (m) cc_final: 0.8680 (p) REVERT: L 61 ASP cc_start: 0.8832 (p0) cc_final: 0.8463 (t70) REVERT: L 80 GLU cc_start: 0.7473 (mp0) cc_final: 0.7268 (mp0) REVERT: A 337 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8131 (tm-30) REVERT: A 386 ASP cc_start: 0.8739 (t0) cc_final: 0.8444 (t0) REVERT: A 417 ASP cc_start: 0.8723 (m-30) cc_final: 0.8404 (m-30) outliers start: 13 outliers final: 11 residues processed: 71 average time/residue: 0.1689 time to fit residues: 14.5097 Evaluate side-chains 74 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.0570 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.088992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.069388 restraints weight = 7447.088| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.67 r_work: 0.2775 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3477 Z= 0.114 Angle : 0.614 11.412 4727 Z= 0.307 Chirality : 0.042 0.128 501 Planarity : 0.004 0.048 611 Dihedral : 4.342 24.360 478 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.53 % Favored : 92.24 % Rotamer: Outliers : 2.72 % Allowed : 18.53 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.62 (0.40), residues: 425 helix: -5.24 (0.34), residues: 14 sheet: 0.09 (0.46), residues: 143 loop : -1.57 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 350 HIS 0.001 0.000 HIS A 516 PHE 0.013 0.001 PHE A 389 TYR 0.017 0.001 TYR H 100 ARG 0.004 0.000 ARG L 46 Details of bonding type rmsd hydrogen bonds : bond 0.02404 ( 83) hydrogen bonds : angle 5.19544 ( 216) SS BOND : bond 0.00288 ( 7) SS BOND : angle 0.85839 ( 14) covalent geometry : bond 0.00267 ( 3470) covalent geometry : angle 0.61272 ( 4713) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.411 Fit side-chains REVERT: H 46 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8292 (mt-10) REVERT: H 73 ASP cc_start: 0.8299 (t70) cc_final: 0.7522 (t0) REVERT: H 91 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7659 (t) REVERT: H 107 ASP cc_start: 0.8841 (t0) cc_final: 0.8503 (t0) REVERT: L 5 THR cc_start: 0.8999 (m) cc_final: 0.8675 (p) REVERT: L 18 ARG cc_start: 0.8581 (ttm-80) cc_final: 0.8312 (ttm-80) REVERT: L 61 ASP cc_start: 0.8856 (p0) cc_final: 0.8483 (t70) REVERT: A 337 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8143 (tm-30) REVERT: A 386 ASP cc_start: 0.8721 (t0) cc_final: 0.8428 (t0) REVERT: A 417 ASP cc_start: 0.8714 (m-30) cc_final: 0.8396 (m-30) outliers start: 10 outliers final: 9 residues processed: 69 average time/residue: 0.1633 time to fit residues: 13.9833 Evaluate side-chains 71 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 41 optimal weight: 0.0000 chunk 13 optimal weight: 0.0170 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.089151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.069702 restraints weight = 7456.364| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.65 r_work: 0.2782 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3477 Z= 0.116 Angle : 0.628 11.301 4727 Z= 0.316 Chirality : 0.042 0.127 501 Planarity : 0.004 0.050 611 Dihedral : 4.299 23.271 478 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.00 % Favored : 91.76 % Rotamer: Outliers : 3.00 % Allowed : 19.07 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.60 (0.40), residues: 425 helix: -5.24 (0.34), residues: 14 sheet: 0.09 (0.46), residues: 143 loop : -1.55 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 350 HIS 0.000 0.000 HIS A 516 PHE 0.012 0.001 PHE A 389 TYR 0.017 0.001 TYR H 100 ARG 0.005 0.000 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.02428 ( 83) hydrogen bonds : angle 5.19224 ( 216) SS BOND : bond 0.00296 ( 7) SS BOND : angle 0.86313 ( 14) covalent geometry : bond 0.00276 ( 3470) covalent geometry : angle 0.62675 ( 4713) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1892.14 seconds wall clock time: 33 minutes 53.52 seconds (2033.52 seconds total)