Starting phenix.real_space_refine on Thu Jul 24 00:55:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k5g_36905/07_2025/8k5g_36905.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k5g_36905/07_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_36905/07_2025/8k5g_36905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k5g_36905/07_2025/8k5g_36905.map" model { file = "/net/cci-nas-00/data/ceres_data/8k5g_36905/07_2025/8k5g_36905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k5g_36905/07_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-5711/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: 2.89, per 1000 atoms: 0.85 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: 0.81 Conformation dependent library (CDL) restraints added in 468.0 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: 0.49 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: 0.94 Time building geometry restraints manager: 0.98 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: 2.070 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.490 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.700 ------------------------------------------------------------------------------- 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 : 0.402 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: 0.2008 time to fit residues: 19.3432 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 : 0.393 ------------------------------------------------------------------------------- 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: 0.0070 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: 0.7980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 62 GLN L 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.085409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.066760 restraints weight = 7477.826| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.54 r_work: 0.2704 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3477 Z= 0.210 Angle : 0.692 11.406 4727 Z= 0.356 Chirality : 0.046 0.154 501 Planarity : 0.005 0.046 611 Dihedral : 5.149 28.550 478 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.65 % Favored : 90.12 % Rotamer: Outliers : 1.36 % Allowed : 8.99 % Favored : 89.65 % 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: -2.08 (0.41), residues: 425 helix: -5.28 (0.33), residues: 14 sheet: -0.23 (0.47), residues: 147 loop : -1.93 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 433 HIS 0.003 0.001 HIS A 516 PHE 0.008 0.001 PHE L 99 TYR 0.015 0.002 TYR L 50 ARG 0.004 0.001 ARG L 46 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 83) hydrogen bonds : angle 6.35444 ( 216) SS BOND : bond 0.00473 ( 7) SS BOND : angle 1.47137 ( 14) covalent geometry : bond 0.00501 ( 3470) covalent geometry : angle 0.68877 ( 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 : 0.396 Fit side-chains REVERT: H 73 ASP cc_start: 0.8306 (t70) cc_final: 0.7612 (t0) REVERT: H 87 ARG cc_start: 0.8192 (mtm-85) cc_final: 0.7864 (mtm110) REVERT: H 100 TYR cc_start: 0.8772 (t80) cc_final: 0.8552 (t80) REVERT: L 5 THR cc_start: 0.9057 (m) cc_final: 0.8673 (p) REVERT: A 337 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8183 (tm-30) REVERT: A 386 ASP cc_start: 0.8691 (t0) cc_final: 0.8428 (t0) REVERT: A 430 VAL cc_start: 0.9386 (OUTLIER) cc_final: 0.9127 (t) outliers start: 5 outliers final: 3 residues processed: 69 average time/residue: 0.2092 time to fit residues: 16.9155 Evaluate side-chains 67 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 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: 1.9990 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 1 optimal weight: 0.0000 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.086231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.067335 restraints weight = 7348.002| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.55 r_work: 0.2721 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3477 Z= 0.151 Angle : 0.646 11.921 4727 Z= 0.326 Chirality : 0.044 0.134 501 Planarity : 0.004 0.045 611 Dihedral : 4.971 28.153 478 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.00 % Favored : 91.76 % Rotamer: Outliers : 2.18 % Allowed : 10.35 % Favored : 87.47 % 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: -2.06 (0.40), residues: 425 helix: -5.12 (0.53), residues: 8 sheet: -0.07 (0.48), residues: 141 loop : -2.09 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 350 HIS 0.002 0.001 HIS A 516 PHE 0.006 0.001 PHE A 397 TYR 0.008 0.001 TYR A 505 ARG 0.005 0.000 ARG L 46 Details of bonding type rmsd hydrogen bonds : bond 0.02958 ( 83) hydrogen bonds : angle 5.95599 ( 216) SS BOND : bond 0.00386 ( 7) SS BOND : angle 1.18459 ( 14) covalent geometry : bond 0.00355 ( 3470) covalent geometry : angle 0.64405 ( 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 74 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.370 Fit side-chains REVERT: H 73 ASP cc_start: 0.8275 (t70) cc_final: 0.7573 (t0) REVERT: H 87 ARG cc_start: 0.8202 (mtm-85) cc_final: 0.7900 (mtm110) REVERT: H 91 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8202 (t) REVERT: H 100 TYR cc_start: 0.8740 (t80) cc_final: 0.8533 (t80) REVERT: L 5 THR cc_start: 0.9056 (m) cc_final: 0.8676 (p) REVERT: A 337 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8128 (tm-30) REVERT: A 386 ASP cc_start: 0.8724 (t0) cc_final: 0.8377 (t0) outliers start: 8 outliers final: 6 residues processed: 70 average time/residue: 0.2078 time to fit residues: 17.7027 Evaluate side-chains 70 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 L residue 73 THR Chi-restraints excluded: chain L residue 98 THR 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: 7.9990 chunk 33 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN A 391 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.086245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.066839 restraints weight = 7430.634| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.64 r_work: 0.2723 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3477 Z= 0.136 Angle : 0.633 12.405 4727 Z= 0.318 Chirality : 0.044 0.135 501 Planarity : 0.004 0.047 611 Dihedral : 4.884 27.593 478 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.24 % Favored : 91.53 % Rotamer: Outliers : 3.27 % Allowed : 13.08 % Favored : 83.65 % 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: -2.04 (0.40), residues: 425 helix: -5.23 (0.33), residues: 14 sheet: -0.02 (0.47), residues: 141 loop : -2.00 (0.34), residues: 270 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 0.000 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.02793 ( 83) hydrogen bonds : angle 5.79259 ( 216) SS BOND : bond 0.00366 ( 7) SS BOND : angle 1.08714 ( 14) covalent geometry : bond 0.00320 ( 3470) covalent geometry : angle 0.63108 ( 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: 12 poor density : 67 time to evaluate : 0.395 Fit side-chains REVERT: H 73 ASP cc_start: 0.8280 (t70) cc_final: 0.7576 (t0) REVERT: H 87 ARG cc_start: 0.8192 (mtm-85) cc_final: 0.7873 (mtm110) REVERT: H 91 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8124 (t) REVERT: L 5 THR cc_start: 0.9033 (m) cc_final: 0.8638 (p) REVERT: A 337 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8164 (tm-30) REVERT: A 386 ASP cc_start: 0.8745 (t0) cc_final: 0.8413 (t0) REVERT: A 430 VAL cc_start: 0.9385 (OUTLIER) cc_final: 0.9118 (t) outliers start: 12 outliers final: 7 residues processed: 76 average time/residue: 0.2154 time to fit residues: 19.8096 Evaluate side-chains 73 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 L residue 73 THR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 430 VAL 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: 0.0010 chunk 30 optimal weight: 0.0870 chunk 2 optimal weight: 0.0870 chunk 0 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 0.0270 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 overall best weight: 0.2000 ------------------------------------------------------------------------------- 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 = 0.3268 r_free = 0.3268 target = 0.089676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.070010 restraints weight = 7485.724| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.70 r_work: 0.2784 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3477 Z= 0.106 Angle : 0.632 11.988 4727 Z= 0.312 Chirality : 0.043 0.142 501 Planarity : 0.004 0.046 611 Dihedral : 4.485 25.424 478 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.82 % Favored : 92.94 % Rotamer: Outliers : 2.45 % Allowed : 15.53 % 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: -1.96 (0.40), residues: 425 helix: -5.29 (0.24), residues: 20 sheet: -0.08 (0.47), residues: 143 loop : -1.76 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 350 HIS 0.000 0.000 HIS A 502 PHE 0.004 0.001 PHE A 371 TYR 0.010 0.001 TYR A 505 ARG 0.004 0.000 ARG L 46 Details of bonding type rmsd hydrogen bonds : bond 0.02432 ( 83) hydrogen bonds : angle 5.44496 ( 216) SS BOND : bond 0.00298 ( 7) SS BOND : angle 0.81499 ( 14) covalent geometry : bond 0.00238 ( 3470) covalent geometry : angle 0.63092 ( 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 76 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.435 Fit side-chains REVERT: H 23 LYS cc_start: 0.8796 (ttmm) cc_final: 0.8203 (ttmm) REVERT: H 73 ASP cc_start: 0.8313 (t70) cc_final: 0.7553 (t0) REVERT: H 87 ARG cc_start: 0.8087 (mtm-85) cc_final: 0.7756 (mtm110) REVERT: H 91 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7653 (t) REVERT: L 5 THR cc_start: 0.8970 (m) cc_final: 0.8585 (p) REVERT: L 21 LEU cc_start: 0.8979 (mt) cc_final: 0.8680 (mp) REVERT: L 61 ASP cc_start: 0.8792 (p0) cc_final: 0.8469 (t70) REVERT: A 337 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8153 (tm-30) REVERT: A 386 ASP cc_start: 0.8722 (t0) cc_final: 0.8456 (t0) outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 0.2262 time to fit residues: 19.9064 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 : 0.446 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 0.0770 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 0.0060 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 0.0770 overall best weight: 0.3312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.089270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.069951 restraints weight = 7409.890| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.63 r_work: 0.2790 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2475 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= 0.106 Angle : 0.606 11.694 4727 Z= 0.301 Chirality : 0.042 0.133 501 Planarity : 0.004 0.047 611 Dihedral : 4.361 24.542 478 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.76 % Favored : 92.00 % Rotamer: Outliers : 2.72 % Allowed : 16.08 % Favored : 81.20 % 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: -1.79 (0.39), residues: 425 helix: -5.24 (0.33), residues: 14 sheet: 0.17 (0.47), residues: 138 loop : -1.80 (0.34), residues: 273 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 0.010 0.001 PHE A 389 TYR 0.015 0.001 TYR H 100 ARG 0.004 0.000 ARG L 46 Details of bonding type rmsd hydrogen bonds : bond 0.02428 ( 83) hydrogen bonds : angle 5.26688 ( 216) SS BOND : bond 0.00257 ( 7) SS BOND : angle 0.83764 ( 14) covalent geometry : bond 0.00244 ( 3470) covalent geometry : angle 0.60546 ( 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 75 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.608 Fit side-chains REVERT: H 46 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8218 (mt-10) REVERT: H 73 ASP cc_start: 0.8352 (t70) cc_final: 0.7573 (t0) REVERT: H 91 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7695 (t) REVERT: L 5 THR cc_start: 0.9011 (m) cc_final: 0.8633 (p) REVERT: A 337 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 386 ASP cc_start: 0.8684 (t0) cc_final: 0.8406 (t0) outliers start: 10 outliers final: 9 residues processed: 73 average time/residue: 0.2121 time to fit residues: 19.3299 Evaluate side-chains 73 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 0.0010 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.087962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.068266 restraints weight = 7464.889| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.67 r_work: 0.2754 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2445 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= 0.133 Angle : 0.618 11.746 4727 Z= 0.308 Chirality : 0.043 0.130 501 Planarity : 0.004 0.049 611 Dihedral : 4.453 25.153 478 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.00 % Favored : 91.76 % Rotamer: Outliers : 3.27 % Allowed : 16.62 % 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: -1.87 (0.39), residues: 425 helix: -5.26 (0.26), residues: 20 sheet: 0.15 (0.47), residues: 138 loop : -1.77 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 433 HIS 0.001 0.001 HIS A 516 PHE 0.012 0.001 PHE A 389 TYR 0.016 0.001 TYR H 100 ARG 0.005 0.000 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.02590 ( 83) hydrogen bonds : angle 5.34645 ( 216) SS BOND : bond 0.00341 ( 7) SS BOND : angle 1.00129 ( 14) covalent geometry : bond 0.00317 ( 3470) covalent geometry : angle 0.61623 ( 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 76 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.421 Fit side-chains REVERT: H 23 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8206 (ttmm) REVERT: H 46 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8307 (mt-10) REVERT: H 73 ASP cc_start: 0.8363 (t70) cc_final: 0.7582 (t0) REVERT: H 87 ARG cc_start: 0.8242 (mtp-110) cc_final: 0.7854 (mtm110) REVERT: H 91 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.7791 (t) REVERT: H 107 ASP cc_start: 0.8956 (t0) cc_final: 0.8570 (t0) REVERT: L 5 THR cc_start: 0.9026 (m) cc_final: 0.8697 (p) REVERT: A 337 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8153 (tm-30) REVERT: A 386 ASP cc_start: 0.8729 (t0) cc_final: 0.8430 (t0) outliers start: 12 outliers final: 10 residues processed: 73 average time/residue: 0.2545 time to fit residues: 21.8325 Evaluate side-chains 73 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 12 SER Chi-restraints excluded: chain L residue 98 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 0.0470 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 0.0770 chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 25 optimal weight: 0.0770 overall best weight: 0.1952 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.090275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.071217 restraints weight = 7353.147| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.55 r_work: 0.2819 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 3477 Z= 0.103 Angle : 0.604 11.623 4727 Z= 0.298 Chirality : 0.042 0.128 501 Planarity : 0.004 0.046 611 Dihedral : 4.220 23.631 478 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.59 % Favored : 93.18 % Rotamer: Outliers : 3.00 % Allowed : 17.17 % Favored : 79.84 % 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: -1.69 (0.39), residues: 425 helix: -5.23 (0.33), residues: 14 sheet: 0.02 (0.46), residues: 143 loop : -1.61 (0.34), 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 502 PHE 0.011 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 0.02333 ( 83) hydrogen bonds : angle 5.10679 ( 216) SS BOND : bond 0.00232 ( 7) SS BOND : angle 0.74300 ( 14) covalent geometry : bond 0.00239 ( 3470) covalent geometry : angle 0.60337 ( 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: 11 poor density : 66 time to evaluate : 0.504 Fit side-chains REVERT: H 46 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8266 (mt-10) REVERT: H 73 ASP cc_start: 0.8307 (t70) cc_final: 0.7544 (t0) REVERT: H 87 ARG cc_start: 0.8145 (mtp-110) cc_final: 0.7866 (mtm110) REVERT: H 91 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7447 (t) REVERT: H 107 ASP cc_start: 0.8888 (t0) cc_final: 0.8535 (t0) REVERT: L 5 THR cc_start: 0.8987 (m) cc_final: 0.8614 (p) REVERT: L 80 GLU cc_start: 0.6913 (mp0) cc_final: 0.6629 (mp0) REVERT: A 337 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8102 (tm-30) REVERT: A 386 ASP cc_start: 0.8647 (t0) cc_final: 0.8419 (t0) REVERT: A 389 PHE cc_start: 0.8640 (m-80) cc_final: 0.8252 (m-80) outliers start: 11 outliers final: 9 residues processed: 74 average time/residue: 0.2639 time to fit residues: 24.8856 Evaluate side-chains 73 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 33 optimal weight: 0.0010 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 = 0.3258 r_free = 0.3258 target = 0.088883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.069348 restraints weight = 7437.352| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.66 r_work: 0.2776 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3477 Z= 0.122 Angle : 0.636 11.491 4727 Z= 0.314 Chirality : 0.043 0.126 501 Planarity : 0.004 0.050 611 Dihedral : 4.298 23.535 478 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.29 % Favored : 92.47 % Rotamer: Outliers : 3.27 % Allowed : 18.80 % 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: -1.67 (0.39), residues: 425 helix: -5.21 (0.35), residues: 14 sheet: 0.09 (0.46), residues: 143 loop : -1.64 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 433 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 0.005 0.000 ARG L 46 Details of bonding type rmsd hydrogen bonds : bond 0.02542 ( 83) hydrogen bonds : angle 5.18585 ( 216) SS BOND : bond 0.00330 ( 7) SS BOND : angle 0.92944 ( 14) covalent geometry : bond 0.00288 ( 3470) covalent geometry : angle 0.63469 ( 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 76 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.437 Fit side-chains REVERT: H 46 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8287 (mt-10) REVERT: H 73 ASP cc_start: 0.8305 (t70) cc_final: 0.7515 (t0) REVERT: H 87 ARG cc_start: 0.8201 (mtp-110) cc_final: 0.7875 (mtm110) REVERT: H 91 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7643 (t) REVERT: H 107 ASP cc_start: 0.8914 (t0) cc_final: 0.8548 (t0) REVERT: L 5 THR cc_start: 0.9014 (m) cc_final: 0.8691 (p) REVERT: L 21 LEU cc_start: 0.8954 (mt) cc_final: 0.8649 (mp) REVERT: L 61 ASP cc_start: 0.8787 (p0) cc_final: 0.8454 (t70) REVERT: A 337 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8161 (tm-30) REVERT: A 386 ASP cc_start: 0.8702 (t0) cc_final: 0.8420 (t0) outliers start: 12 outliers final: 11 residues processed: 73 average time/residue: 0.3109 time to fit residues: 27.1874 Evaluate side-chains 76 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 12 SER 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: 4.9990 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 0.0000 chunk 29 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.3252 r_free = 0.3252 target = 0.088580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.068992 restraints weight = 7460.252| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.69 r_work: 0.2769 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2670 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= 0.125 Angle : 0.648 11.562 4727 Z= 0.320 Chirality : 0.043 0.128 501 Planarity : 0.004 0.046 611 Dihedral : 4.393 24.613 478 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.06 % Favored : 92.71 % Rotamer: Outliers : 3.27 % Allowed : 18.80 % 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: -1.66 (0.40), residues: 425 helix: -5.25 (0.25), residues: 20 sheet: 0.32 (0.47), residues: 138 loop : -1.63 (0.35), residues: 267 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 0.013 0.001 PHE A 389 TYR 0.018 0.001 TYR H 100 ARG 0.005 0.000 ARG L 46 Details of bonding type rmsd hydrogen bonds : bond 0.02548 ( 83) hydrogen bonds : angle 5.15044 ( 216) SS BOND : bond 0.00305 ( 7) SS BOND : angle 0.92382 ( 14) covalent geometry : bond 0.00295 ( 3470) covalent geometry : angle 0.64751 ( 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 76 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.379 Fit side-chains REVERT: H 46 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8301 (mt-10) REVERT: H 73 ASP cc_start: 0.8289 (t70) cc_final: 0.7504 (t0) REVERT: H 87 ARG cc_start: 0.8375 (mtp-110) cc_final: 0.8037 (mtm110) REVERT: H 91 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.7743 (t) REVERT: H 107 ASP cc_start: 0.8882 (t0) cc_final: 0.8532 (t0) REVERT: L 5 THR cc_start: 0.9025 (m) cc_final: 0.8702 (p) REVERT: L 18 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.8194 (ttm-80) REVERT: L 61 ASP cc_start: 0.8794 (p0) cc_final: 0.8476 (t70) REVERT: L 80 GLU cc_start: 0.6981 (mp0) cc_final: 0.6684 (mp0) REVERT: A 337 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8191 (tm-30) REVERT: A 386 ASP cc_start: 0.8719 (t0) cc_final: 0.8442 (t0) outliers start: 12 outliers final: 11 residues processed: 73 average time/residue: 0.2898 time to fit residues: 25.3613 Evaluate side-chains 75 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 12 SER 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: 0.7980 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 41 optimal weight: 0.2980 chunk 13 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3240 r_free = 0.3240 target = 0.087916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.068308 restraints weight = 7501.161| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.69 r_work: 0.2756 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3477 Z= 0.134 Angle : 0.642 11.505 4727 Z= 0.320 Chirality : 0.043 0.131 501 Planarity : 0.004 0.050 611 Dihedral : 4.419 24.113 478 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.53 % Favored : 92.24 % Rotamer: Outliers : 3.27 % Allowed : 18.80 % 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: -1.69 (0.40), residues: 425 helix: -5.25 (0.26), residues: 20 sheet: 0.28 (0.47), residues: 138 loop : -1.64 (0.35), residues: 267 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 0.014 0.001 PHE A 389 TYR 0.017 0.001 TYR H 100 ARG 0.006 0.000 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.02620 ( 83) hydrogen bonds : angle 5.26249 ( 216) SS BOND : bond 0.00335 ( 7) SS BOND : angle 0.98303 ( 14) covalent geometry : bond 0.00321 ( 3470) covalent geometry : angle 0.64102 ( 4713) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2721.18 seconds wall clock time: 50 minutes 36.86 seconds (3036.86 seconds total)