Starting phenix.real_space_refine on Tue Feb 3 17:02:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nn6_49565/02_2026/9nn6_49565.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nn6_49565/02_2026/9nn6_49565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nn6_49565/02_2026/9nn6_49565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nn6_49565/02_2026/9nn6_49565.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nn6_49565/02_2026/9nn6_49565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nn6_49565/02_2026/9nn6_49565.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 3254 2.51 5 N 910 2.21 5 O 1046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5224 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 4974 Classifications: {'peptide': 632} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 606} Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 250 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 28} Time building chain proxies: 1.37, per 1000 atoms: 0.26 Number of scatterers: 5224 At special positions: 0 Unit cell: (87.15, 69.72, 71.38, 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 14 16.00 O 1046 8.00 N 910 7.00 C 3254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.41 Conformation dependent library (CDL) restraints added in 389.4 milliseconds 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1210 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 7 sheets defined 7.2% alpha, 49.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 55 through 62 removed outlier: 4.501A pdb=" N LYS A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 72 removed outlier: 4.246A pdb=" N VAL A 70 " --> pdb=" O ASN A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.797A pdb=" N LEU A 122 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 422 through 427 removed outlier: 3.534A pdb=" N LEU A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 422 through 427' Processing helix chain 'A' and resid 496 through 501 removed outlier: 4.201A pdb=" N GLN A 501 " --> pdb=" O PRO A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 561 Processing helix chain 'A' and resid 642 through 647 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 54 removed outlier: 4.268A pdb=" N SER A 50 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU A 100 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE A 155 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A 102 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR A 157 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE A 101 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 83 removed outlier: 5.817A pdb=" N ARG A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 563 through 564 removed outlier: 3.794A pdb=" N LYS A 563 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU A 199 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A 264 " --> pdb=" O ASP A 268 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 362 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 383 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS A 387 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N TRP A 394 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE A 418 " --> pdb=" O TRP A 394 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 416 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASN A 524 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE A 486 " --> pdb=" O ASN A 522 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN A 522 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA6, first strand: chain 'A' and resid 431 through 434 removed outlier: 6.398A pdb=" N LYS A 440 " --> pdb=" O PHE A 518 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE A 515 " --> pdb=" O PHE A 506 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE A 506 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL A 517 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 68 through 69 280 hydrogen bonds defined for protein. 774 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: 0.54 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 911 1.32 - 1.44: 1482 1.44 - 1.56: 2925 1.56 - 1.68: 0 1.68 - 1.81: 24 Bond restraints: 5342 Sorted by residual: bond pdb=" C ASP A 286 " pdb=" O ASP A 286 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.19e-02 7.06e+03 1.08e+01 bond pdb=" N TYR A 287 " pdb=" CA TYR A 287 " ideal model delta sigma weight residual 1.456 1.484 -0.029 1.35e-02 5.49e+03 4.49e+00 bond pdb=" N THR A 32 " pdb=" CA THR A 32 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N LYS B 57 " pdb=" CA LYS B 57 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N ARG B 74 " pdb=" CA ARG B 74 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.41e-02 5.03e+03 2.82e+00 ... (remaining 5337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.77: 6857 0.77 - 1.54: 320 1.54 - 2.31: 37 2.31 - 3.08: 19 3.08 - 3.85: 21 Bond angle restraints: 7254 Sorted by residual: angle pdb=" N TYR A 287 " pdb=" CA TYR A 287 " pdb=" C TYR A 287 " ideal model delta sigma weight residual 113.38 110.30 3.08 1.23e+00 6.61e-01 6.27e+00 angle pdb=" N GLN A 501 " pdb=" CA GLN A 501 " pdb=" CB GLN A 501 " ideal model delta sigma weight residual 113.65 110.10 3.55 1.47e+00 4.63e-01 5.83e+00 angle pdb=" CA GLY B 73 " pdb=" C GLY B 73 " pdb=" N ARG B 74 " ideal model delta sigma weight residual 118.42 115.62 2.80 1.26e+00 6.30e-01 4.93e+00 angle pdb=" CA ARG B 74 " pdb=" C ARG B 74 " pdb=" O ARG B 74 " ideal model delta sigma weight residual 121.40 118.96 2.44 1.11e+00 8.12e-01 4.85e+00 angle pdb=" CA ASP A 286 " pdb=" C ASP A 286 " pdb=" O ASP A 286 " ideal model delta sigma weight residual 120.42 118.12 2.30 1.06e+00 8.90e-01 4.71e+00 ... (remaining 7249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 2900 15.92 - 31.84: 218 31.84 - 47.76: 37 47.76 - 63.68: 4 63.68 - 79.59: 3 Dihedral angle restraints: 3162 sinusoidal: 1261 harmonic: 1901 Sorted by residual: dihedral pdb=" CA ASN B 77 " pdb=" C ASN B 77 " pdb=" N TRP B 78 " pdb=" CA TRP B 78 " ideal model delta harmonic sigma weight residual 180.00 -165.25 -14.75 0 5.00e+00 4.00e-02 8.70e+00 dihedral pdb=" CA GLN A 501 " pdb=" CB GLN A 501 " pdb=" CG GLN A 501 " pdb=" CD GLN A 501 " ideal model delta sinusoidal sigma weight residual -60.00 -103.64 43.64 3 1.50e+01 4.44e-03 7.85e+00 dihedral pdb=" CA TYR A 402 " pdb=" CB TYR A 402 " pdb=" CG TYR A 402 " pdb=" CD1 TYR A 402 " ideal model delta sinusoidal sigma weight residual 90.00 36.46 53.54 2 2.00e+01 2.50e-03 7.76e+00 ... (remaining 3159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 425 0.026 - 0.052: 247 0.052 - 0.078: 33 0.078 - 0.105: 28 0.105 - 0.131: 40 Chirality restraints: 773 Sorted by residual: chirality pdb=" CA VAL A 279 " pdb=" N VAL A 279 " pdb=" C VAL A 279 " pdb=" CB VAL A 279 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA ILE A 195 " pdb=" N ILE A 195 " pdb=" C ILE A 195 " pdb=" CB ILE A 195 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA VAL A 74 " pdb=" N VAL A 74 " pdb=" C VAL A 74 " pdb=" CB VAL A 74 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 770 not shown) Planarity restraints: 958 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 63 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO B 64 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 64 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 64 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 286 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C ASP A 286 " -0.024 2.00e-02 2.50e+03 pdb=" O ASP A 286 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR A 287 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 286 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" CG ASP A 286 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASP A 286 " -0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP A 286 " -0.007 2.00e-02 2.50e+03 ... (remaining 955 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 500 2.74 - 3.28: 5147 3.28 - 3.82: 8282 3.82 - 4.36: 9822 4.36 - 4.90: 18326 Nonbonded interactions: 42077 Sorted by model distance: nonbonded pdb=" N SER A 206 " pdb=" OD1 ASP A 236 " model vdw 2.203 3.120 nonbonded pdb=" OG SER A 52 " pdb=" NH1 ARG A 137 " model vdw 2.224 3.120 nonbonded pdb=" O VAL A 523 " pdb=" NZ LYS A 525 " model vdw 2.239 3.120 nonbonded pdb=" OE2 GLU A 82 " pdb=" OG SER A 96 " model vdw 2.242 3.040 nonbonded pdb=" O SER A 38 " pdb=" OG SER A 39 " model vdw 2.256 3.040 ... (remaining 42072 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.140 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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 : 0.002 0.039 5342 Z= 0.124 Angle : 0.419 3.847 7254 Z= 0.230 Chirality : 0.042 0.131 773 Planarity : 0.003 0.050 958 Dihedral : 11.423 79.594 1952 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.35), residues: 660 helix: 0.44 (1.87), residues: 12 sheet: 1.07 (0.28), residues: 353 loop : 0.45 (0.40), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 107 TYR 0.006 0.001 TYR A 500 PHE 0.005 0.001 PHE A 418 TRP 0.012 0.001 TRP B 78 HIS 0.001 0.000 HIS A 393 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 5342) covalent geometry : angle 0.41879 ( 7254) hydrogen bonds : bond 0.20059 ( 280) hydrogen bonds : angle 9.72696 ( 774) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9248 (ptpt) cc_final: 0.8893 (ptpp) REVERT: A 58 ASP cc_start: 0.8958 (m-30) cc_final: 0.8610 (m-30) REVERT: A 131 GLU cc_start: 0.8609 (tp30) cc_final: 0.8301 (tp30) REVERT: A 384 MET cc_start: 0.8487 (tmm) cc_final: 0.8098 (tmm) REVERT: A 393 HIS cc_start: 0.8291 (t-90) cc_final: 0.7761 (t70) REVERT: A 450 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7281 (mt-10) REVERT: A 487 SER cc_start: 0.8933 (t) cc_final: 0.8681 (t) REVERT: A 536 LYS cc_start: 0.8765 (mttt) cc_final: 0.8560 (mttp) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.3495 time to fit residues: 47.3961 Evaluate side-chains 105 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.096710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.075212 restraints weight = 8339.795| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.39 r_work: 0.2795 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5342 Z= 0.194 Angle : 0.587 6.441 7254 Z= 0.317 Chirality : 0.046 0.151 773 Planarity : 0.004 0.054 958 Dihedral : 4.026 17.158 730 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.81 % Allowed : 9.49 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.34), residues: 660 helix: 1.97 (2.18), residues: 7 sheet: 0.69 (0.27), residues: 356 loop : 0.63 (0.40), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 383 TYR 0.019 0.002 TYR A 294 PHE 0.013 0.002 PHE A 656 TRP 0.009 0.001 TRP B 68 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 5342) covalent geometry : angle 0.58660 ( 7254) hydrogen bonds : bond 0.03788 ( 280) hydrogen bonds : angle 6.38182 ( 774) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9313 (ptpt) cc_final: 0.8954 (ptpp) REVERT: A 62 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8550 (ttpp) REVERT: A 82 GLU cc_start: 0.9122 (tp30) cc_final: 0.8838 (mm-30) REVERT: A 131 GLU cc_start: 0.8678 (tp30) cc_final: 0.8448 (tp30) REVERT: A 140 MET cc_start: 0.7589 (mmm) cc_final: 0.7341 (mmm) REVERT: A 345 ASP cc_start: 0.8387 (t0) cc_final: 0.8115 (t0) REVERT: A 384 MET cc_start: 0.8725 (tmm) cc_final: 0.8240 (tmm) REVERT: A 393 HIS cc_start: 0.7964 (t-90) cc_final: 0.7298 (t-90) REVERT: A 419 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8405 (ttmp) REVERT: A 450 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7348 (mt-10) REVERT: A 487 SER cc_start: 0.9109 (t) cc_final: 0.8550 (p) outliers start: 16 outliers final: 9 residues processed: 121 average time/residue: 0.3582 time to fit residues: 45.5003 Evaluate side-chains 113 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain B residue 83 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.094041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.072664 restraints weight = 8365.669| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.41 r_work: 0.2765 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5342 Z= 0.248 Angle : 0.582 5.727 7254 Z= 0.312 Chirality : 0.046 0.148 773 Planarity : 0.004 0.050 958 Dihedral : 4.187 23.612 730 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.81 % Allowed : 11.42 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.34), residues: 660 helix: 0.50 (1.91), residues: 7 sheet: 0.39 (0.27), residues: 356 loop : 0.47 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 383 TYR 0.020 0.002 TYR A 590 PHE 0.011 0.002 PHE A 418 TRP 0.007 0.001 TRP B 68 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 5342) covalent geometry : angle 0.58227 ( 7254) hydrogen bonds : bond 0.03374 ( 280) hydrogen bonds : angle 5.91269 ( 774) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9314 (ptpt) cc_final: 0.8948 (ptpp) REVERT: A 62 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8631 (ttpp) REVERT: A 131 GLU cc_start: 0.8770 (tp30) cc_final: 0.8469 (tp30) REVERT: A 140 MET cc_start: 0.7689 (mmm) cc_final: 0.7379 (mmm) REVERT: A 345 ASP cc_start: 0.8472 (t0) cc_final: 0.8197 (t0) REVERT: A 384 MET cc_start: 0.8822 (tmm) cc_final: 0.8325 (tmm) REVERT: A 419 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8522 (ttmp) REVERT: A 450 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7898 (mt-10) REVERT: A 487 SER cc_start: 0.9135 (t) cc_final: 0.8655 (p) outliers start: 16 outliers final: 9 residues processed: 111 average time/residue: 0.3871 time to fit residues: 44.9361 Evaluate side-chains 110 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 83 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 0.0570 chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- 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 = 0.3246 r_free = 0.3246 target = 0.093872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.072937 restraints weight = 8354.541| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.39 r_work: 0.2755 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 5342 Z= 0.216 Angle : 0.569 6.155 7254 Z= 0.305 Chirality : 0.045 0.149 773 Planarity : 0.004 0.049 958 Dihedral : 4.257 29.547 730 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.64 % Allowed : 12.65 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.34), residues: 660 helix: 0.08 (1.93), residues: 7 sheet: 0.25 (0.27), residues: 354 loop : 0.47 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 383 TYR 0.022 0.002 TYR A 590 PHE 0.029 0.002 PHE A 418 TRP 0.008 0.001 TRP B 68 HIS 0.002 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 5342) covalent geometry : angle 0.56912 ( 7254) hydrogen bonds : bond 0.02985 ( 280) hydrogen bonds : angle 5.65202 ( 774) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9319 (ptpt) cc_final: 0.8958 (ptpp) REVERT: A 82 GLU cc_start: 0.9095 (tp30) cc_final: 0.8834 (mm-30) REVERT: A 131 GLU cc_start: 0.8780 (tp30) cc_final: 0.8459 (tp30) REVERT: A 140 MET cc_start: 0.7653 (mmm) cc_final: 0.7389 (mmm) REVERT: A 345 ASP cc_start: 0.8574 (t0) cc_final: 0.8304 (t0) REVERT: A 384 MET cc_start: 0.8864 (tmm) cc_final: 0.8345 (tmm) REVERT: A 393 HIS cc_start: 0.8120 (t-90) cc_final: 0.7556 (t-90) REVERT: A 450 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7866 (mt-10) REVERT: A 480 ASN cc_start: 0.8808 (t0) cc_final: 0.8540 (t0) REVERT: A 487 SER cc_start: 0.9147 (t) cc_final: 0.8668 (p) outliers start: 15 outliers final: 10 residues processed: 114 average time/residue: 0.3244 time to fit residues: 38.8703 Evaluate side-chains 109 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 83 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3256 r_free = 0.3256 target = 0.094526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.073456 restraints weight = 8479.784| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.43 r_work: 0.2754 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 5342 Z= 0.211 Angle : 0.571 6.246 7254 Z= 0.305 Chirality : 0.045 0.148 773 Planarity : 0.004 0.049 958 Dihedral : 4.291 32.804 730 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.51 % Allowed : 11.95 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.33), residues: 660 helix: 0.06 (1.90), residues: 7 sheet: 0.17 (0.27), residues: 354 loop : 0.40 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 662 TYR 0.024 0.001 TYR A 590 PHE 0.022 0.002 PHE A 418 TRP 0.009 0.001 TRP B 68 HIS 0.002 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 5342) covalent geometry : angle 0.57149 ( 7254) hydrogen bonds : bond 0.02870 ( 280) hydrogen bonds : angle 5.51982 ( 774) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9313 (ptpt) cc_final: 0.8946 (ptpp) REVERT: A 58 ASP cc_start: 0.9038 (m-30) cc_final: 0.8722 (m-30) REVERT: A 131 GLU cc_start: 0.8789 (tp30) cc_final: 0.8475 (tp30) REVERT: A 140 MET cc_start: 0.7767 (mmm) cc_final: 0.7421 (mmm) REVERT: A 287 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.7827 (m-10) REVERT: A 345 ASP cc_start: 0.8623 (t0) cc_final: 0.8339 (t0) REVERT: A 367 GLU cc_start: 0.8915 (tt0) cc_final: 0.8472 (mt-10) REVERT: A 384 MET cc_start: 0.8912 (tmm) cc_final: 0.8380 (tmm) REVERT: A 450 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7849 (mt-10) REVERT: A 480 ASN cc_start: 0.8768 (t0) cc_final: 0.8536 (t0) outliers start: 20 outliers final: 11 residues processed: 113 average time/residue: 0.3726 time to fit residues: 44.2570 Evaluate side-chains 113 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 83 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 4 optimal weight: 0.0970 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- 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 = 0.3253 r_free = 0.3253 target = 0.094237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.073316 restraints weight = 8378.343| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.41 r_work: 0.2758 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5342 Z= 0.197 Angle : 0.578 6.597 7254 Z= 0.310 Chirality : 0.045 0.156 773 Planarity : 0.004 0.049 958 Dihedral : 4.303 34.810 730 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.64 % Allowed : 13.18 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.33), residues: 660 helix: -0.18 (1.74), residues: 7 sheet: 0.17 (0.27), residues: 354 loop : 0.42 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 662 TYR 0.019 0.001 TYR A 461 PHE 0.030 0.002 PHE A 418 TRP 0.010 0.001 TRP B 68 HIS 0.002 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 5342) covalent geometry : angle 0.57836 ( 7254) hydrogen bonds : bond 0.02761 ( 280) hydrogen bonds : angle 5.41603 ( 774) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9320 (ptpt) cc_final: 0.8961 (ptpp) REVERT: A 131 GLU cc_start: 0.8778 (tp30) cc_final: 0.8463 (tp30) REVERT: A 140 MET cc_start: 0.7734 (mmm) cc_final: 0.7315 (mmm) REVERT: A 163 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8396 (mmtt) REVERT: A 345 ASP cc_start: 0.8600 (t0) cc_final: 0.8297 (t0) REVERT: A 384 MET cc_start: 0.8919 (tmm) cc_final: 0.8374 (tmm) REVERT: A 450 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7841 (mt-10) REVERT: A 480 ASN cc_start: 0.8766 (t0) cc_final: 0.8528 (t0) REVERT: A 542 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7828 (mm-30) outliers start: 15 outliers final: 12 residues processed: 112 average time/residue: 0.3297 time to fit residues: 38.8572 Evaluate side-chains 119 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 83 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 65 optimal weight: 0.0170 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- 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 = 0.3265 r_free = 0.3265 target = 0.094986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.074066 restraints weight = 8336.959| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.41 r_work: 0.2777 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5342 Z= 0.162 Angle : 0.576 6.450 7254 Z= 0.309 Chirality : 0.045 0.167 773 Planarity : 0.004 0.050 958 Dihedral : 4.265 36.132 730 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.99 % Allowed : 13.88 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.33), residues: 660 helix: -0.72 (1.65), residues: 7 sheet: 0.20 (0.27), residues: 353 loop : 0.45 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 662 TYR 0.026 0.001 TYR A 590 PHE 0.030 0.002 PHE A 418 TRP 0.011 0.001 TRP B 68 HIS 0.002 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 5342) covalent geometry : angle 0.57632 ( 7254) hydrogen bonds : bond 0.02638 ( 280) hydrogen bonds : angle 5.31388 ( 774) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9325 (ptpt) cc_final: 0.9001 (ptpp) REVERT: A 131 GLU cc_start: 0.8741 (tp30) cc_final: 0.8399 (tp30) REVERT: A 163 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8396 (mmtt) REVERT: A 345 ASP cc_start: 0.8640 (t0) cc_final: 0.8354 (t0) REVERT: A 367 GLU cc_start: 0.8904 (tt0) cc_final: 0.8497 (mt-10) REVERT: A 384 MET cc_start: 0.8881 (tmm) cc_final: 0.8363 (tmm) REVERT: A 450 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7834 (mt-10) REVERT: A 480 ASN cc_start: 0.8670 (t0) cc_final: 0.8403 (t0) outliers start: 17 outliers final: 11 residues processed: 117 average time/residue: 0.3577 time to fit residues: 44.0468 Evaluate side-chains 116 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 517 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.0060 chunk 57 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.095472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.074544 restraints weight = 8317.253| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.41 r_work: 0.2783 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5342 Z= 0.160 Angle : 0.616 7.948 7254 Z= 0.322 Chirality : 0.045 0.168 773 Planarity : 0.004 0.051 958 Dihedral : 4.253 36.619 730 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.99 % Allowed : 15.82 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.33), residues: 660 helix: -0.60 (1.67), residues: 7 sheet: 0.20 (0.27), residues: 353 loop : 0.51 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 662 TYR 0.018 0.001 TYR A 294 PHE 0.028 0.002 PHE A 418 TRP 0.011 0.001 TRP B 68 HIS 0.002 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 5342) covalent geometry : angle 0.61615 ( 7254) hydrogen bonds : bond 0.02604 ( 280) hydrogen bonds : angle 5.23167 ( 774) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9314 (ptpt) cc_final: 0.8986 (ptpp) REVERT: A 131 GLU cc_start: 0.8701 (tp30) cc_final: 0.8336 (tp30) REVERT: A 163 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8437 (mmtt) REVERT: A 345 ASP cc_start: 0.8623 (t0) cc_final: 0.8358 (t0) REVERT: A 367 GLU cc_start: 0.8904 (tt0) cc_final: 0.8477 (mt-10) REVERT: A 384 MET cc_start: 0.8889 (tmm) cc_final: 0.8370 (tmm) REVERT: A 450 GLU cc_start: 0.8426 (mt-10) cc_final: 0.7845 (mt-10) REVERT: A 624 THR cc_start: 0.8993 (p) cc_final: 0.8793 (p) outliers start: 17 outliers final: 12 residues processed: 117 average time/residue: 0.3525 time to fit residues: 43.5227 Evaluate side-chains 119 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 83 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 31 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 0.0270 chunk 63 optimal weight: 0.0870 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.5016 ------------------------------------------------------------------------------- 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 = 0.3311 r_free = 0.3311 target = 0.097461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.076516 restraints weight = 8284.168| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.41 r_work: 0.2818 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5342 Z= 0.118 Angle : 0.598 7.656 7254 Z= 0.316 Chirality : 0.045 0.249 773 Planarity : 0.004 0.052 958 Dihedral : 4.133 37.195 730 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.11 % Allowed : 16.70 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.34), residues: 660 helix: -0.21 (1.75), residues: 7 sheet: 0.35 (0.27), residues: 357 loop : 0.57 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 662 TYR 0.019 0.001 TYR A 590 PHE 0.021 0.001 PHE A 418 TRP 0.013 0.001 TRP B 68 HIS 0.002 0.000 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 5342) covalent geometry : angle 0.59828 ( 7254) hydrogen bonds : bond 0.02455 ( 280) hydrogen bonds : angle 5.10995 ( 774) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9306 (ptpt) cc_final: 0.8946 (ptpp) REVERT: A 58 ASP cc_start: 0.8946 (m-30) cc_final: 0.8703 (m-30) REVERT: A 131 GLU cc_start: 0.8603 (tp30) cc_final: 0.8278 (tp30) REVERT: A 163 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8458 (mmtt) REVERT: A 345 ASP cc_start: 0.8644 (t0) cc_final: 0.8380 (t0) REVERT: A 367 GLU cc_start: 0.8879 (tt0) cc_final: 0.8480 (mt-10) REVERT: A 383 ARG cc_start: 0.8804 (ttm-80) cc_final: 0.8351 (ttm-80) REVERT: A 384 MET cc_start: 0.8878 (tmm) cc_final: 0.8387 (tmm) REVERT: A 450 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7624 (mt-10) outliers start: 12 outliers final: 10 residues processed: 119 average time/residue: 0.3316 time to fit residues: 41.5568 Evaluate side-chains 124 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 83 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.0170 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.097989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.076793 restraints weight = 8361.007| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.47 r_work: 0.2814 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5342 Z= 0.130 Angle : 0.621 7.904 7254 Z= 0.325 Chirality : 0.046 0.328 773 Planarity : 0.004 0.052 958 Dihedral : 4.139 37.002 730 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.93 % Allowed : 17.57 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.33), residues: 660 helix: -0.08 (1.80), residues: 7 sheet: 0.40 (0.27), residues: 357 loop : 0.59 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 662 TYR 0.020 0.001 TYR A 590 PHE 0.023 0.001 PHE A 418 TRP 0.012 0.001 TRP B 68 HIS 0.004 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5342) covalent geometry : angle 0.62121 ( 7254) hydrogen bonds : bond 0.02464 ( 280) hydrogen bonds : angle 5.04424 ( 774) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9300 (ptpt) cc_final: 0.8957 (ptpp) REVERT: A 58 ASP cc_start: 0.8975 (m-30) cc_final: 0.8753 (m-30) REVERT: A 131 GLU cc_start: 0.8600 (tp30) cc_final: 0.8277 (tp30) REVERT: A 163 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8412 (mmtt) REVERT: A 345 ASP cc_start: 0.8634 (t0) cc_final: 0.8371 (t0) REVERT: A 357 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.8961 (p) REVERT: A 367 GLU cc_start: 0.8896 (tt0) cc_final: 0.8471 (mt-10) REVERT: A 383 ARG cc_start: 0.8826 (ttm-80) cc_final: 0.8365 (ttm-80) REVERT: A 384 MET cc_start: 0.8920 (tmm) cc_final: 0.8438 (tmm) REVERT: A 450 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7582 (mt-10) outliers start: 11 outliers final: 8 residues processed: 119 average time/residue: 0.3412 time to fit residues: 42.6957 Evaluate side-chains 118 residues out of total 569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 83 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 63 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.093608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.072760 restraints weight = 8449.412| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.42 r_work: 0.2746 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 5342 Z= 0.258 Angle : 0.650 7.341 7254 Z= 0.344 Chirality : 0.048 0.408 773 Planarity : 0.004 0.051 958 Dihedral : 4.486 36.265 730 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.93 % Allowed : 17.57 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.33), residues: 660 helix: -0.50 (1.78), residues: 7 sheet: 0.25 (0.27), residues: 353 loop : 0.52 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 662 TYR 0.029 0.002 TYR A 399 PHE 0.025 0.002 PHE A 418 TRP 0.007 0.001 TRP B 68 HIS 0.006 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 5342) covalent geometry : angle 0.65026 ( 7254) hydrogen bonds : bond 0.02852 ( 280) hydrogen bonds : angle 5.28994 ( 774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1332.21 seconds wall clock time: 23 minutes 30.66 seconds (1410.66 seconds total)