Starting phenix.real_space_refine on Tue Feb 3 13:17:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gs9_34226/02_2026/8gs9_34226.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gs9_34226/02_2026/8gs9_34226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gs9_34226/02_2026/8gs9_34226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gs9_34226/02_2026/8gs9_34226.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gs9_34226/02_2026/8gs9_34226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gs9_34226/02_2026/8gs9_34226.map" } resolution = 2.66 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= -0.003 sd= 0.041 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 12 5.16 5 C 1984 2.51 5 N 531 2.21 5 O 589 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: 3116 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1462 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 171} Chain: "H" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 881 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "K" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 773 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 96} Time building chain proxies: 0.61, per 1000 atoms: 0.20 Number of scatterers: 3116 At special positions: 0 Unit cell: (67.545, 58.995, 94.905, 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 12 16.00 O 589 8.00 N 531 7.00 C 1984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 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: 0.15 Conformation dependent library (CDL) restraints added in 75.9 milliseconds 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 724 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 12.1% alpha, 38.6% 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 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 4.143A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 371' Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.515A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.017A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.954A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.687A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR H 33 " --> pdb=" O SER H 98 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE H 105 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.687A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR H 33 " --> pdb=" O SER H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.535A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 11 through 12 130 hydrogen bonds defined for protein. 300 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: 0.31 Time building geometry restraints manager: 0.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1009 1.34 - 1.46: 845 1.46 - 1.58: 1326 1.58 - 1.70: 0 1.70 - 1.82: 14 Bond restraints: 3194 Sorted by residual: bond pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 8.98e+00 bond pdb=" N ASN A 360 " pdb=" CA ASN A 360 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.39e+00 bond pdb=" N CYS A 361 " pdb=" CA CYS A 361 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.26e-02 6.30e+03 6.87e+00 bond pdb=" N SER A 359 " pdb=" CA SER A 359 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.81e+00 bond pdb=" N ALA A 363 " pdb=" CA ALA A 363 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.24e-02 6.50e+03 4.10e+00 ... (remaining 3189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 4007 0.92 - 1.84: 260 1.84 - 2.76: 45 2.76 - 3.68: 18 3.68 - 4.60: 5 Bond angle restraints: 4335 Sorted by residual: angle pdb=" CA VAL A 362 " pdb=" C VAL A 362 " pdb=" O VAL A 362 " ideal model delta sigma weight residual 121.36 117.47 3.89 1.10e+00 8.26e-01 1.25e+01 angle pdb=" N ALA K 51 " pdb=" CA ALA K 51 " pdb=" CB ALA K 51 " ideal model delta sigma weight residual 114.17 110.62 3.55 1.14e+00 7.69e-01 9.68e+00 angle pdb=" CA SER A 359 " pdb=" C SER A 359 " pdb=" O SER A 359 " ideal model delta sigma weight residual 120.51 116.68 3.83 1.43e+00 4.89e-01 7.17e+00 angle pdb=" C ASN A 450 " pdb=" N TYR A 451 " pdb=" CA TYR A 451 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.80e+00 angle pdb=" CA ALA A 363 " pdb=" C ALA A 363 " pdb=" O ALA A 363 " ideal model delta sigma weight residual 120.32 117.78 2.54 1.11e+00 8.12e-01 5.25e+00 ... (remaining 4330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.49: 1681 13.49 - 26.98: 138 26.98 - 40.48: 38 40.48 - 53.97: 9 53.97 - 67.46: 6 Dihedral angle restraints: 1872 sinusoidal: 729 harmonic: 1143 Sorted by residual: dihedral pdb=" CA PHE A 490 " pdb=" C PHE A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta harmonic sigma weight residual -180.00 -162.67 -17.33 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA GLN H 13 " pdb=" C GLN H 13 " pdb=" N PRO H 14 " pdb=" CA PRO H 14 " ideal model delta harmonic sigma weight residual 180.00 -163.10 -16.90 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA LYS A 478 " pdb=" C LYS A 478 " pdb=" N PRO A 479 " pdb=" CA PRO A 479 " ideal model delta harmonic sigma weight residual -180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 1869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 300 0.035 - 0.070: 109 0.070 - 0.105: 30 0.105 - 0.140: 20 0.140 - 0.175: 2 Chirality restraints: 461 Sorted by residual: chirality pdb=" CA VAL A 362 " pdb=" N VAL A 362 " pdb=" C VAL A 362 " pdb=" CB VAL A 362 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE K 21 " pdb=" N ILE K 21 " pdb=" C ILE K 21 " pdb=" CB ILE K 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 458 not shown) Planarity restraints: 564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 358 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C ILE A 358 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE A 358 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A 359 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 478 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO A 479 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 32 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C ASN H 32 " 0.020 2.00e-02 2.50e+03 pdb=" O ASN H 32 " -0.008 2.00e-02 2.50e+03 pdb=" N TYR H 33 " -0.007 2.00e-02 2.50e+03 ... (remaining 561 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 940 2.82 - 3.34: 2496 3.34 - 3.86: 4712 3.86 - 4.38: 5702 4.38 - 4.90: 10174 Nonbonded interactions: 24024 Sorted by model distance: nonbonded pdb=" NE2 GLN K 89 " pdb=" O GLU K 91 " model vdw 2.297 3.120 nonbonded pdb=" N GLU H 6 " pdb=" OE1 GLU H 6 " model vdw 2.347 3.120 nonbonded pdb=" OH TYR A 473 " pdb=" O ARG H 31 " model vdw 2.378 3.040 nonbonded pdb=" NE ARG H 38 " pdb=" OE1 GLU H 46 " model vdw 2.428 3.120 nonbonded pdb=" N GLY H 15 " pdb=" O LEU H 85 " model vdw 2.437 3.120 ... (remaining 24019 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: 5.430 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.340 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:8.180 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 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 0.037 3198 Z= 0.186 Angle : 0.549 4.601 4343 Z= 0.320 Chirality : 0.045 0.175 461 Planarity : 0.003 0.034 564 Dihedral : 11.977 67.459 1136 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.64 % Favored : 93.85 % Rotamer: Outliers : 0.60 % Allowed : 5.37 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.51 (0.40), residues: 390 helix: -3.37 (0.74), residues: 27 sheet: 0.37 (0.44), residues: 124 loop : -0.30 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 18 TYR 0.007 0.001 TYR H 52 PHE 0.008 0.001 PHE A 456 TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3194) covalent geometry : angle 0.54727 ( 4335) SS BOND : bond 0.00535 ( 4) SS BOND : angle 1.07145 ( 8) hydrogen bonds : bond 0.14007 ( 114) hydrogen bonds : angle 7.64017 ( 300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.129 Fit side-chains REVERT: A 456 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6797 (p90) REVERT: A 516 GLU cc_start: 0.6176 (mt-10) cc_final: 0.5760 (mt-10) REVERT: K 83 PHE cc_start: 0.5818 (m-80) cc_final: 0.5538 (m-80) outliers start: 2 outliers final: 0 residues processed: 90 average time/residue: 0.4673 time to fit residues: 43.2447 Evaluate side-chains 52 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.0170 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.0020 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.4628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.148951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.137186 restraints weight = 6970.918| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.25 r_work: 0.4029 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3198 Z= 0.111 Angle : 0.547 7.336 4343 Z= 0.299 Chirality : 0.045 0.160 461 Planarity : 0.004 0.025 564 Dihedral : 4.615 31.926 444 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.33 % Favored : 96.41 % Rotamer: Outliers : 4.78 % Allowed : 15.22 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 (0.41), residues: 390 helix: -3.34 (0.73), residues: 26 sheet: 0.60 (0.48), residues: 113 loop : -0.27 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.009 0.001 TYR H 52 PHE 0.008 0.001 PHE A 456 TRP 0.008 0.001 TRP A 436 HIS 0.001 0.000 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 3194) covalent geometry : angle 0.53737 ( 4335) SS BOND : bond 0.00321 ( 4) SS BOND : angle 2.42716 ( 8) hydrogen bonds : bond 0.03135 ( 114) hydrogen bonds : angle 5.72759 ( 300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: A 456 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6681 (p90) REVERT: K 18 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.5919 (ttp-170) REVERT: K 83 PHE cc_start: 0.6165 (m-80) cc_final: 0.5868 (m-80) outliers start: 16 outliers final: 7 residues processed: 64 average time/residue: 0.4335 time to fit residues: 28.6036 Evaluate side-chains 58 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.0570 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.148468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.136132 restraints weight = 6899.191| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.27 r_work: 0.4017 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 3198 Z= 0.129 Angle : 0.591 8.208 4343 Z= 0.312 Chirality : 0.046 0.250 461 Planarity : 0.004 0.027 564 Dihedral : 4.663 33.092 444 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.85 % Favored : 95.90 % Rotamer: Outliers : 4.18 % Allowed : 17.01 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.17 (0.40), residues: 390 helix: -3.42 (0.87), residues: 20 sheet: 0.69 (0.48), residues: 114 loop : -0.16 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 24 TYR 0.010 0.001 TYR H 52 PHE 0.010 0.001 PHE H 105 TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3194) covalent geometry : angle 0.57456 ( 4335) SS BOND : bond 0.01046 ( 4) SS BOND : angle 3.24998 ( 8) hydrogen bonds : bond 0.03243 ( 114) hydrogen bonds : angle 5.36174 ( 300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.186 Fit side-chains REVERT: A 456 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6699 (p90) REVERT: H 20 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7250 (mm) REVERT: K 18 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.5850 (ttp-170) REVERT: K 83 PHE cc_start: 0.6262 (m-80) cc_final: 0.5960 (m-80) outliers start: 14 outliers final: 8 residues processed: 61 average time/residue: 0.3974 time to fit residues: 25.1177 Evaluate side-chains 57 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.0470 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.0030 chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.2094 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.147139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.134733 restraints weight = 6862.657| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.28 r_work: 0.4000 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 3198 Z= 0.157 Angle : 0.649 13.827 4343 Z= 0.336 Chirality : 0.047 0.269 461 Planarity : 0.004 0.027 564 Dihedral : 5.024 36.268 444 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.59 % Favored : 96.15 % Rotamer: Outliers : 4.78 % Allowed : 17.91 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.47 (0.41), residues: 390 helix: -3.33 (0.81), residues: 26 sheet: 0.36 (0.46), residues: 133 loop : -0.29 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 24 TYR 0.014 0.001 TYR H 52 PHE 0.011 0.001 PHE H 105 TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 3194) covalent geometry : angle 0.63458 ( 4335) SS BOND : bond 0.01007 ( 4) SS BOND : angle 3.21607 ( 8) hydrogen bonds : bond 0.03631 ( 114) hydrogen bonds : angle 5.47835 ( 300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.158 Fit side-chains REVERT: A 456 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.7085 (p90) REVERT: H 20 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7274 (mm) REVERT: K 18 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.5931 (ttp-170) REVERT: K 81 GLU cc_start: 0.6363 (pm20) cc_final: 0.6154 (pm20) outliers start: 16 outliers final: 8 residues processed: 61 average time/residue: 0.4703 time to fit residues: 29.6622 Evaluate side-chains 57 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 0.7980 chunk 2 optimal weight: 0.0470 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** 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 = 0.4240 r_free = 0.4240 target = 0.147236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.135258 restraints weight = 6856.516| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.22 r_work: 0.4013 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 3198 Z= 0.128 Angle : 0.607 10.090 4343 Z= 0.315 Chirality : 0.045 0.222 461 Planarity : 0.003 0.024 564 Dihedral : 4.772 35.688 444 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.18 % Allowed : 20.00 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 (0.41), residues: 390 helix: -3.34 (0.82), residues: 26 sheet: 0.76 (0.49), residues: 119 loop : -0.39 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.009 0.001 TYR H 52 PHE 0.008 0.001 PHE A 456 TRP 0.008 0.001 TRP H 47 HIS 0.000 0.000 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3194) covalent geometry : angle 0.58796 ( 4335) SS BOND : bond 0.01016 ( 4) SS BOND : angle 3.58171 ( 8) hydrogen bonds : bond 0.03201 ( 114) hydrogen bonds : angle 5.24177 ( 300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.125 Fit side-chains REVERT: A 456 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.7005 (p90) REVERT: H 20 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7290 (mm) REVERT: K 18 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.5817 (ttp-170) outliers start: 14 outliers final: 6 residues processed: 59 average time/residue: 0.5339 time to fit residues: 32.4331 Evaluate side-chains 54 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.146018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.133931 restraints weight = 6946.253| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 2.20 r_work: 0.3994 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 3198 Z= 0.215 Angle : 0.726 12.123 4343 Z= 0.374 Chirality : 0.047 0.203 461 Planarity : 0.004 0.030 564 Dihedral : 5.464 45.242 444 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.37 % Allowed : 21.49 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.74 (0.41), residues: 390 helix: -3.40 (0.80), residues: 26 sheet: 0.32 (0.47), residues: 133 loop : -0.59 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 38 TYR 0.017 0.002 TYR H 52 PHE 0.012 0.001 PHE A 456 TRP 0.009 0.002 TRP H 47 HIS 0.001 0.000 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 3194) covalent geometry : angle 0.70435 ( 4335) SS BOND : bond 0.01450 ( 4) SS BOND : angle 4.13691 ( 8) hydrogen bonds : bond 0.04012 ( 114) hydrogen bonds : angle 5.85984 ( 300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.077 Fit side-chains REVERT: A 456 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.6824 (p90) REVERT: H 20 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7301 (mm) REVERT: K 18 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.5958 (ttp-170) outliers start: 18 outliers final: 9 residues processed: 61 average time/residue: 0.3613 time to fit residues: 22.7605 Evaluate side-chains 56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.147245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.134911 restraints weight = 6943.604| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 2.28 r_work: 0.4008 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3198 Z= 0.119 Angle : 0.622 13.340 4343 Z= 0.321 Chirality : 0.045 0.219 461 Planarity : 0.003 0.027 564 Dihedral : 4.993 44.013 444 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.37 % Allowed : 22.09 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.69 (0.41), residues: 390 helix: -3.37 (0.81), residues: 26 sheet: 0.42 (0.47), residues: 133 loop : -0.60 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.008 0.001 TYR H 52 PHE 0.010 0.001 PHE A 456 TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3194) covalent geometry : angle 0.61563 ( 4335) SS BOND : bond 0.01023 ( 4) SS BOND : angle 2.15381 ( 8) hydrogen bonds : bond 0.03218 ( 114) hydrogen bonds : angle 5.45159 ( 300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.127 Fit side-chains REVERT: A 389 ASP cc_start: 0.7653 (m-30) cc_final: 0.7395 (m-30) REVERT: A 456 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.6965 (p90) REVERT: H 20 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7324 (mm) REVERT: K 18 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.5817 (ttp-170) REVERT: K 38 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7752 (tt0) outliers start: 18 outliers final: 6 residues processed: 61 average time/residue: 0.4865 time to fit residues: 30.6843 Evaluate side-chains 57 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.147272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.134821 restraints weight = 7038.007| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.32 r_work: 0.4001 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3198 Z= 0.147 Angle : 0.653 12.492 4343 Z= 0.338 Chirality : 0.046 0.220 461 Planarity : 0.004 0.027 564 Dihedral : 5.133 45.485 444 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.78 % Allowed : 22.99 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.78 (0.41), residues: 390 helix: -3.39 (0.71), residues: 29 sheet: 0.43 (0.48), residues: 133 loop : -0.68 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.010 0.001 TYR H 52 PHE 0.011 0.001 PHE A 456 TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 3194) covalent geometry : angle 0.64745 ( 4335) SS BOND : bond 0.01040 ( 4) SS BOND : angle 2.09948 ( 8) hydrogen bonds : bond 0.03528 ( 114) hydrogen bonds : angle 5.44938 ( 300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.122 Fit side-chains REVERT: A 456 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7013 (p90) REVERT: H 20 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7325 (mm) REVERT: K 18 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.5830 (ttp-170) REVERT: K 38 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7726 (tt0) outliers start: 16 outliers final: 9 residues processed: 56 average time/residue: 0.5159 time to fit residues: 29.7904 Evaluate side-chains 57 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.147774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.135289 restraints weight = 6909.989| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.32 r_work: 0.4008 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3198 Z= 0.128 Angle : 0.642 12.177 4343 Z= 0.334 Chirality : 0.045 0.214 461 Planarity : 0.003 0.026 564 Dihedral : 4.974 44.682 444 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.18 % Allowed : 24.18 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.73 (0.41), residues: 390 helix: -3.39 (0.70), residues: 29 sheet: 0.47 (0.48), residues: 133 loop : -0.64 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.008 0.001 TYR H 52 PHE 0.010 0.001 PHE A 456 TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3194) covalent geometry : angle 0.63736 ( 4335) SS BOND : bond 0.01086 ( 4) SS BOND : angle 1.92740 ( 8) hydrogen bonds : bond 0.03259 ( 114) hydrogen bonds : angle 5.30832 ( 300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 456 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.6997 (p90) REVERT: H 20 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7324 (mm) REVERT: K 18 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.5748 (ttp-170) REVERT: K 38 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7746 (tt0) outliers start: 14 outliers final: 9 residues processed: 54 average time/residue: 0.5139 time to fit residues: 28.6785 Evaluate side-chains 57 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.148267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.135960 restraints weight = 6807.723| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.29 r_work: 0.4019 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3198 Z= 0.121 Angle : 0.627 11.844 4343 Z= 0.326 Chirality : 0.045 0.206 461 Planarity : 0.003 0.025 564 Dihedral : 4.784 42.142 444 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.18 % Allowed : 23.88 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.67 (0.41), residues: 390 helix: -3.36 (0.71), residues: 29 sheet: 0.78 (0.49), residues: 123 loop : -0.73 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.008 0.001 TYR K 49 PHE 0.009 0.001 PHE A 456 TRP 0.008 0.001 TRP H 47 HIS 0.001 0.000 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3194) covalent geometry : angle 0.62277 ( 4335) SS BOND : bond 0.00968 ( 4) SS BOND : angle 1.84065 ( 8) hydrogen bonds : bond 0.03147 ( 114) hydrogen bonds : angle 5.14677 ( 300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.7044 (p90) REVERT: H 20 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7290 (mm) REVERT: K 18 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.5755 (ttp-170) REVERT: K 38 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7738 (tt0) outliers start: 14 outliers final: 9 residues processed: 53 average time/residue: 0.4349 time to fit residues: 23.7342 Evaluate side-chains 58 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.0020 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** 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 = 0.4250 r_free = 0.4250 target = 0.147863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.135501 restraints weight = 6856.946| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.27 r_work: 0.4015 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3198 Z= 0.129 Angle : 0.635 11.735 4343 Z= 0.329 Chirality : 0.045 0.207 461 Planarity : 0.003 0.024 564 Dihedral : 4.838 42.108 444 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.48 % Allowed : 24.78 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.69 (0.41), residues: 390 helix: -3.36 (0.71), residues: 29 sheet: 0.76 (0.50), residues: 123 loop : -0.74 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.008 0.001 TYR H 52 PHE 0.009 0.001 PHE A 456 TRP 0.008 0.001 TRP H 47 HIS 0.001 0.000 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3194) covalent geometry : angle 0.62983 ( 4335) SS BOND : bond 0.01002 ( 4) SS BOND : angle 1.90713 ( 8) hydrogen bonds : bond 0.03256 ( 114) hydrogen bonds : angle 5.18866 ( 300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1339.21 seconds wall clock time: 23 minutes 32.27 seconds (1412.27 seconds total)