Starting phenix.real_space_refine on Wed Jul 23 10:39:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gs9_34226/07_2025/8gs9_34226.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gs9_34226/07_2025/8gs9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gs9_34226/07_2025/8gs9_34226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gs9_34226/07_2025/8gs9_34226.map" model { file = "/net/cci-nas-00/data/ceres_data/8gs9_34226/07_2025/8gs9_34226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gs9_34226/07_2025/8gs9_34226.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.26, per 1000 atoms: 1.69 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: 0.90 Conformation dependent library (CDL) restraints added in 549.1 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: 0.45 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: 0.74 Time building geometry restraints manager: 1.08 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: 8.120 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.320 Find NCS groups from input model: 0.020 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:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS A 505 PHE 0.008 0.001 PHE A 456 TYR 0.007 0.001 TYR H 52 ARG 0.002 0.000 ARG K 18 Details of bonding type rmsd hydrogen bonds : bond 0.14007 ( 114) hydrogen bonds : angle 7.64017 ( 300) SS BOND : bond 0.00535 ( 4) SS BOND : angle 1.07145 ( 8) covalent geometry : bond 0.00330 ( 3194) covalent geometry : angle 0.54727 ( 4335) *********************** 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 : 0.341 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: 0.9751 time to fit residues: 90.5366 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 : 0.392 ------------------------------------------------------------------------------- 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 32 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.0570 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN H 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.148671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.136953 restraints weight = 6897.891| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.23 r_work: 0.4026 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3198 Z= 0.117 Angle : 0.551 7.273 4343 Z= 0.300 Chirality : 0.045 0.157 461 Planarity : 0.004 0.025 564 Dihedral : 4.637 32.022 444 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.24 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.41), residues: 390 helix: -3.33 (0.73), residues: 26 sheet: 0.59 (0.48), residues: 113 loop : -0.28 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.001 0.000 HIS K 90 PHE 0.008 0.001 PHE A 456 TYR 0.009 0.001 TYR H 52 ARG 0.005 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03178 ( 114) hydrogen bonds : angle 5.71574 ( 300) SS BOND : bond 0.00703 ( 4) SS BOND : angle 2.41146 ( 8) covalent geometry : bond 0.00269 ( 3194) covalent geometry : angle 0.54122 ( 4335) *********************** 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 : 0.381 Fit side-chains REVERT: A 456 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.6698 (p90) REVERT: K 18 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.5916 (ttp-170) REVERT: K 83 PHE cc_start: 0.6169 (m-80) cc_final: 0.5875 (m-80) outliers start: 16 outliers final: 7 residues processed: 64 average time/residue: 0.9578 time to fit residues: 63.4527 Evaluate side-chains 57 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 20 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.146286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.134163 restraints weight = 6856.946| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.19 r_work: 0.3990 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 3198 Z= 0.254 Angle : 0.759 8.946 4343 Z= 0.397 Chirality : 0.050 0.276 461 Planarity : 0.005 0.036 564 Dihedral : 5.691 47.226 444 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.64 % Favored : 94.10 % Rotamer: Outliers : 5.37 % Allowed : 17.01 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.41), residues: 390 helix: -3.48 (0.72), residues: 26 sheet: -0.00 (0.45), residues: 140 loop : -0.47 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 353 HIS 0.001 0.000 HIS K 90 PHE 0.016 0.002 PHE H 105 TYR 0.022 0.002 TYR H 52 ARG 0.006 0.001 ARG K 24 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 114) hydrogen bonds : angle 6.05296 ( 300) SS BOND : bond 0.01322 ( 4) SS BOND : angle 3.72497 ( 8) covalent geometry : bond 0.00615 ( 3194) covalent geometry : angle 0.74229 ( 4335) *********************** 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 71 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.379 Fit side-chains REVERT: A 456 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.6754 (p90) REVERT: H 20 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7238 (mm) REVERT: K 18 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.5877 (ttp-170) outliers start: 18 outliers final: 8 residues processed: 64 average time/residue: 1.0885 time to fit residues: 71.8765 Evaluate side-chains 56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.4220 r_free = 0.4220 target = 0.145936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.133885 restraints weight = 6911.966| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.18 r_work: 0.3991 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 3198 Z= 0.191 Angle : 0.687 13.503 4343 Z= 0.359 Chirality : 0.047 0.270 461 Planarity : 0.004 0.032 564 Dihedral : 5.603 52.464 444 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 6.27 % Allowed : 18.81 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.41), residues: 390 helix: -3.48 (0.76), residues: 26 sheet: 0.14 (0.46), residues: 138 loop : -0.55 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 436 HIS 0.001 0.000 HIS K 90 PHE 0.014 0.001 PHE A 456 TYR 0.018 0.002 TYR H 52 ARG 0.007 0.001 ARG K 24 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 114) hydrogen bonds : angle 5.77270 ( 300) SS BOND : bond 0.01372 ( 4) SS BOND : angle 3.24317 ( 8) covalent geometry : bond 0.00466 ( 3194) covalent geometry : angle 0.67375 ( 4335) *********************** 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 72 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.377 Fit side-chains REVERT: H 20 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7298 (mm) REVERT: K 18 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.5890 (ttp-170) REVERT: K 38 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7732 (tt0) outliers start: 21 outliers final: 10 residues processed: 64 average time/residue: 1.0588 time to fit residues: 70.0391 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 : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 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 H residue 20 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 105 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4228 r_free = 0.4228 target = 0.146290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.134275 restraints weight = 6913.059| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.21 r_work: 0.4001 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 3198 Z= 0.133 Angle : 0.623 9.804 4343 Z= 0.323 Chirality : 0.045 0.228 461 Planarity : 0.004 0.028 564 Dihedral : 5.189 52.866 444 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.78 % Allowed : 21.79 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.42), residues: 390 helix: -3.38 (0.81), residues: 26 sheet: 0.34 (0.47), residues: 133 loop : -0.51 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.001 0.000 HIS K 90 PHE 0.013 0.001 PHE A 456 TYR 0.013 0.001 TYR H 33 ARG 0.004 0.000 ARG K 42 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 114) hydrogen bonds : angle 5.38617 ( 300) SS BOND : bond 0.01016 ( 4) SS BOND : angle 3.49455 ( 8) covalent geometry : bond 0.00334 ( 3194) covalent geometry : angle 0.60514 ( 4335) *********************** 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 68 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.469 Fit side-chains REVERT: H 20 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7337 (mm) REVERT: K 18 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.5831 (ttp-170) outliers start: 16 outliers final: 9 residues processed: 62 average time/residue: 1.0310 time to fit residues: 66.2759 Evaluate side-chains 56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 105 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 29 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 0.0050 chunk 14 optimal weight: 0.0070 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6614 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.147213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.135001 restraints weight = 7048.562| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 2.24 r_work: 0.4010 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 3198 Z= 0.130 Angle : 0.632 12.187 4343 Z= 0.326 Chirality : 0.044 0.203 461 Planarity : 0.004 0.027 564 Dihedral : 5.097 52.374 444 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.78 % Allowed : 22.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.41), residues: 390 helix: -3.30 (0.74), residues: 29 sheet: 0.40 (0.48), residues: 133 loop : -0.51 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.001 0.000 HIS K 90 PHE 0.012 0.001 PHE A 456 TYR 0.012 0.001 TYR H 33 ARG 0.004 0.000 ARG K 42 Details of bonding type rmsd hydrogen bonds : bond 0.03117 ( 114) hydrogen bonds : angle 5.28623 ( 300) SS BOND : bond 0.01340 ( 4) SS BOND : angle 3.87608 ( 8) covalent geometry : bond 0.00329 ( 3194) covalent geometry : angle 0.61037 ( 4335) *********************** 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 66 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.342 Fit side-chains REVERT: H 20 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7324 (mm) REVERT: K 18 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.5751 (ttp-170) REVERT: K 38 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7788 (tt0) outliers start: 16 outliers final: 10 residues processed: 61 average time/residue: 0.9761 time to fit residues: 61.6331 Evaluate side-chains 60 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 361 CYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 37 optimal weight: 0.0010 chunk 21 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.146425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.134106 restraints weight = 6779.177| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.26 r_work: 0.3999 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3198 Z= 0.150 Angle : 0.653 13.146 4343 Z= 0.337 Chirality : 0.045 0.232 461 Planarity : 0.004 0.028 564 Dihedral : 5.327 55.532 444 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.37 % Allowed : 22.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.41), residues: 390 helix: -3.35 (0.72), residues: 29 sheet: 0.39 (0.48), residues: 133 loop : -0.68 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.001 0.000 HIS K 90 PHE 0.013 0.001 PHE A 456 TYR 0.014 0.001 TYR H 33 ARG 0.005 0.000 ARG K 42 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 114) hydrogen bonds : angle 5.38634 ( 300) SS BOND : bond 0.01073 ( 4) SS BOND : angle 2.25655 ( 8) covalent geometry : bond 0.00362 ( 3194) covalent geometry : angle 0.64666 ( 4335) *********************** 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 66 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.436 Fit side-chains REVERT: A 389 ASP cc_start: 0.7676 (m-30) cc_final: 0.7411 (m-30) REVERT: H 20 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7300 (mm) REVERT: K 18 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.5835 (ttp-170) REVERT: K 38 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7738 (tt0) outliers start: 18 outliers final: 11 residues processed: 60 average time/residue: 1.1781 time to fit residues: 73.0509 Evaluate side-chains 57 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 85 LEU Chi-restraints excluded: chain H residue 99 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 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 5 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.0270 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.145450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.133265 restraints weight = 6880.735| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.18 r_work: 0.3987 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3198 Z= 0.203 Angle : 0.729 12.632 4343 Z= 0.378 Chirality : 0.047 0.237 461 Planarity : 0.004 0.029 564 Dihedral : 5.599 53.002 444 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.37 % Allowed : 23.28 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.41), residues: 390 helix: -3.49 (0.68), residues: 29 sheet: 0.31 (0.48), residues: 133 loop : -0.95 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 47 HIS 0.001 0.001 HIS K 90 PHE 0.016 0.001 PHE A 456 TYR 0.016 0.002 TYR H 52 ARG 0.005 0.001 ARG K 42 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 114) hydrogen bonds : angle 5.71551 ( 300) SS BOND : bond 0.01224 ( 4) SS BOND : angle 2.32784 ( 8) covalent geometry : bond 0.00485 ( 3194) covalent geometry : angle 0.72291 ( 4335) *********************** 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 61 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.372 Fit side-chains REVERT: H 20 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7314 (mm) REVERT: K 18 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.5914 (ttp-170) REVERT: K 38 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7770 (tt0) outliers start: 18 outliers final: 11 residues processed: 56 average time/residue: 1.0648 time to fit residues: 61.6253 Evaluate side-chains 56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 78 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 9 SER 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 21 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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** H 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.146176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.133698 restraints weight = 6867.465| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.26 r_work: 0.3991 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3198 Z= 0.157 Angle : 0.681 12.213 4343 Z= 0.356 Chirality : 0.045 0.226 461 Planarity : 0.004 0.033 564 Dihedral : 5.225 46.977 444 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.48 % Allowed : 24.18 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.41), residues: 390 helix: -3.30 (0.73), residues: 29 sheet: 0.34 (0.48), residues: 133 loop : -0.83 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS K 90 PHE 0.014 0.001 PHE A 456 TYR 0.014 0.001 TYR H 33 ARG 0.008 0.001 ARG K 42 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 114) hydrogen bonds : angle 5.45721 ( 300) SS BOND : bond 0.01146 ( 4) SS BOND : angle 2.13719 ( 8) covalent geometry : bond 0.00378 ( 3194) covalent geometry : angle 0.67520 ( 4335) *********************** 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 63 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: H 20 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7288 (mm) REVERT: K 18 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.5786 (ttp-170) REVERT: K 38 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7791 (tt0) outliers start: 15 outliers final: 10 residues processed: 56 average time/residue: 1.0768 time to fit residues: 62.2323 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 : 0.354 ------------------------------------------------------------------------------- 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 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 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 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** H 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.146795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.134469 restraints weight = 6767.116| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.25 r_work: 0.4002 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3198 Z= 0.138 Angle : 0.662 11.770 4343 Z= 0.347 Chirality : 0.045 0.215 461 Planarity : 0.004 0.035 564 Dihedral : 4.894 40.062 444 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.48 % Allowed : 24.48 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.41), residues: 390 helix: -3.16 (0.80), residues: 29 sheet: 0.43 (0.49), residues: 133 loop : -0.76 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.000 HIS K 90 PHE 0.012 0.001 PHE A 456 TYR 0.012 0.001 TYR H 33 ARG 0.009 0.001 ARG K 42 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 114) hydrogen bonds : angle 5.24390 ( 300) SS BOND : bond 0.01028 ( 4) SS BOND : angle 2.01709 ( 8) covalent geometry : bond 0.00334 ( 3194) covalent geometry : angle 0.65695 ( 4335) ********************** 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 61 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.362 Fit side-chains REVERT: H 20 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7315 (mm) REVERT: K 18 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.5745 (ttp-170) REVERT: K 38 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7786 (tt0) outliers start: 15 outliers final: 9 residues processed: 57 average time/residue: 1.0959 time to fit residues: 64.5346 Evaluate side-chains 57 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 9 SER 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 36 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 0.0870 chunk 12 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.8562 ------------------------------------------------------------------------------- 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 = 0.4232 r_free = 0.4232 target = 0.146306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.134165 restraints weight = 6828.306| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.22 r_work: 0.4002 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3198 Z= 0.144 Angle : 0.679 11.727 4343 Z= 0.353 Chirality : 0.045 0.215 461 Planarity : 0.004 0.034 564 Dihedral : 4.578 20.391 442 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.88 % Allowed : 25.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.41), residues: 390 helix: -3.16 (0.79), residues: 29 sheet: 0.48 (0.49), residues: 133 loop : -0.81 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS K 90 PHE 0.012 0.001 PHE A 456 TYR 0.013 0.001 TYR H 33 ARG 0.008 0.001 ARG K 42 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 114) hydrogen bonds : angle 5.26328 ( 300) SS BOND : bond 0.01088 ( 4) SS BOND : angle 2.03038 ( 8) covalent geometry : bond 0.00350 ( 3194) covalent geometry : angle 0.67447 ( 4335) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2974.41 seconds wall clock time: 51 minutes 45.04 seconds (3105.04 seconds total)