Starting phenix.real_space_refine on Thu Jul 24 10:56:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kmj_62435/07_2025/9kmj_62435.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kmj_62435/07_2025/9kmj_62435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kmj_62435/07_2025/9kmj_62435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kmj_62435/07_2025/9kmj_62435.map" model { file = "/net/cci-nas-00/data/ceres_data/9kmj_62435/07_2025/9kmj_62435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kmj_62435/07_2025/9kmj_62435.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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: 6 Type Number sf(0) Gaussians S 43 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3953 2.51 5 N 950 2.21 5 O 1070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6019 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4282 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 27, 'TRANS': 508} Chain breaks: 1 Chain: "H" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 922 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 804 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 11 Unusual residues: {' CL': 1, ' NA': 2, 'TAU': 1} Classifications: {'undetermined': 4, 'water': 1} Link IDs: {None: 4} Time building chain proxies: 4.63, per 1000 atoms: 0.77 Number of scatterers: 6019 At special positions: 0 Unit cell: (77.08, 82.82, 113.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 43 16.00 Na 2 11.00 O 1070 8.00 N 950 7.00 C 3953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 851.9 milliseconds 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1386 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 55.4% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 46 through 56 removed outlier: 4.024A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.614A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.699A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 110 through 116 removed outlier: 3.605A pdb=" N LYS A 115 " --> pdb=" O CYS A 112 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 116 " --> pdb=" O TRP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 121 through 151 removed outlier: 3.733A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 247 through 267 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.586A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.558A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 286' Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.362A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.572A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.593A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.619A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.906A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.804A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 496 Processing helix chain 'A' and resid 501 through 510 removed outlier: 3.529A pdb=" N TYR A 506 " --> pdb=" O PRO A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.734A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.617A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.928A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 removed outlier: 3.552A pdb=" N TYR A 532 " --> pdb=" O TYR A 536 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.756A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.756A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.125A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.927A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.623A pdb=" N SER L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.999A pdb=" N SER L 68 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 11.429A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 12.104A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.895A pdb=" N MET L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'L' and resid 54 through 55 removed outlier: 5.540A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN L 91 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 963 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: 1.70 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1761 1.34 - 1.46: 1514 1.46 - 1.58: 2855 1.58 - 1.70: 0 1.70 - 1.82: 63 Bond restraints: 6193 Sorted by residual: bond pdb=" CB PRO A 68 " pdb=" CG PRO A 68 " ideal model delta sigma weight residual 1.492 1.410 0.082 5.00e-02 4.00e+02 2.68e+00 bond pdb=" CD GLU A 406 " pdb=" OE1 GLU A 406 " ideal model delta sigma weight residual 1.249 1.220 0.029 1.90e-02 2.77e+03 2.32e+00 bond pdb=" C TYR L 95 " pdb=" N PRO L 96 " ideal model delta sigma weight residual 1.334 1.368 -0.035 2.34e-02 1.83e+03 2.18e+00 bond pdb=" CB CYS A 476 " pdb=" SG CYS A 476 " ideal model delta sigma weight residual 1.808 1.760 0.048 3.30e-02 9.18e+02 2.13e+00 bond pdb=" CB ILE A 141 " pdb=" CG1 ILE A 141 " ideal model delta sigma weight residual 1.530 1.501 0.029 2.00e-02 2.50e+03 2.04e+00 ... (remaining 6188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 8112 2.02 - 4.04: 257 4.04 - 6.06: 33 6.06 - 8.08: 11 8.08 - 10.10: 9 Bond angle restraints: 8422 Sorted by residual: angle pdb=" C SER L 51 " pdb=" N THR L 52 " pdb=" CA THR L 52 " ideal model delta sigma weight residual 121.54 131.64 -10.10 1.91e+00 2.74e-01 2.80e+01 angle pdb=" CA PRO A 208 " pdb=" N PRO A 208 " pdb=" CD PRO A 208 " ideal model delta sigma weight residual 112.00 106.14 5.86 1.40e+00 5.10e-01 1.75e+01 angle pdb=" C GLY A 425 " pdb=" N TYR A 426 " pdb=" CA TYR A 426 " ideal model delta sigma weight residual 121.54 128.59 -7.05 1.91e+00 2.74e-01 1.36e+01 angle pdb=" C PRO A 68 " pdb=" N TYR A 69 " pdb=" CA TYR A 69 " ideal model delta sigma weight residual 121.14 114.89 6.25 1.75e+00 3.27e-01 1.27e+01 angle pdb=" C VAL A 136 " pdb=" N TYR A 137 " pdb=" CA TYR A 137 " ideal model delta sigma weight residual 121.14 114.90 6.24 1.75e+00 3.27e-01 1.27e+01 ... (remaining 8417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 3173 16.96 - 33.92: 306 33.92 - 50.88: 60 50.88 - 67.84: 4 67.84 - 84.79: 5 Dihedral angle restraints: 3548 sinusoidal: 1358 harmonic: 2190 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 49.65 43.35 1 1.00e+01 1.00e-02 2.62e+01 dihedral pdb=" CA TYR L 95 " pdb=" C TYR L 95 " pdb=" N PRO L 96 " pdb=" CA PRO L 96 " ideal model delta harmonic sigma weight residual 180.00 156.62 23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA SER A 301 " pdb=" C SER A 301 " pdb=" N TYR A 302 " pdb=" CA TYR A 302 " ideal model delta harmonic sigma weight residual 180.00 159.99 20.01 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 3545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 654 0.048 - 0.096: 196 0.096 - 0.143: 52 0.143 - 0.191: 14 0.191 - 0.239: 4 Chirality restraints: 920 Sorted by residual: chirality pdb=" CA GLU A 406 " pdb=" N GLU A 406 " pdb=" C GLU A 406 " pdb=" CB GLU A 406 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL A 357 " pdb=" CA VAL A 357 " pdb=" CG1 VAL A 357 " pdb=" CG2 VAL A 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CG LEU A 261 " pdb=" CB LEU A 261 " pdb=" CD1 LEU A 261 " pdb=" CD2 LEU A 261 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 917 not shown) Planarity restraints: 1036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 207 " -0.045 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO A 208 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 402 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C SER A 402 " 0.045 2.00e-02 2.50e+03 pdb=" O SER A 402 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 403 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 252 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO A 253 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " 0.036 5.00e-02 4.00e+02 ... (remaining 1033 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1422 2.78 - 3.31: 5637 3.31 - 3.84: 10901 3.84 - 4.37: 12917 4.37 - 4.90: 22504 Nonbonded interactions: 53381 Sorted by model distance: nonbonded pdb=" OD1 ASP A 494 " pdb=" OH TYR H 59 " model vdw 2.251 3.040 nonbonded pdb=" NE ARG A 493 " pdb=" O GLU H 100 " model vdw 2.332 3.120 nonbonded pdb=" O ALA A 343 " pdb=" OG SER A 346 " model vdw 2.334 3.040 nonbonded pdb=" ND2 ASN A 63 " pdb=" OG SER A 337 " model vdw 2.357 3.120 nonbonded pdb=" O ASN L 2 " pdb=" OG1 THR L 98 " model vdw 2.362 3.040 ... (remaining 53376 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: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.420 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.006 0.082 6196 Z= 0.253 Angle : 0.877 10.105 8428 Z= 0.465 Chirality : 0.052 0.239 920 Planarity : 0.007 0.065 1036 Dihedral : 13.752 84.794 2153 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.43 (0.29), residues: 754 helix: -0.67 (0.24), residues: 364 sheet: -1.15 (0.52), residues: 103 loop : -0.99 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 44 HIS 0.003 0.001 HIS A 161 PHE 0.042 0.003 PHE A 338 TYR 0.026 0.002 TYR A 137 ARG 0.010 0.001 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.16404 ( 329) hydrogen bonds : angle 7.43160 ( 963) SS BOND : bond 0.00372 ( 3) SS BOND : angle 1.60857 ( 6) covalent geometry : bond 0.00619 ( 6193) covalent geometry : angle 0.87585 ( 8422) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.587 Fit side-chains REVERT: H 32 TYR cc_start: 0.7454 (m-80) cc_final: 0.7181 (m-80) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1572 time to fit residues: 21.6433 Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 43 optimal weight: 0.0670 chunk 67 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.173890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.139216 restraints weight = 6399.383| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.99 r_work: 0.3278 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6196 Z= 0.167 Angle : 0.607 7.663 8428 Z= 0.316 Chirality : 0.041 0.152 920 Planarity : 0.005 0.051 1036 Dihedral : 5.356 58.433 835 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.15 % Allowed : 5.24 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.30), residues: 754 helix: 0.41 (0.26), residues: 366 sheet: -0.80 (0.52), residues: 98 loop : -0.77 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 470 HIS 0.003 0.001 HIS A 161 PHE 0.022 0.002 PHE A 338 TYR 0.020 0.001 TYR A 137 ARG 0.004 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04818 ( 329) hydrogen bonds : angle 5.43088 ( 963) SS BOND : bond 0.00224 ( 3) SS BOND : angle 0.99040 ( 6) covalent geometry : bond 0.00391 ( 6193) covalent geometry : angle 0.60652 ( 8422) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.588 Fit side-chains REVERT: H 93 MET cc_start: 0.7784 (tpt) cc_final: 0.7566 (tpp) outliers start: 1 outliers final: 1 residues processed: 102 average time/residue: 0.1606 time to fit residues: 22.3639 Evaluate side-chains 97 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.167007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.132306 restraints weight = 6642.956| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.98 r_work: 0.3399 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6196 Z= 0.195 Angle : 0.595 7.716 8428 Z= 0.310 Chirality : 0.042 0.154 920 Planarity : 0.005 0.051 1036 Dihedral : 5.248 59.216 835 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.08 % Allowed : 9.55 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.31), residues: 754 helix: 0.86 (0.27), residues: 362 sheet: -0.93 (0.51), residues: 103 loop : -0.67 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 470 HIS 0.004 0.001 HIS A 161 PHE 0.020 0.002 PHE A 350 TYR 0.023 0.001 TYR A 137 ARG 0.004 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 329) hydrogen bonds : angle 5.20510 ( 963) SS BOND : bond 0.00281 ( 3) SS BOND : angle 0.77572 ( 6) covalent geometry : bond 0.00463 ( 6193) covalent geometry : angle 0.59498 ( 8422) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.652 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 102 average time/residue: 0.1761 time to fit residues: 24.0872 Evaluate side-chains 99 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 21 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 64 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.171178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137318 restraints weight = 6581.094| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.95 r_work: 0.3365 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6196 Z= 0.160 Angle : 0.565 7.671 8428 Z= 0.294 Chirality : 0.040 0.155 920 Planarity : 0.005 0.049 1036 Dihedral : 5.100 57.612 835 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.23 % Allowed : 11.40 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.31), residues: 754 helix: 1.11 (0.27), residues: 362 sheet: -0.75 (0.49), residues: 110 loop : -0.58 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.003 0.001 HIS A 161 PHE 0.023 0.002 PHE A 404 TYR 0.022 0.001 TYR A 137 ARG 0.003 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04515 ( 329) hydrogen bonds : angle 4.99882 ( 963) SS BOND : bond 0.00246 ( 3) SS BOND : angle 0.60406 ( 6) covalent geometry : bond 0.00378 ( 6193) covalent geometry : angle 0.56510 ( 8422) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.652 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 95 average time/residue: 0.1827 time to fit residues: 23.0633 Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain L residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 34 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.172983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.140751 restraints weight = 6544.688| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.00 r_work: 0.3307 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6196 Z= 0.151 Angle : 0.551 7.763 8428 Z= 0.286 Chirality : 0.040 0.153 920 Planarity : 0.005 0.048 1036 Dihedral : 5.003 59.853 835 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.08 % Allowed : 12.48 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.31), residues: 754 helix: 1.26 (0.27), residues: 363 sheet: -0.58 (0.50), residues: 103 loop : -0.49 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.026 0.002 PHE A 404 TYR 0.022 0.001 TYR A 137 ARG 0.003 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 329) hydrogen bonds : angle 4.86619 ( 963) SS BOND : bond 0.00242 ( 3) SS BOND : angle 0.57663 ( 6) covalent geometry : bond 0.00355 ( 6193) covalent geometry : angle 0.55107 ( 8422) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.721 Fit side-chains REVERT: A 69 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.6346 (p90) outliers start: 7 outliers final: 6 residues processed: 100 average time/residue: 0.2796 time to fit residues: 36.9854 Evaluate side-chains 102 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain L residue 21 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 9 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 54 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.172779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.140556 restraints weight = 6422.695| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.98 r_work: 0.3430 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6196 Z= 0.156 Angle : 0.556 7.787 8428 Z= 0.287 Chirality : 0.040 0.154 920 Planarity : 0.005 0.073 1036 Dihedral : 4.990 59.346 835 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.39 % Allowed : 12.79 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.31), residues: 754 helix: 1.32 (0.27), residues: 363 sheet: -0.54 (0.50), residues: 103 loop : -0.44 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.027 0.002 PHE A 404 TYR 0.022 0.001 TYR A 137 ARG 0.006 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 329) hydrogen bonds : angle 4.84089 ( 963) SS BOND : bond 0.00242 ( 3) SS BOND : angle 0.55169 ( 6) covalent geometry : bond 0.00369 ( 6193) covalent geometry : angle 0.55611 ( 8422) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.680 Fit side-chains REVERT: A 69 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.6377 (p90) REVERT: H 108 TYR cc_start: 0.8365 (m-80) cc_final: 0.8149 (m-10) outliers start: 9 outliers final: 6 residues processed: 97 average time/residue: 0.2108 time to fit residues: 28.1884 Evaluate side-chains 96 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain L residue 21 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.172309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.137440 restraints weight = 6582.841| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.01 r_work: 0.3378 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6196 Z= 0.164 Angle : 0.565 7.964 8428 Z= 0.291 Chirality : 0.041 0.154 920 Planarity : 0.005 0.070 1036 Dihedral : 4.989 59.522 835 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.23 % Allowed : 13.71 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.56 (0.31), residues: 754 helix: 1.33 (0.27), residues: 363 sheet: -0.50 (0.50), residues: 103 loop : -0.43 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.030 0.002 PHE A 404 TYR 0.022 0.001 TYR A 137 ARG 0.007 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 329) hydrogen bonds : angle 4.83299 ( 963) SS BOND : bond 0.00248 ( 3) SS BOND : angle 0.53010 ( 6) covalent geometry : bond 0.00390 ( 6193) covalent geometry : angle 0.56527 ( 8422) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.6385 (p90) REVERT: L 91 GLN cc_start: 0.9082 (pp30) cc_final: 0.8287 (pp30) outliers start: 8 outliers final: 6 residues processed: 94 average time/residue: 0.1823 time to fit residues: 23.0148 Evaluate side-chains 98 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain L residue 21 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 1 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 15 optimal weight: 0.0470 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.170941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.137099 restraints weight = 6545.726| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.95 r_work: 0.3368 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6196 Z= 0.152 Angle : 0.558 7.967 8428 Z= 0.287 Chirality : 0.040 0.154 920 Planarity : 0.005 0.067 1036 Dihedral : 4.964 59.773 835 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.39 % Allowed : 14.18 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.32), residues: 754 helix: 1.38 (0.27), residues: 363 sheet: -0.42 (0.50), residues: 103 loop : -0.38 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 PHE 0.033 0.002 PHE A 404 TYR 0.022 0.001 TYR A 137 ARG 0.006 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04334 ( 329) hydrogen bonds : angle 4.81989 ( 963) SS BOND : bond 0.00239 ( 3) SS BOND : angle 0.52265 ( 6) covalent geometry : bond 0.00361 ( 6193) covalent geometry : angle 0.55795 ( 8422) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.6441 (p90) REVERT: L 91 GLN cc_start: 0.9076 (pp30) cc_final: 0.8264 (pp30) outliers start: 9 outliers final: 7 residues processed: 98 average time/residue: 0.3023 time to fit residues: 39.9183 Evaluate side-chains 99 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain L residue 21 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.168126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133704 restraints weight = 6639.109| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.98 r_work: 0.3403 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6196 Z= 0.149 Angle : 0.567 8.122 8428 Z= 0.290 Chirality : 0.041 0.154 920 Planarity : 0.005 0.064 1036 Dihedral : 4.931 59.080 835 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.23 % Allowed : 14.79 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.32), residues: 754 helix: 1.42 (0.27), residues: 363 sheet: -0.42 (0.50), residues: 103 loop : -0.36 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.002 0.000 HIS A 161 PHE 0.034 0.002 PHE A 404 TYR 0.021 0.001 TYR A 137 ARG 0.007 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 329) hydrogen bonds : angle 4.81149 ( 963) SS BOND : bond 0.00229 ( 3) SS BOND : angle 0.49165 ( 6) covalent geometry : bond 0.00353 ( 6193) covalent geometry : angle 0.56718 ( 8422) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.6408 (p90) REVERT: L 91 GLN cc_start: 0.9080 (pp30) cc_final: 0.8277 (pp30) outliers start: 8 outliers final: 7 residues processed: 95 average time/residue: 0.2129 time to fit residues: 26.8327 Evaluate side-chains 99 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain L residue 21 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.0870 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.168509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134061 restraints weight = 6710.898| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.99 r_work: 0.3381 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6196 Z= 0.168 Angle : 0.583 8.377 8428 Z= 0.299 Chirality : 0.041 0.156 920 Planarity : 0.005 0.067 1036 Dihedral : 4.974 58.203 835 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.23 % Allowed : 14.64 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.32), residues: 754 helix: 1.39 (0.27), residues: 363 sheet: -0.43 (0.50), residues: 103 loop : -0.37 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.003 0.001 HIS A 161 PHE 0.036 0.002 PHE A 404 TYR 0.022 0.001 TYR A 137 ARG 0.007 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04447 ( 329) hydrogen bonds : angle 4.87180 ( 963) SS BOND : bond 0.00231 ( 3) SS BOND : angle 0.49067 ( 6) covalent geometry : bond 0.00401 ( 6193) covalent geometry : angle 0.58275 ( 8422) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.574 Fit side-chains REVERT: A 69 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.6411 (p90) REVERT: H 90 ASP cc_start: 0.8646 (t0) cc_final: 0.8195 (t0) REVERT: L 91 GLN cc_start: 0.9089 (pp30) cc_final: 0.8272 (pp30) outliers start: 8 outliers final: 7 residues processed: 95 average time/residue: 0.1949 time to fit residues: 24.5088 Evaluate side-chains 97 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain L residue 21 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 23 optimal weight: 0.0060 chunk 44 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 32 optimal weight: 0.0570 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 43 optimal weight: 0.0770 chunk 13 optimal weight: 0.7980 overall best weight: 0.2072 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.177604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.146386 restraints weight = 6666.493| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.04 r_work: 0.3500 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6196 Z= 0.119 Angle : 0.545 8.462 8428 Z= 0.279 Chirality : 0.040 0.158 920 Planarity : 0.005 0.052 1036 Dihedral : 4.762 56.930 835 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.23 % Allowed : 14.48 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.32), residues: 754 helix: 1.57 (0.28), residues: 363 sheet: -0.22 (0.52), residues: 98 loop : -0.28 (0.39), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.001 0.000 HIS H 80 PHE 0.036 0.002 PHE A 404 TYR 0.023 0.001 TYR A 137 ARG 0.004 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 329) hydrogen bonds : angle 4.65636 ( 963) SS BOND : bond 0.00200 ( 3) SS BOND : angle 0.51997 ( 6) covalent geometry : bond 0.00265 ( 6193) covalent geometry : angle 0.54523 ( 8422) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3887.02 seconds wall clock time: 69 minutes 18.01 seconds (4158.01 seconds total)