Starting phenix.real_space_refine on Thu Jul 2 02:22:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kmk_62436/07_2026/9kmk_62436.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kmk_62436/07_2026/9kmk_62436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kmk_62436/07_2026/9kmk_62436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kmk_62436/07_2026/9kmk_62436.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kmk_62436/07_2026/9kmk_62436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kmk_62436/07_2026/9kmk_62436.map" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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: 5 Type Number sf(0) Gaussians S 41 5.16 5 Cl 1 4.86 5 C 3854 2.51 5 N 931 2.21 5 O 1045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5872 Number of models: 1 Model: "" Number of chains: 4 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: 4145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4145 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 25, 'TRANS': 494} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Time building chain proxies: 1.03, per 1000 atoms: 0.18 Number of scatterers: 5872 At special positions: 0 Unit cell: (75.44, 82.82, 113.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 41 16.00 O 1045 8.00 N 931 7.00 C 3854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 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 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 141.5 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 6 sheets defined 53.4% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.978A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.940A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.837A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 removed outlier: 4.118A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 90 through 105 removed outlier: 3.524A pdb=" N THR A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 removed outlier: 4.313A pdb=" N THR A 111 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP A 113 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 121 through 151 removed outlier: 4.074A 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 236 removed outlier: 3.982A pdb=" N TRP A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 266 removed outlier: 3.710A pdb=" N TYR A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.664A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.571A pdb=" N GLY A 286 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 312 removed outlier: 3.991A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 355 removed outlier: 3.513A pdb=" N CYS A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.574A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 444 removed outlier: 3.692A pdb=" N ILE A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.680A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 removed outlier: 3.778A pdb=" N LEU A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 496 Processing helix chain 'A' and resid 501 through 510 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 581 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.040A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N CYS H 96 " --> pdb=" O GLY H 110 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR H 94 " --> pdb=" O GLY H 112 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR H 114 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA H 92 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 6 removed outlier: 12.362A pdb=" N CYS L 23 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 11.583A pdb=" N THR L 75 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N ALA L 25 " --> pdb=" O SER L 73 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N SER L 73 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 11.616A pdb=" N SER L 27 " --> pdb=" O SER L 71 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER L 71 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY L 69 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.469A pdb=" N MET L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'L' and resid 54 through 55 removed outlier: 5.793A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 531 through 532 318 hydrogen bonds defined for protein. 921 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: 0.57 Time building geometry restraints manager: 0.47 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: 1737 1.34 - 1.46: 1399 1.46 - 1.58: 2845 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6041 Sorted by residual: bond pdb=" CB ILE A 141 " pdb=" CG1 ILE A 141 " ideal model delta sigma weight residual 1.530 1.493 0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" CB VAL A 140 " pdb=" CG1 VAL A 140 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.39e+00 bond pdb=" CG1 ILE A 292 " pdb=" CD1 ILE A 292 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.70e+00 bond pdb=" SD MET A 452 " pdb=" CE MET A 452 " ideal model delta sigma weight residual 1.791 1.750 0.041 2.50e-02 1.60e+03 2.69e+00 bond pdb=" CB VAL A 94 " pdb=" CG2 VAL A 94 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.27e+00 ... (remaining 6036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 7934 2.23 - 4.46: 222 4.46 - 6.69: 43 6.69 - 8.92: 11 8.92 - 11.15: 3 Bond angle restraints: 8213 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 121.54 132.69 -11.15 1.91e+00 2.74e-01 3.41e+01 angle pdb=" C LYS A 317 " pdb=" N TYR A 318 " pdb=" CA TYR A 318 " ideal model delta sigma weight residual 120.79 127.27 -6.48 1.39e+00 5.18e-01 2.17e+01 angle pdb=" N GLY A 62 " pdb=" CA GLY A 62 " pdb=" C GLY A 62 " ideal model delta sigma weight residual 113.18 103.70 9.48 2.37e+00 1.78e-01 1.60e+01 angle pdb=" N TYR A 318 " pdb=" CA TYR A 318 " pdb=" C TYR A 318 " ideal model delta sigma weight residual 111.02 115.88 -4.86 1.22e+00 6.72e-01 1.59e+01 angle pdb=" C ARG A 427 " pdb=" N ARG A 428 " pdb=" CA ARG A 428 " ideal model delta sigma weight residual 121.54 129.00 -7.46 1.91e+00 2.74e-01 1.52e+01 ... (remaining 8208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 3109 17.40 - 34.81: 299 34.81 - 52.21: 44 52.21 - 69.62: 6 69.62 - 87.02: 5 Dihedral angle restraints: 3463 sinusoidal: 1323 harmonic: 2140 Sorted by residual: dihedral pdb=" CA TYR A 320 " pdb=" C TYR A 320 " pdb=" N ASN A 321 " pdb=" CA ASN A 321 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA CYS A 171 " pdb=" C CYS A 171 " pdb=" N MET A 172 " pdb=" CA MET A 172 " ideal model delta harmonic sigma weight residual 180.00 156.92 23.08 0 5.00e+00 4.00e-02 2.13e+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 180.00 158.06 21.94 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 3460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 828 0.104 - 0.208: 68 0.208 - 0.312: 2 0.312 - 0.417: 0 0.417 - 0.521: 1 Chirality restraints: 899 Sorted by residual: chirality pdb=" CB VAL A 447 " pdb=" CA VAL A 447 " pdb=" CG1 VAL A 447 " pdb=" CG2 VAL A 447 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.52 2.00e-01 2.50e+01 6.78e+00 chirality pdb=" CB VAL A 140 " pdb=" CA VAL A 140 " pdb=" CG1 VAL A 140 " pdb=" CG2 VAL A 140 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB THR H 28 " pdb=" CA THR H 28 " pdb=" OG1 THR H 28 " pdb=" CG2 THR H 28 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 896 not shown) Planarity restraints: 1013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 67 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO A 68 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.26e+00 pdb=" N PRO L 8 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 40 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO H 41 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " 0.030 5.00e-02 4.00e+02 ... (remaining 1010 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1413 2.78 - 3.31: 5450 3.31 - 3.84: 10532 3.84 - 4.37: 12363 4.37 - 4.90: 21317 Nonbonded interactions: 51075 Sorted by model distance: nonbonded pdb=" O SER H 52 " pdb=" NH1 ARG H 72 " model vdw 2.256 3.120 nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR A 168 " pdb=" OE2 GLU A 197 " model vdw 2.284 3.040 nonbonded pdb=" OH TYR H 59 " pdb=" OD1 ASP A 494 " model vdw 2.286 3.040 nonbonded pdb=" O SER A 464 " pdb=" OG SER A 464 " model vdw 2.291 3.040 ... (remaining 51070 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: 3.120 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: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.900 Find NCS groups from input model: 0.030 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:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 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 : 0.007 0.072 6044 Z= 0.278 Angle : 0.938 11.151 8219 Z= 0.512 Chirality : 0.058 0.521 899 Planarity : 0.007 0.057 1013 Dihedral : 13.803 87.023 2102 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.28), residues: 738 helix: -1.03 (0.23), residues: 367 sheet: -0.64 (0.52), residues: 104 loop : -1.81 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 66 TYR 0.022 0.002 TYR A 318 PHE 0.031 0.003 PHE L 92 TRP 0.016 0.002 TRP A 65 HIS 0.003 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.28 ( 6041) covalent geometry : angle 0.93681 / 0.51 ( 8213) SS BOND : bond 0.00148 / 0.07 ( 3) SS BOND : angle 1.70254 / 0.93 ( 6) hydrogen bonds : bond 0.16568 / 11.03 ( 318) hydrogen bonds : angle 7.64460 / 5.08 ( 921) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.137 Fit side-chains REVERT: A 140 VAL cc_start: 0.8443 (p) cc_final: 0.8127 (m) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0568 time to fit residues: 7.8587 Evaluate side-chains 90 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.172607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140141 restraints weight = 6573.073| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.05 r_work: 0.3450 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6044 Z= 0.136 Angle : 0.591 7.638 8219 Z= 0.311 Chirality : 0.042 0.151 899 Planarity : 0.005 0.042 1013 Dihedral : 4.917 23.805 819 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.32 % Allowed : 6.80 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.30), residues: 738 helix: 0.27 (0.25), residues: 376 sheet: -1.00 (0.49), residues: 113 loop : -1.40 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 240 TYR 0.019 0.001 TYR A 137 PHE 0.018 0.001 PHE A 455 TRP 0.010 0.001 TRP A 470 HIS 0.002 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 6041) covalent geometry : angle 0.58962 / 0.31 ( 8213) SS BOND : bond 0.00114 / 0.06 ( 3) SS BOND : angle 1.48724 / 0.80 ( 6) hydrogen bonds : bond 0.04581 / 3.08 ( 318) hydrogen bonds : angle 5.28392 / 3.53 ( 921) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.229 Fit side-chains REVERT: A 83 TYR cc_start: 0.9087 (t80) cc_final: 0.8835 (t80) REVERT: A 441 LEU cc_start: 0.8486 (mp) cc_final: 0.8178 (mm) outliers start: 2 outliers final: 1 residues processed: 105 average time/residue: 0.0924 time to fit residues: 12.4496 Evaluate side-chains 90 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 17 optimal weight: 0.0070 chunk 64 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.172658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.141069 restraints weight = 6597.499| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.88 r_work: 0.3464 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6044 Z= 0.186 Angle : 0.601 8.972 8219 Z= 0.316 Chirality : 0.042 0.156 899 Planarity : 0.004 0.039 1013 Dihedral : 4.730 21.678 819 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.11 % Allowed : 8.70 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.30), residues: 738 helix: 0.68 (0.26), residues: 376 sheet: -0.90 (0.48), residues: 113 loop : -1.21 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 98 TYR 0.019 0.002 TYR A 137 PHE 0.020 0.002 PHE A 455 TRP 0.009 0.001 TRP A 218 HIS 0.002 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 ( 6041) covalent geometry : angle 0.59988 / 0.32 ( 8213) SS BOND : bond 0.00105 / 0.05 ( 3) SS BOND : angle 1.44427 / 0.75 ( 6) hydrogen bonds : bond 0.04642 / 3.14 ( 318) hydrogen bonds : angle 5.08751 / 3.39 ( 921) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.227 Fit side-chains REVERT: A 138 TYR cc_start: 0.8007 (t80) cc_final: 0.7539 (m-80) REVERT: A 441 LEU cc_start: 0.8516 (mp) cc_final: 0.8226 (mm) REVERT: A 567 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7770 (mtt180) outliers start: 7 outliers final: 6 residues processed: 100 average time/residue: 0.0879 time to fit residues: 11.5528 Evaluate side-chains 93 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 38 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 65 optimal weight: 0.3980 chunk 46 optimal weight: 0.0030 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.176997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145272 restraints weight = 6618.044| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.92 r_work: 0.3509 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6044 Z= 0.128 Angle : 0.550 7.637 8219 Z= 0.289 Chirality : 0.040 0.160 899 Planarity : 0.004 0.039 1013 Dihedral : 4.463 19.830 819 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.27 % Allowed : 11.08 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.31), residues: 738 helix: 1.12 (0.26), residues: 376 sheet: -0.82 (0.47), residues: 113 loop : -1.12 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 98 TYR 0.022 0.001 TYR A 137 PHE 0.018 0.001 PHE A 300 TRP 0.011 0.001 TRP A 218 HIS 0.003 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 6041) covalent geometry : angle 0.54954 / 0.29 ( 8213) SS BOND : bond 0.00132 / 0.07 ( 3) SS BOND : angle 1.09077 / 0.55 ( 6) hydrogen bonds : bond 0.04148 / 2.80 ( 318) hydrogen bonds : angle 4.75738 / 3.18 ( 921) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.135 Fit side-chains REVERT: A 83 TYR cc_start: 0.9152 (t80) cc_final: 0.8848 (t80) REVERT: A 138 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: A 441 LEU cc_start: 0.8531 (mp) cc_final: 0.8244 (mm) REVERT: A 567 ARG cc_start: 0.8271 (mtm-85) cc_final: 0.7788 (mtt180) outliers start: 8 outliers final: 7 residues processed: 104 average time/residue: 0.0690 time to fit residues: 9.3842 Evaluate side-chains 102 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 62 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.171619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.139445 restraints weight = 6780.661| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.93 r_work: 0.3443 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6044 Z= 0.205 Angle : 0.617 13.842 8219 Z= 0.319 Chirality : 0.043 0.161 899 Planarity : 0.004 0.037 1013 Dihedral : 4.532 19.237 819 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.37 % Allowed : 11.39 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.31), residues: 738 helix: 1.06 (0.26), residues: 377 sheet: -0.86 (0.47), residues: 113 loop : -1.09 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 98 TYR 0.019 0.002 TYR A 137 PHE 0.018 0.002 PHE A 455 TRP 0.010 0.001 TRP A 218 HIS 0.002 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 ( 6041) covalent geometry : angle 0.61583 / 0.32 ( 8213) SS BOND : bond 0.00142 / 0.07 ( 3) SS BOND : angle 1.29387 / 0.62 ( 6) hydrogen bonds : bond 0.04585 / 3.11 ( 318) hydrogen bonds : angle 4.89740 / 3.28 ( 921) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.153 Fit side-chains REVERT: A 441 LEU cc_start: 0.8533 (mp) cc_final: 0.8250 (mm) REVERT: A 498 TYR cc_start: 0.8953 (p90) cc_final: 0.8666 (p90) REVERT: A 567 ARG cc_start: 0.8275 (mtm-85) cc_final: 0.7814 (mtt180) outliers start: 15 outliers final: 9 residues processed: 107 average time/residue: 0.0785 time to fit residues: 11.1206 Evaluate side-chains 102 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.173391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.141506 restraints weight = 6676.258| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.92 r_work: 0.3461 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6044 Z= 0.161 Angle : 0.602 15.542 8219 Z= 0.309 Chirality : 0.042 0.163 899 Planarity : 0.004 0.037 1013 Dihedral : 4.447 18.616 819 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.06 % Allowed : 12.50 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.31), residues: 738 helix: 1.15 (0.26), residues: 377 sheet: -0.93 (0.46), residues: 114 loop : -1.03 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 98 TYR 0.020 0.001 TYR A 137 PHE 0.020 0.002 PHE A 232 TRP 0.015 0.001 TRP A 218 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 6041) covalent geometry : angle 0.60144 / 0.31 ( 8213) SS BOND : bond 0.00139 / 0.07 ( 3) SS BOND : angle 1.10659 / 0.54 ( 6) hydrogen bonds : bond 0.04357 / 2.95 ( 318) hydrogen bonds : angle 4.82333 / 3.23 ( 921) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.215 Fit side-chains REVERT: L 107 MET cc_start: 0.8322 (mmm) cc_final: 0.8014 (mmt) REVERT: A 388 SER cc_start: 0.8948 (t) cc_final: 0.8357 (p) REVERT: A 441 LEU cc_start: 0.8535 (mp) cc_final: 0.8251 (mm) REVERT: A 498 TYR cc_start: 0.8950 (p90) cc_final: 0.8676 (p90) REVERT: A 567 ARG cc_start: 0.8246 (mtm-85) cc_final: 0.7806 (mtt180) outliers start: 13 outliers final: 12 residues processed: 107 average time/residue: 0.1026 time to fit residues: 14.3117 Evaluate side-chains 105 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.170803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138855 restraints weight = 6746.723| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.92 r_work: 0.3435 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6044 Z= 0.197 Angle : 0.627 13.703 8219 Z= 0.324 Chirality : 0.043 0.171 899 Planarity : 0.004 0.036 1013 Dihedral : 4.520 18.263 819 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.22 % Allowed : 13.45 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.30), residues: 738 helix: 1.07 (0.26), residues: 375 sheet: -0.96 (0.45), residues: 115 loop : -1.05 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 98 TYR 0.020 0.002 TYR A 137 PHE 0.019 0.002 PHE A 455 TRP 0.015 0.001 TRP A 218 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 ( 6041) covalent geometry : angle 0.62594 / 0.32 ( 8213) SS BOND : bond 0.00194 / 0.10 ( 3) SS BOND : angle 1.25321 / 0.63 ( 6) hydrogen bonds : bond 0.04630 / 3.16 ( 318) hydrogen bonds : angle 4.91709 / 3.30 ( 921) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.210 Fit side-chains REVERT: A 441 LEU cc_start: 0.8544 (mp) cc_final: 0.8246 (mm) REVERT: A 498 TYR cc_start: 0.8952 (p90) cc_final: 0.8679 (p90) REVERT: A 567 ARG cc_start: 0.8278 (mtm-85) cc_final: 0.7855 (mtt180) outliers start: 14 outliers final: 12 residues processed: 105 average time/residue: 0.0820 time to fit residues: 11.2377 Evaluate side-chains 104 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 25 optimal weight: 0.4980 chunk 30 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 0.0060 chunk 53 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.174425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.142867 restraints weight = 6709.063| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.91 r_work: 0.3482 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6044 Z= 0.141 Angle : 0.584 13.020 8219 Z= 0.303 Chirality : 0.041 0.176 899 Planarity : 0.004 0.037 1013 Dihedral : 4.364 17.517 819 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.90 % Allowed : 14.40 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.31), residues: 738 helix: 1.24 (0.26), residues: 377 sheet: -0.83 (0.46), residues: 114 loop : -0.96 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 98 TYR 0.023 0.001 TYR A 137 PHE 0.022 0.002 PHE A 232 TRP 0.013 0.001 TRP A 218 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 6041) covalent geometry : angle 0.58388 / 0.30 ( 8213) SS BOND : bond 0.00205 / 0.11 ( 3) SS BOND : angle 0.93297 / 0.45 ( 6) hydrogen bonds : bond 0.04213 / 2.87 ( 318) hydrogen bonds : angle 4.73774 / 3.18 ( 921) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: H 67 ARG cc_start: 0.8509 (ptt90) cc_final: 0.8072 (ptm-80) REVERT: L 107 MET cc_start: 0.8301 (mmm) cc_final: 0.8096 (mmt) REVERT: A 83 TYR cc_start: 0.9117 (t80) cc_final: 0.8857 (t80) REVERT: A 388 SER cc_start: 0.8936 (t) cc_final: 0.8363 (p) REVERT: A 441 LEU cc_start: 0.8521 (mp) cc_final: 0.8235 (mm) REVERT: A 498 TYR cc_start: 0.8918 (p90) cc_final: 0.8652 (p90) REVERT: A 567 ARG cc_start: 0.8257 (mtm-85) cc_final: 0.7839 (mtt180) outliers start: 12 outliers final: 10 residues processed: 106 average time/residue: 0.0873 time to fit residues: 12.1096 Evaluate side-chains 107 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 66 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.172526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.143172 restraints weight = 6730.162| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.85 r_work: 0.3485 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6044 Z= 0.173 Angle : 0.602 12.315 8219 Z= 0.313 Chirality : 0.042 0.171 899 Planarity : 0.004 0.037 1013 Dihedral : 4.416 17.275 819 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.37 % Allowed : 14.08 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.31), residues: 738 helix: 1.19 (0.26), residues: 377 sheet: -0.84 (0.46), residues: 114 loop : -0.93 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 98 TYR 0.020 0.001 TYR A 137 PHE 0.021 0.002 PHE A 232 TRP 0.014 0.001 TRP A 218 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 6041) covalent geometry : angle 0.60131 / 0.31 ( 8213) SS BOND : bond 0.00189 / 0.10 ( 3) SS BOND : angle 1.05173 / 0.51 ( 6) hydrogen bonds : bond 0.04412 / 3.00 ( 318) hydrogen bonds : angle 4.80784 / 3.23 ( 921) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: H 67 ARG cc_start: 0.8525 (ptt90) cc_final: 0.8108 (ptm-80) REVERT: A 83 TYR cc_start: 0.9114 (t80) cc_final: 0.8869 (t80) REVERT: A 388 SER cc_start: 0.8961 (t) cc_final: 0.8398 (p) REVERT: A 441 LEU cc_start: 0.8542 (mp) cc_final: 0.8257 (mm) REVERT: A 498 TYR cc_start: 0.8925 (p90) cc_final: 0.8679 (p90) REVERT: A 567 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.7846 (mtt180) outliers start: 15 outliers final: 11 residues processed: 106 average time/residue: 0.0874 time to fit residues: 12.1276 Evaluate side-chains 106 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 44 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.171242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.139448 restraints weight = 6718.102| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.92 r_work: 0.3444 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6044 Z= 0.193 Angle : 0.623 12.102 8219 Z= 0.325 Chirality : 0.043 0.167 899 Planarity : 0.004 0.037 1013 Dihedral : 4.498 17.248 819 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.06 % Allowed : 14.87 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.31), residues: 738 helix: 1.15 (0.26), residues: 375 sheet: -0.90 (0.45), residues: 115 loop : -0.96 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 98 TYR 0.019 0.002 TYR A 137 PHE 0.022 0.002 PHE A 232 TRP 0.015 0.001 TRP A 218 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 ( 6041) covalent geometry : angle 0.62281 / 0.32 ( 8213) SS BOND : bond 0.00189 / 0.10 ( 3) SS BOND : angle 1.10177 / 0.54 ( 6) hydrogen bonds : bond 0.04550 / 3.10 ( 318) hydrogen bonds : angle 4.87384 / 3.27 ( 921) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 388 SER cc_start: 0.8968 (t) cc_final: 0.8390 (p) REVERT: A 441 LEU cc_start: 0.8505 (mp) cc_final: 0.8204 (mm) REVERT: A 498 TYR cc_start: 0.8911 (p90) cc_final: 0.8643 (p90) REVERT: A 567 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.7791 (mtt180) outliers start: 13 outliers final: 11 residues processed: 101 average time/residue: 0.0897 time to fit residues: 11.8219 Evaluate side-chains 105 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.171928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.140280 restraints weight = 6661.758| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.90 r_work: 0.3447 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6044 Z= 0.181 Angle : 0.616 11.889 8219 Z= 0.321 Chirality : 0.042 0.169 899 Planarity : 0.004 0.037 1013 Dihedral : 4.487 17.179 819 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.06 % Allowed : 15.19 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.31), residues: 738 helix: 1.09 (0.26), residues: 377 sheet: -0.89 (0.45), residues: 115 loop : -0.97 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 98 TYR 0.020 0.002 TYR A 137 PHE 0.016 0.002 PHE A 455 TRP 0.014 0.001 TRP A 218 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 6041) covalent geometry : angle 0.61599 / 0.32 ( 8213) SS BOND : bond 0.00210 / 0.11 ( 3) SS BOND : angle 1.01099 / 0.49 ( 6) hydrogen bonds : bond 0.04465 / 3.04 ( 318) hydrogen bonds : angle 4.85646 / 3.26 ( 921) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1746.96 seconds wall clock time: 30 minutes 42.87 seconds (1842.87 seconds total)