Starting phenix.real_space_refine on Wed Jul 1 23:52:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wfi_37492/07_2026/8wfi_37492.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wfi_37492/07_2026/8wfi_37492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wfi_37492/07_2026/8wfi_37492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wfi_37492/07_2026/8wfi_37492.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wfi_37492/07_2026/8wfi_37492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wfi_37492/07_2026/8wfi_37492.map" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.067 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 35 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2877 2.51 5 N 676 2.21 5 O 756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 4347 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4302 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 25, 'TRANS': 516} Chain breaks: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 37 Ad-hoc single atom residues: {' CL': 1, ' NA': 2} Classifications: {'water': 37} Link IDs: {None: 36} Chain breaks: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY A 701 " occ=0.00 ... (3 atoms not shown) pdb=" OXT GLY A 701 " occ=0.00 Time building chain proxies: 0.84, per 1000 atoms: 0.19 Number of scatterers: 4347 At special positions: 0 Unit cell: (75.65, 65.45, 93.5, 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 35 16.00 Na 2 11.00 O 756 8.00 N 676 7.00 C 2877 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 175 " 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: 0.22 Conformation dependent library (CDL) restraints added in 97.8 milliseconds 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 988 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 78.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.594A pdb=" N PHE A 55 " --> pdb=" O ASN A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.054A pdb=" N VAL A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 79 removed outlier: 4.124A pdb=" N TYR A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 83 Processing helix chain 'A' and resid 84 through 95 Processing helix chain 'A' and resid 95 through 111 removed outlier: 3.942A pdb=" N ALA A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.719A pdb=" N TRP A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 119 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 120 " --> pdb=" O VAL A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 115 through 120' Processing helix chain 'A' and resid 121 through 124 Processing helix chain 'A' and resid 125 through 156 removed outlier: 3.649A pdb=" N TYR A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 218 Processing helix chain 'A' and resid 233 through 253 Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 258 through 266 removed outlier: 3.873A pdb=" N VAL A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 281 removed outlier: 3.587A pdb=" N VAL A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.569A pdb=" N GLY A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.897A pdb=" N TRP A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.721A pdb=" N THR A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 372 removed outlier: 3.929A pdb=" N ASP A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 342 " --> pdb=" O CYS A 338 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 395 removed outlier: 4.555A pdb=" N TYR A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Proline residue: A 391 - end of helix Processing helix chain 'A' and resid 399 through 435 removed outlier: 3.804A pdb=" N TRP A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.692A pdb=" N LEU A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 459 Processing helix chain 'A' and resid 460 through 463 removed outlier: 3.777A pdb=" N SER A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 460 through 463' Processing helix chain 'A' and resid 465 through 477 removed outlier: 3.676A pdb=" N TRP A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 498 through 511 Processing helix chain 'A' and resid 515 through 540 removed outlier: 5.656A pdb=" N SER A 526 " --> pdb=" O TRP A 522 " (cutoff:3.500A) Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 552 through 568 removed outlier: 4.272A pdb=" N SER A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL A 567 " --> pdb=" O ALA A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 579 Processing helix chain 'A' and resid 585 through 595 removed outlier: 3.534A pdb=" N LYS A 595 " --> pdb=" O LYS A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 Processing sheet with id=AA1, first strand: chain 'A' and resid 545 through 546 273 hydrogen bonds defined for protein. 801 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: 0.40 Time building geometry restraints manager: 0.29 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: 1269 1.34 - 1.46: 1078 1.46 - 1.58: 2045 1.58 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 4445 Sorted by residual: bond pdb=" N GLY A 701 " pdb=" CA GLY A 701 " ideal model delta sigma weight residual 1.451 1.477 -0.026 1.60e-02 3.91e+03 2.62e+00 bond pdb=" N GLY A 610 " pdb=" CA GLY A 610 " ideal model delta sigma weight residual 1.449 1.468 -0.018 1.45e-02 4.76e+03 1.61e+00 bond pdb=" C TYR A 141 " pdb=" O TYR A 141 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.28e-02 6.10e+03 6.97e-01 bond pdb=" CA PHE A 268 " pdb=" C PHE A 268 " ideal model delta sigma weight residual 1.522 1.531 -0.009 1.26e-02 6.30e+03 5.51e-01 bond pdb=" CA ILE A 97 " pdb=" C ILE A 97 " ideal model delta sigma weight residual 1.520 1.526 -0.007 8.80e-03 1.29e+04 5.46e-01 ... (remaining 4440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 5931 1.55 - 3.11: 97 3.11 - 4.66: 28 4.66 - 6.21: 5 6.21 - 7.77: 1 Bond angle restraints: 6062 Sorted by residual: angle pdb=" C THR A 267 " pdb=" N PHE A 268 " pdb=" CA PHE A 268 " ideal model delta sigma weight residual 120.09 123.98 -3.89 1.25e+00 6.40e-01 9.69e+00 angle pdb=" O GLY A 701 " pdb=" C GLY A 701 " pdb=" OXT GLY A 701 " ideal model delta sigma weight residual 118.00 125.77 -7.77 3.00e+00 1.11e-01 6.70e+00 angle pdb=" C PRO A 73 " pdb=" N TYR A 74 " pdb=" CA TYR A 74 " ideal model delta sigma weight residual 121.14 117.03 4.11 1.75e+00 3.27e-01 5.53e+00 angle pdb=" C PRO A 398 " pdb=" N ILE A 399 " pdb=" CA ILE A 399 " ideal model delta sigma weight residual 121.97 125.99 -4.02 1.80e+00 3.09e-01 4.99e+00 angle pdb=" CA TYR A 74 " pdb=" CB TYR A 74 " pdb=" CG TYR A 74 " ideal model delta sigma weight residual 113.90 117.82 -3.92 1.80e+00 3.09e-01 4.74e+00 ... (remaining 6057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 2274 16.39 - 32.77: 191 32.77 - 49.16: 30 49.16 - 65.54: 6 65.54 - 81.93: 3 Dihedral angle restraints: 2504 sinusoidal: 942 harmonic: 1562 Sorted by residual: dihedral pdb=" CA PHE A 524 " pdb=" C PHE A 524 " pdb=" N VAL A 525 " pdb=" CA VAL A 525 " ideal model delta harmonic sigma weight residual -180.00 -157.65 -22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA TRP A 118 " pdb=" C TRP A 118 " pdb=" N ARG A 119 " pdb=" CA ARG A 119 " ideal model delta harmonic sigma weight residual 180.00 163.39 16.61 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB MET A 102 " pdb=" CG MET A 102 " pdb=" SD MET A 102 " pdb=" CE MET A 102 " ideal model delta sinusoidal sigma weight residual -60.00 -111.29 51.29 3 1.50e+01 4.44e-03 9.00e+00 ... (remaining 2501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 378 0.026 - 0.051: 174 0.051 - 0.077: 80 0.077 - 0.102: 29 0.102 - 0.128: 8 Chirality restraints: 669 Sorted by residual: chirality pdb=" CA PRO A 73 " pdb=" N PRO A 73 " pdb=" C PRO A 73 " pdb=" CB PRO A 73 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA VAL A 160 " pdb=" N VAL A 160 " pdb=" C VAL A 160 " pdb=" CB VAL A 160 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.33e-01 chirality pdb=" CA PRO A 122 " pdb=" N PRO A 122 " pdb=" C PRO A 122 " pdb=" CB PRO A 122 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.24e-01 ... (remaining 666 not shown) Planarity restraints: 744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 106 " -0.020 2.00e-02 2.50e+03 1.97e-02 6.77e+00 pdb=" CG PHE A 106 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 106 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 106 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 106 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 106 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 106 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 521 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C CYS A 521 " 0.032 2.00e-02 2.50e+03 pdb=" O CYS A 521 " -0.012 2.00e-02 2.50e+03 pdb=" N TRP A 522 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 355 " 0.013 2.00e-02 2.50e+03 9.92e-03 1.97e+00 pdb=" CG TYR A 355 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 355 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 355 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 355 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 355 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 355 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 355 " 0.002 2.00e-02 2.50e+03 ... (remaining 741 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1148 2.80 - 3.33: 3991 3.33 - 3.85: 7270 3.85 - 4.38: 8505 4.38 - 4.90: 14699 Nonbonded interactions: 35613 Sorted by model distance: nonbonded pdb=" OG SER A 597 " pdb=" OD1 ASP A 599 " model vdw 2.278 3.040 nonbonded pdb=" O PRO A 602 " pdb=" NH2 ARG A 608 " model vdw 2.278 3.120 nonbonded pdb=" O SER A 479 " pdb=" O HOH A 801 " model vdw 2.280 3.040 nonbonded pdb=" O TYR A 476 " pdb=" O HOH A 801 " model vdw 2.307 3.040 nonbonded pdb=" OE1 GLN A 52 " pdb=" NH2 ARG A 340 " model vdw 2.372 3.120 ... (remaining 35608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.00 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.030 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4446 Z= 0.132 Angle : 0.568 7.766 6064 Z= 0.305 Chirality : 0.038 0.128 669 Planarity : 0.004 0.033 744 Dihedral : 12.583 81.926 1513 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 1.63 (0.36), residues: 538 helix: 2.12 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -1.16 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 71 TYR 0.024 0.002 TYR A 355 PHE 0.045 0.002 PHE A 106 TRP 0.015 0.001 TRP A 215 HIS 0.002 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 ( 4445) covalent geometry : angle 0.56781 / 0.30 ( 6062) SS BOND : bond 0.00235 / 0.12 ( 1) SS BOND : angle 0.95539 / 0.53 ( 2) hydrogen bonds : bond 0.14329 / 9.17 ( 273) hydrogen bonds : angle 5.11487 / 3.63 ( 801) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.098 Fit side-chains REVERT: A 212 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7561 (tp30) REVERT: A 260 LYS cc_start: 0.7546 (mttm) cc_final: 0.6799 (mmpt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.4603 time to fit residues: 36.7382 Evaluate side-chains 65 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.147991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128519 restraints weight = 4243.478| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.20 r_work: 0.3371 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4446 Z= 0.153 Angle : 0.570 6.115 6064 Z= 0.306 Chirality : 0.040 0.127 669 Planarity : 0.005 0.040 744 Dihedral : 4.019 22.656 594 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.32 % Allowed : 7.03 % Favored : 91.65 % 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: 1.61 (0.36), residues: 538 helix: 2.07 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.30 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 608 TYR 0.025 0.002 TYR A 74 PHE 0.042 0.002 PHE A 106 TRP 0.019 0.001 TRP A 215 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 ( 4445) covalent geometry : angle 0.56966 / 0.31 ( 6062) SS BOND : bond 0.00578 / 0.30 ( 1) SS BOND : angle 1.11701 / 0.61 ( 2) hydrogen bonds : bond 0.06899 / 4.43 ( 273) hydrogen bonds : angle 4.04259 / 2.84 ( 801) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.109 Fit side-chains REVERT: A 507 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: A 606 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7299 (pm20) outliers start: 6 outliers final: 2 residues processed: 61 average time/residue: 0.4545 time to fit residues: 28.8134 Evaluate side-chains 59 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 44 optimal weight: 0.0060 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 607 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.158172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.142851 restraints weight = 4248.915| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 0.88 r_work: 0.3480 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4446 Z= 0.131 Angle : 0.528 6.044 6064 Z= 0.281 Chirality : 0.039 0.126 669 Planarity : 0.005 0.041 744 Dihedral : 3.904 22.929 594 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.98 % Allowed : 7.91 % Favored : 90.11 % 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: 1.80 (0.37), residues: 538 helix: 2.23 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.29 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 608 TYR 0.022 0.002 TYR A 74 PHE 0.029 0.002 PHE A 106 TRP 0.017 0.001 TRP A 215 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 4445) covalent geometry : angle 0.52756 / 0.28 ( 6062) SS BOND : bond 0.00455 / 0.24 ( 1) SS BOND : angle 0.95303 / 0.53 ( 2) hydrogen bonds : bond 0.06195 / 3.97 ( 273) hydrogen bonds : angle 3.90227 / 2.74 ( 801) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 507 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: A 550 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7082 (mm-40) REVERT: A 606 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7432 (pm20) outliers start: 9 outliers final: 4 residues processed: 65 average time/residue: 0.4788 time to fit residues: 32.3065 Evaluate side-chains 67 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 0.0770 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.153787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.135378 restraints weight = 4293.118| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.14 r_work: 0.3484 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4446 Z= 0.133 Angle : 0.528 6.127 6064 Z= 0.281 Chirality : 0.039 0.128 669 Planarity : 0.005 0.041 744 Dihedral : 3.890 22.962 594 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.98 % Allowed : 8.79 % Favored : 89.23 % 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: 1.84 (0.37), residues: 538 helix: 2.25 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -1.28 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 233 TYR 0.022 0.002 TYR A 74 PHE 0.022 0.002 PHE A 106 TRP 0.017 0.001 TRP A 215 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 4445) covalent geometry : angle 0.52773 / 0.28 ( 6062) SS BOND : bond 0.00459 / 0.24 ( 1) SS BOND : angle 0.91370 / 0.50 ( 2) hydrogen bonds : bond 0.06217 / 4.00 ( 273) hydrogen bonds : angle 3.87896 / 2.72 ( 801) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 507 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: A 550 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.6960 (mm-40) outliers start: 9 outliers final: 4 residues processed: 64 average time/residue: 0.4331 time to fit residues: 28.8417 Evaluate side-chains 65 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 550 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 0.0670 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.0570 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.158484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.142876 restraints weight = 4279.211| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 0.90 r_work: 0.3489 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4446 Z= 0.123 Angle : 0.505 6.004 6064 Z= 0.268 Chirality : 0.038 0.123 669 Planarity : 0.004 0.040 744 Dihedral : 3.807 22.885 594 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.10 % Allowed : 10.77 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.37), residues: 538 helix: 2.37 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -1.27 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 608 TYR 0.020 0.001 TYR A 74 PHE 0.016 0.001 PHE A 106 TRP 0.015 0.001 TRP A 215 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 ( 4445) covalent geometry : angle 0.50508 / 0.27 ( 6062) SS BOND : bond 0.00384 / 0.20 ( 1) SS BOND : angle 0.81384 / 0.45 ( 2) hydrogen bonds : bond 0.05739 / 3.69 ( 273) hydrogen bonds : angle 3.80565 / 2.67 ( 801) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.100 Fit side-chains REVERT: A 507 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: A 550 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7105 (mm-40) REVERT: A 606 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7196 (pm20) outliers start: 5 outliers final: 2 residues processed: 63 average time/residue: 0.4336 time to fit residues: 28.4125 Evaluate side-chains 60 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.148538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.130124 restraints weight = 4345.309| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.13 r_work: 0.3383 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4446 Z= 0.216 Angle : 0.672 6.302 6064 Z= 0.362 Chirality : 0.045 0.147 669 Planarity : 0.006 0.049 744 Dihedral : 4.336 23.437 594 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.42 % Allowed : 9.45 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.36), residues: 538 helix: 1.91 (0.26), residues: 369 sheet: None (None), residues: 0 loop : -1.48 (0.45), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 233 TYR 0.026 0.003 TYR A 74 PHE 0.028 0.003 PHE A 106 TRP 0.023 0.002 TRP A 215 HIS 0.007 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 ( 4445) covalent geometry : angle 0.67128 / 0.36 ( 6062) SS BOND : bond 0.01048 / 0.55 ( 1) SS BOND : angle 1.61274 / 0.88 ( 2) hydrogen bonds : bond 0.08798 / 5.68 ( 273) hydrogen bonds : angle 4.14711 / 2.92 ( 801) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.135 Fit side-chains REVERT: A 71 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7902 (ttt-90) REVERT: A 507 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: A 550 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7074 (mm-40) REVERT: A 606 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7065 (pm20) outliers start: 11 outliers final: 6 residues processed: 68 average time/residue: 0.4573 time to fit residues: 32.3133 Evaluate side-chains 72 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.152895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.134590 restraints weight = 4314.579| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.13 r_work: 0.3477 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4446 Z= 0.136 Angle : 0.536 6.202 6064 Z= 0.285 Chirality : 0.039 0.127 669 Planarity : 0.005 0.043 744 Dihedral : 3.978 23.439 594 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.42 % Allowed : 10.11 % Favored : 87.47 % 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: 1.73 (0.37), residues: 538 helix: 2.20 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.36 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 377 TYR 0.020 0.002 TYR A 74 PHE 0.014 0.001 PHE A 106 TRP 0.016 0.001 TRP A 215 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 ( 4445) covalent geometry : angle 0.53551 / 0.28 ( 6062) SS BOND : bond 0.00476 / 0.25 ( 1) SS BOND : angle 1.01961 / 0.57 ( 2) hydrogen bonds : bond 0.06408 / 4.12 ( 273) hydrogen bonds : angle 3.93132 / 2.76 ( 801) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 402 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7046 (tp) REVERT: A 507 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: A 550 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.6995 (mm-40) REVERT: A 606 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7013 (pm20) outliers start: 11 outliers final: 5 residues processed: 65 average time/residue: 0.4482 time to fit residues: 30.3687 Evaluate side-chains 69 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.151050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.132544 restraints weight = 4323.695| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.14 r_work: 0.3453 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4446 Z= 0.154 Angle : 0.566 6.182 6064 Z= 0.303 Chirality : 0.040 0.133 669 Planarity : 0.005 0.045 744 Dihedral : 4.052 23.392 594 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.98 % Allowed : 10.55 % Favored : 87.47 % 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: 1.66 (0.36), residues: 538 helix: 2.15 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.38 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 233 TYR 0.023 0.002 TYR A 74 PHE 0.017 0.002 PHE A 106 TRP 0.018 0.002 TRP A 215 HIS 0.005 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 4445) covalent geometry : angle 0.56568 / 0.30 ( 6062) SS BOND : bond 0.00602 / 0.32 ( 1) SS BOND : angle 1.11466 / 0.61 ( 2) hydrogen bonds : bond 0.07037 / 4.53 ( 273) hydrogen bonds : angle 3.97333 / 2.79 ( 801) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: A 507 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: A 550 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7028 (mm-40) REVERT: A 606 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.6986 (pm20) outliers start: 9 outliers final: 6 residues processed: 64 average time/residue: 0.5000 time to fit residues: 33.2861 Evaluate side-chains 70 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.151620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133141 restraints weight = 4356.237| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.15 r_work: 0.3460 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4446 Z= 0.149 Angle : 0.559 6.144 6064 Z= 0.298 Chirality : 0.040 0.130 669 Planarity : 0.005 0.045 744 Dihedral : 4.023 23.424 594 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.42 % Allowed : 10.11 % Favored : 87.47 % 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: 1.68 (0.36), residues: 538 helix: 2.17 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.39 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 233 TYR 0.022 0.002 TYR A 74 PHE 0.016 0.002 PHE A 106 TRP 0.017 0.001 TRP A 215 HIS 0.005 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 ( 4445) covalent geometry : angle 0.55893 / 0.30 ( 6062) SS BOND : bond 0.00562 / 0.30 ( 1) SS BOND : angle 1.06655 / 0.59 ( 2) hydrogen bonds : bond 0.06857 / 4.41 ( 273) hydrogen bonds : angle 3.96130 / 2.78 ( 801) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 402 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.7034 (tp) REVERT: A 507 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: A 550 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7022 (mm-40) REVERT: A 606 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.6988 (pm20) outliers start: 11 outliers final: 6 residues processed: 66 average time/residue: 0.4893 time to fit residues: 33.6269 Evaluate side-chains 72 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.151475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.132988 restraints weight = 4329.510| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.14 r_work: 0.3459 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4446 Z= 0.149 Angle : 0.556 6.132 6064 Z= 0.297 Chirality : 0.040 0.130 669 Planarity : 0.005 0.045 744 Dihedral : 4.030 23.396 594 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.20 % Allowed : 10.11 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.68 (0.36), residues: 538 helix: 2.17 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.39 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 233 TYR 0.022 0.002 TYR A 74 PHE 0.016 0.002 PHE A 106 TRP 0.018 0.001 TRP A 215 HIS 0.005 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 ( 4445) covalent geometry : angle 0.55562 / 0.30 ( 6062) SS BOND : bond 0.00559 / 0.29 ( 1) SS BOND : angle 1.07033 / 0.59 ( 2) hydrogen bonds : bond 0.06865 / 4.41 ( 273) hydrogen bonds : angle 3.96588 / 2.78 ( 801) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: A 402 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7028 (tp) REVERT: A 507 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: A 550 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7027 (mm-40) REVERT: A 606 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.6982 (pm20) outliers start: 10 outliers final: 6 residues processed: 65 average time/residue: 0.4713 time to fit residues: 31.8143 Evaluate side-chains 71 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 606 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 11 optimal weight: 0.0770 chunk 2 optimal weight: 0.9980 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.154416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.135969 restraints weight = 4365.187| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.15 r_work: 0.3493 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4446 Z= 0.126 Angle : 0.522 6.861 6064 Z= 0.275 Chirality : 0.039 0.119 669 Planarity : 0.005 0.042 744 Dihedral : 3.863 23.180 594 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.98 % Allowed : 10.33 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.88 (0.37), residues: 538 helix: 2.29 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -1.29 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 611 TYR 0.019 0.001 TYR A 74 PHE 0.012 0.001 PHE A 106 TRP 0.015 0.001 TRP A 215 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 ( 4445) covalent geometry : angle 0.52141 / 0.27 ( 6062) SS BOND : bond 0.00371 / 0.20 ( 1) SS BOND : angle 0.86058 / 0.47 ( 2) hydrogen bonds : bond 0.05912 / 3.79 ( 273) hydrogen bonds : angle 3.86788 / 2.71 ( 801) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1425.82 seconds wall clock time: 25 minutes 0.21 seconds (1500.21 seconds total)