Starting phenix.real_space_refine on Sat May 10 00:34:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wfi_37492/05_2025/8wfi_37492.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wfi_37492/05_2025/8wfi_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wfi_37492/05_2025/8wfi_37492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wfi_37492/05_2025/8wfi_37492.map" model { file = "/net/cci-nas-00/data/ceres_data/8wfi_37492/05_2025/8wfi_37492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wfi_37492/05_2025/8wfi_37492.cif" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 40 Unusual residues: {' CL': 1, ' NA': 2} Classifications: {'undetermined': 3, 'water': 37} Link IDs: {None: 39} 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: 3.47, per 1000 atoms: 0.80 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: 0.97 Conformation dependent library (CDL) restraints added in 471.0 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: 0.39 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: 1.11 Time building geometry restraints manager: 1.16 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.060 Find NCS groups from input model: 0.050 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:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (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 TRP 0.015 0.001 TRP A 215 HIS 0.002 0.001 HIS A 499 PHE 0.045 0.002 PHE A 106 TYR 0.024 0.002 TYR A 355 ARG 0.006 0.001 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.14329 ( 273) hydrogen bonds : angle 5.11487 ( 801) SS BOND : bond 0.00235 ( 1) SS BOND : angle 0.95539 ( 2) covalent geometry : bond 0.00244 ( 4445) covalent geometry : angle 0.56781 ( 6062) *********************** 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 : 0.464 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: 1.1432 time to fit residues: 91.6228 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 : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.0370 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.0870 chunk 42 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.150110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.130842 restraints weight = 4205.352| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.18 r_work: 0.3401 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0825 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= 0.131 Angle : 0.528 5.989 6064 Z= 0.282 Chirality : 0.039 0.123 669 Planarity : 0.005 0.039 744 Dihedral : 3.926 22.422 594 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.10 % Allowed : 6.59 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.37), residues: 538 helix: 2.21 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.24 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 215 HIS 0.003 0.001 HIS A 499 PHE 0.036 0.002 PHE A 106 TYR 0.024 0.002 TYR A 74 ARG 0.003 0.000 ARG A 608 Details of bonding type rmsd hydrogen bonds : bond 0.06045 ( 273) hydrogen bonds : angle 3.95234 ( 801) SS BOND : bond 0.00422 ( 1) SS BOND : angle 0.85404 ( 2) covalent geometry : bond 0.00249 ( 4445) covalent geometry : angle 0.52772 ( 6062) *********************** 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: 5 poor density : 60 time to evaluate : 0.428 Fit side-chains REVERT: A 507 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: A 606 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7293 (pm20) outliers start: 5 outliers final: 1 residues processed: 62 average time/residue: 1.2266 time to fit residues: 78.9276 Evaluate side-chains 60 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 606 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 24 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.158741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143288 restraints weight = 4219.296| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 0.88 r_work: 0.3489 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0976 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= 0.128 Angle : 0.522 6.067 6064 Z= 0.277 Chirality : 0.039 0.125 669 Planarity : 0.005 0.041 744 Dihedral : 3.886 22.755 594 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.76 % Allowed : 7.91 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.37), residues: 538 helix: 2.32 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.28 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 215 HIS 0.004 0.001 HIS A 499 PHE 0.029 0.002 PHE A 106 TYR 0.022 0.002 TYR A 74 ARG 0.002 0.000 ARG A 608 Details of bonding type rmsd hydrogen bonds : bond 0.05996 ( 273) hydrogen bonds : angle 3.86915 ( 801) SS BOND : bond 0.00422 ( 1) SS BOND : angle 0.87001 ( 2) covalent geometry : bond 0.00248 ( 4445) covalent geometry : angle 0.52203 ( 6062) *********************** 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 68 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.462 Fit side-chains REVERT: A 507 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: A 550 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7077 (mm-40) REVERT: A 606 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7423 (pm20) outliers start: 8 outliers final: 4 residues processed: 62 average time/residue: 1.1693 time to fit residues: 75.4679 Evaluate side-chains 65 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.157354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.141839 restraints weight = 4278.533| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 0.89 r_work: 0.3475 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1068 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= 0.134 Angle : 0.529 5.957 6064 Z= 0.282 Chirality : 0.039 0.127 669 Planarity : 0.005 0.041 744 Dihedral : 3.910 22.917 594 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.76 % Allowed : 9.45 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.37), residues: 538 helix: 2.33 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.28 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 215 HIS 0.004 0.001 HIS A 499 PHE 0.025 0.002 PHE A 106 TYR 0.022 0.002 TYR A 74 ARG 0.002 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.06239 ( 273) hydrogen bonds : angle 3.87906 ( 801) SS BOND : bond 0.00486 ( 1) SS BOND : angle 0.94237 ( 2) covalent geometry : bond 0.00266 ( 4445) covalent geometry : angle 0.52900 ( 6062) *********************** 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: 8 poor density : 61 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 507 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: A 550 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7100 (mm-40) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 1.2534 time to fit residues: 84.6041 Evaluate side-chains 63 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 31 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 17 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.156828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.141265 restraints weight = 4319.605| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 0.89 r_work: 0.3469 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 : 0.003 0.030 4446 Z= 0.134 Angle : 0.529 6.070 6064 Z= 0.281 Chirality : 0.039 0.128 669 Planarity : 0.005 0.042 744 Dihedral : 3.905 23.003 594 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.76 % Allowed : 10.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.37), residues: 538 helix: 2.35 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.26 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 215 HIS 0.004 0.001 HIS A 499 PHE 0.020 0.002 PHE A 106 TYR 0.022 0.002 TYR A 74 ARG 0.002 0.000 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.06200 ( 273) hydrogen bonds : angle 3.86892 ( 801) SS BOND : bond 0.00475 ( 1) SS BOND : angle 0.93067 ( 2) covalent geometry : bond 0.00266 ( 4445) covalent geometry : angle 0.52910 ( 6062) *********************** 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 67 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 507 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: A 550 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7125 (mm-40) REVERT: A 606 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7195 (pm20) outliers start: 8 outliers final: 4 residues processed: 62 average time/residue: 1.1533 time to fit residues: 74.4813 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 : 0.496 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.150928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.132365 restraints weight = 4321.368| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.14 r_work: 0.3450 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1204 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= 0.155 Angle : 0.568 6.114 6064 Z= 0.303 Chirality : 0.041 0.134 669 Planarity : 0.005 0.045 744 Dihedral : 4.052 23.204 594 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.98 % Allowed : 10.11 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.37), residues: 538 helix: 2.24 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.31 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 215 HIS 0.005 0.001 HIS A 499 PHE 0.021 0.002 PHE A 106 TYR 0.023 0.002 TYR A 74 ARG 0.003 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.07027 ( 273) hydrogen bonds : angle 3.96358 ( 801) SS BOND : bond 0.00636 ( 1) SS BOND : angle 1.12511 ( 2) covalent geometry : bond 0.00322 ( 4445) covalent geometry : angle 0.56790 ( 6062) *********************** 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 69 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 507 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: A 550 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7050 (mm-40) REVERT: A 606 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7016 (pm20) outliers start: 9 outliers final: 5 residues processed: 64 average time/residue: 1.1625 time to fit residues: 77.5262 Evaluate side-chains 66 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 12 optimal weight: 0.0970 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.158616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.140783 restraints weight = 4260.345| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.10 r_work: 0.3498 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1188 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= 0.119 Angle : 0.498 5.975 6064 Z= 0.263 Chirality : 0.038 0.117 669 Planarity : 0.004 0.041 744 Dihedral : 3.806 23.102 594 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.98 % Allowed : 10.11 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.37), residues: 538 helix: 2.46 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.20 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 215 HIS 0.003 0.001 HIS A 499 PHE 0.012 0.001 PHE A 106 TYR 0.018 0.001 TYR A 74 ARG 0.002 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.05495 ( 273) hydrogen bonds : angle 3.81307 ( 801) SS BOND : bond 0.00333 ( 1) SS BOND : angle 0.77082 ( 2) covalent geometry : bond 0.00224 ( 4445) covalent geometry : angle 0.49740 ( 6062) *********************** 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: 9 poor density : 62 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6185 (ppt-90) REVERT: A 402 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6936 (tp) REVERT: A 507 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: A 550 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.6989 (mm-40) REVERT: A 606 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7046 (pm20) outliers start: 9 outliers final: 2 residues processed: 67 average time/residue: 1.1467 time to fit residues: 79.9156 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 : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 377 ARG 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 12 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.152163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.133615 restraints weight = 4286.281| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.14 r_work: 0.3459 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1229 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= 0.143 Angle : 0.544 6.010 6064 Z= 0.290 Chirality : 0.040 0.129 669 Planarity : 0.005 0.044 744 Dihedral : 3.961 23.075 594 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.76 % Allowed : 10.33 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.37), residues: 538 helix: 2.28 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -1.22 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 215 HIS 0.005 0.001 HIS A 499 PHE 0.017 0.002 PHE A 106 TYR 0.022 0.002 TYR A 74 ARG 0.003 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.06546 ( 273) hydrogen bonds : angle 3.89907 ( 801) SS BOND : bond 0.00553 ( 1) SS BOND : angle 0.99431 ( 2) covalent geometry : bond 0.00293 ( 4445) covalent geometry : angle 0.54347 ( 6062) *********************** 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: 8 poor density : 62 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6219 (ppt-90) REVERT: A 507 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: A 550 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7021 (mm-40) REVERT: A 606 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.6993 (pm20) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 1.2417 time to fit residues: 83.9322 Evaluate side-chains 66 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 377 ARG 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 52 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.150627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132028 restraints weight = 4363.538| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.14 r_work: 0.3443 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1277 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= 0.157 Angle : 0.574 6.140 6064 Z= 0.306 Chirality : 0.041 0.134 669 Planarity : 0.005 0.045 744 Dihedral : 4.085 23.309 594 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.42 % Allowed : 9.67 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.36), residues: 538 helix: 2.21 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.31 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 215 HIS 0.005 0.001 HIS A 499 PHE 0.019 0.002 PHE A 106 TYR 0.023 0.002 TYR A 74 ARG 0.003 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.07115 ( 273) hydrogen bonds : angle 3.97412 ( 801) SS BOND : bond 0.00638 ( 1) SS BOND : angle 1.08892 ( 2) covalent geometry : bond 0.00329 ( 4445) covalent geometry : angle 0.57376 ( 6062) *********************** 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 74 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.6217 (ppt-90) REVERT: A 507 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: A 550 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7053 (mm-40) REVERT: A 606 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.6996 (pm20) outliers start: 11 outliers final: 6 residues processed: 69 average time/residue: 1.1193 time to fit residues: 80.4986 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 : 0.468 ------------------------------------------------------------------------------- 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 374 ASP Chi-restraints excluded: chain A residue 377 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 25 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.0020 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.154109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.135689 restraints weight = 4296.479| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.14 r_work: 0.3490 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1226 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= 0.125 Angle : 0.513 5.998 6064 Z= 0.272 Chirality : 0.039 0.121 669 Planarity : 0.004 0.042 744 Dihedral : 3.879 23.234 594 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.76 % Allowed : 10.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.37), residues: 538 helix: 2.35 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -1.21 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 215 HIS 0.004 0.001 HIS A 499 PHE 0.013 0.001 PHE A 106 TYR 0.019 0.001 TYR A 74 ARG 0.002 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.05827 ( 273) hydrogen bonds : angle 3.85706 ( 801) SS BOND : bond 0.00376 ( 1) SS BOND : angle 0.83695 ( 2) covalent geometry : bond 0.00240 ( 4445) covalent geometry : angle 0.51326 ( 6062) ********************** 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 70 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 507 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: A 550 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.6987 (mm-40) REVERT: A 606 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7004 (pm20) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 1.1154 time to fit residues: 75.6168 Evaluate side-chains 68 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.152095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.133572 restraints weight = 4336.248| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.13 r_work: 0.3463 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1262 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= 0.144 Angle : 0.552 6.333 6064 Z= 0.293 Chirality : 0.040 0.119 669 Planarity : 0.005 0.044 744 Dihedral : 3.980 23.140 594 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.98 % Allowed : 10.11 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.37), residues: 538 helix: 2.26 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -1.24 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 215 HIS 0.005 0.001 HIS A 499 PHE 0.016 0.002 PHE A 106 TYR 0.014 0.002 TYR A 74 ARG 0.002 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.06580 ( 273) hydrogen bonds : angle 3.91114 ( 801) SS BOND : bond 0.00529 ( 1) SS BOND : angle 0.97662 ( 2) covalent geometry : bond 0.00294 ( 4445) covalent geometry : angle 0.55224 ( 6062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3381.77 seconds wall clock time: 58 minutes 59.41 seconds (3539.41 seconds total)