Starting phenix.real_space_refine on Fri Aug 22 14:46:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wfi_37492/08_2025/8wfi_37492.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wfi_37492/08_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_37492/08_2025/8wfi_37492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wfi_37492/08_2025/8wfi_37492.map" model { file = "/net/cci-nas-00/data/ceres_data/8wfi_37492/08_2025/8wfi_37492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wfi_37492/08_2025/8wfi_37492.cif" } 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-2.0-5787/lib/python3.9/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, 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: 1.20, per 1000 atoms: 0.28 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: 0.28 Conformation dependent library (CDL) restraints added in 157.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.12 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: 0.64 Time building geometry restraints manager: 0.41 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: 2.000 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.610 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.610 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00244 ( 4445) covalent geometry : angle 0.56781 ( 6062) SS BOND : bond 0.00235 ( 1) SS BOND : angle 0.95539 ( 2) hydrogen bonds : bond 0.14329 ( 273) hydrogen bonds : angle 5.11487 ( 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 : 0.121 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: 0.4888 time to fit residues: 38.9475 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 : 0.160 ------------------------------------------------------------------------------- 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: 0.9990 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: 2.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.146908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128179 restraints weight = 4253.140| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.10 r_work: 0.3368 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.0888 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= 0.152 Angle : 0.570 6.077 6064 Z= 0.306 Chirality : 0.040 0.128 669 Planarity : 0.005 0.041 744 Dihedral : 4.088 22.700 594 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.54 % Allowed : 7.47 % Favored : 90.99 % 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 aren 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 355 PHE 0.042 0.002 PHE A 106 TRP 0.020 0.001 TRP A 215 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4445) covalent geometry : angle 0.56973 ( 6062) SS BOND : bond 0.00617 ( 1) SS BOND : angle 1.12570 ( 2) hydrogen bonds : bond 0.06919 ( 273) hydrogen bonds : angle 4.03798 ( 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 66 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.112 Fit side-chains REVERT: A 507 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: A 550 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.6896 (mm-40) REVERT: A 606 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7348 (pm20) outliers start: 7 outliers final: 2 residues processed: 61 average time/residue: 0.4986 time to fit residues: 31.6475 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 : 0.099 ------------------------------------------------------------------------------- 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 550 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 26 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.0050 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.146781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127412 restraints weight = 4254.238| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.18 r_work: 0.3361 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1031 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= 0.142 Angle : 0.548 6.393 6064 Z= 0.293 Chirality : 0.039 0.131 669 Planarity : 0.005 0.043 744 Dihedral : 4.013 23.045 594 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.98 % Allowed : 7.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.37), residues: 538 helix: 2.17 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.33 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 608 TYR 0.023 0.002 TYR A 74 PHE 0.030 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 covalent geometry : bond 0.00282 ( 4445) covalent geometry : angle 0.54741 ( 6062) SS BOND : bond 0.00544 ( 1) SS BOND : angle 1.06658 ( 2) hydrogen bonds : bond 0.06654 ( 273) hydrogen bonds : angle 3.95506 ( 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 70 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 507 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: A 550 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.6919 (mm-40) REVERT: A 606 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7289 (pm20) outliers start: 9 outliers final: 4 residues processed: 64 average time/residue: 0.5690 time to fit residues: 37.6955 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 : 0.103 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.153889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.138407 restraints weight = 4224.329| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 0.87 r_work: 0.3434 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1190 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= 0.163 Angle : 0.588 6.292 6064 Z= 0.315 Chirality : 0.041 0.137 669 Planarity : 0.005 0.045 744 Dihedral : 4.141 23.271 594 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.42 % Allowed : 8.35 % 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 aren not related in a simple way. whole: 1.62 (0.36), residues: 538 helix: 2.11 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.38 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 233 TYR 0.024 0.002 TYR A 74 PHE 0.026 0.002 PHE A 106 TRP 0.019 0.002 TRP A 215 HIS 0.006 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 4445) covalent geometry : angle 0.58734 ( 6062) SS BOND : bond 0.00692 ( 1) SS BOND : angle 1.25627 ( 2) hydrogen bonds : bond 0.07373 ( 273) hydrogen bonds : angle 4.01637 ( 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: 11 poor density : 58 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 507 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: A 550 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7147 (mm-40) outliers start: 11 outliers final: 6 residues processed: 64 average time/residue: 0.5131 time to fit residues: 34.2171 Evaluate side-chains 65 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 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 242 VAL 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 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: 0.8980 chunk 42 optimal weight: 0.0770 chunk 5 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.0000 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 overall best weight: 0.4342 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.154503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.136087 restraints weight = 4351.121| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.15 r_work: 0.3492 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1137 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= 0.123 Angle : 0.510 6.268 6064 Z= 0.270 Chirality : 0.038 0.122 669 Planarity : 0.004 0.041 744 Dihedral : 3.871 23.173 594 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.37), residues: 538 helix: 2.36 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.24 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 377 TYR 0.019 0.001 TYR A 74 PHE 0.013 0.001 PHE A 106 TRP 0.015 0.001 TRP A 215 HIS 0.003 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 4445) covalent geometry : angle 0.50958 ( 6062) SS BOND : bond 0.00354 ( 1) SS BOND : angle 0.84166 ( 2) hydrogen bonds : bond 0.05779 ( 273) hydrogen bonds : angle 3.85098 ( 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 67 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6195 (ppt-90) REVERT: A 402 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6917 (tp) REVERT: A 507 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: A 606 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7020 (pm20) outliers start: 8 outliers final: 2 residues processed: 63 average time/residue: 0.5513 time to fit residues: 36.0517 Evaluate side-chains 66 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 377 ARG Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 507 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: 0.5980 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.148879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130174 restraints weight = 4419.713| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.16 r_work: 0.3423 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4446 Z= 0.182 Angle : 0.613 6.282 6064 Z= 0.330 Chirality : 0.043 0.142 669 Planarity : 0.005 0.047 744 Dihedral : 4.213 23.364 594 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.64 % Allowed : 9.67 % 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 aren not related in a simple way. whole: 1.58 (0.36), residues: 538 helix: 2.09 (0.26), residues: 369 sheet: None (None), residues: 0 loop : -1.38 (0.46), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 233 TYR 0.025 0.002 TYR A 74 PHE 0.021 0.002 PHE A 106 TRP 0.020 0.002 TRP A 215 HIS 0.006 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 4445) covalent geometry : angle 0.61274 ( 6062) SS BOND : bond 0.00815 ( 1) SS BOND : angle 1.36867 ( 2) hydrogen bonds : bond 0.07900 ( 273) hydrogen bonds : angle 4.04501 ( 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 76 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.131 Fit side-chains REVERT: A 71 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7871 (ttt-90) REVERT: A 507 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: A 550 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7067 (mm-40) REVERT: A 606 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7004 (pm20) outliers start: 12 outliers final: 7 residues processed: 69 average time/residue: 0.4930 time to fit residues: 35.3828 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 : 0.098 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 25 optimal weight: 0.0980 chunk 46 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 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 = 0.3762 r_free = 0.3762 target = 0.156164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.140838 restraints weight = 4245.314| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 0.87 r_work: 0.3457 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1206 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 : 0.539 6.232 6064 Z= 0.286 Chirality : 0.039 0.127 669 Planarity : 0.005 0.043 744 Dihedral : 3.997 23.429 594 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.42 % Allowed : 9.89 % 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 aren not related in a simple way. whole: 1.81 (0.37), residues: 538 helix: 2.25 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.31 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 233 TYR 0.021 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 covalent geometry : bond 0.00269 ( 4445) covalent geometry : angle 0.53885 ( 6062) SS BOND : bond 0.00472 ( 1) SS BOND : angle 0.98042 ( 2) hydrogen bonds : bond 0.06439 ( 273) hydrogen bonds : angle 3.92077 ( 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 74 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6291 (ppt-90) REVERT: A 402 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7197 (tp) REVERT: A 507 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: A 550 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7173 (mm-40) REVERT: A 606 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7175 (pm20) outliers start: 11 outliers final: 5 residues processed: 67 average time/residue: 0.4838 time to fit residues: 33.7204 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 : 0.156 ------------------------------------------------------------------------------- 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 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 22 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.150944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.132353 restraints weight = 4331.559| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.15 r_work: 0.3453 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1233 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= 0.150 Angle : 0.559 6.151 6064 Z= 0.299 Chirality : 0.040 0.131 669 Planarity : 0.005 0.045 744 Dihedral : 4.063 23.385 594 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.20 % Allowed : 10.55 % Favored : 87.25 % 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 aren not related in a simple way. whole: 1.72 (0.36), residues: 538 helix: 2.19 (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 233 TYR 0.022 0.002 TYR A 74 PHE 0.015 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 covalent geometry : bond 0.00307 ( 4445) covalent geometry : angle 0.55878 ( 6062) SS BOND : bond 0.00583 ( 1) SS BOND : angle 1.10139 ( 2) hydrogen bonds : bond 0.06920 ( 273) hydrogen bonds : angle 3.95808 ( 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 72 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 377 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6224 (ppt-90) REVERT: A 402 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7024 (tp) REVERT: A 507 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: A 550 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7025 (mm-40) REVERT: A 606 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.6967 (pm20) outliers start: 10 outliers final: 4 residues processed: 65 average time/residue: 0.4813 time to fit residues: 32.4884 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 : 0.153 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.0030 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.157006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.141608 restraints weight = 4280.602| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 0.88 r_work: 0.3473 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1207 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= 0.132 Angle : 0.531 6.103 6064 Z= 0.281 Chirality : 0.039 0.123 669 Planarity : 0.005 0.043 744 Dihedral : 3.934 23.290 594 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.20 % Allowed : 10.77 % Favored : 87.03 % 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 aren not related in a simple way. whole: 1.86 (0.37), residues: 538 helix: 2.28 (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 0.020 0.002 TYR A 74 PHE 0.012 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 covalent geometry : bond 0.00258 ( 4445) covalent geometry : angle 0.53064 ( 6062) SS BOND : bond 0.00421 ( 1) SS BOND : angle 0.94504 ( 2) hydrogen bonds : bond 0.06205 ( 273) hydrogen bonds : angle 3.88950 ( 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 70 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: A 402 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7161 (tp) REVERT: A 507 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8122 (tt0) REVERT: A 550 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7147 (mm-40) REVERT: A 606 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7145 (pm20) outliers start: 10 outliers final: 4 residues processed: 64 average time/residue: 0.4953 time to fit residues: 32.7935 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 : 0.112 ------------------------------------------------------------------------------- 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 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: 0.0030 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 44 optimal weight: 0.0670 chunk 28 optimal weight: 4.9990 overall best weight: 0.4930 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.154048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.135571 restraints weight = 4335.421| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.14 r_work: 0.3490 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1198 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 : 0.514 6.060 6064 Z= 0.273 Chirality : 0.039 0.121 669 Planarity : 0.005 0.043 744 Dihedral : 3.866 23.093 594 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.98 % Allowed : 10.77 % Favored : 87.25 % 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 aren not related in a simple way. whole: 1.96 (0.37), residues: 538 helix: 2.35 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -1.26 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 377 TYR 0.019 0.001 TYR A 74 PHE 0.011 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 covalent geometry : bond 0.00243 ( 4445) covalent geometry : angle 0.51414 ( 6062) SS BOND : bond 0.00384 ( 1) SS BOND : angle 0.87036 ( 2) hydrogen bonds : bond 0.05847 ( 273) hydrogen bonds : angle 3.83588 ( 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: 9 poor density : 63 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 402 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6935 (tp) REVERT: A 507 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: A 550 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.6987 (mm-40) REVERT: A 606 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7020 (pm20) outliers start: 9 outliers final: 5 residues processed: 66 average time/residue: 0.4366 time to fit residues: 29.9518 Evaluate side-chains 68 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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 378 VAL 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: 1.9990 chunk 26 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 11 optimal weight: 0.0270 chunk 2 optimal weight: 0.6980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.154450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135729 restraints weight = 4377.764| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.17 r_work: 0.3494 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1234 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= 0.124 Angle : 0.512 5.952 6064 Z= 0.271 Chirality : 0.038 0.117 669 Planarity : 0.004 0.043 744 Dihedral : 3.839 22.926 594 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.76 % Allowed : 10.99 % Favored : 87.25 % 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 aren not related in a simple way. whole: 1.99 (0.37), residues: 538 helix: 2.38 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -1.25 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 377 TYR 0.013 0.001 TYR A 74 PHE 0.010 0.001 PHE A 366 TRP 0.015 0.001 TRP A 215 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 4445) covalent geometry : angle 0.51173 ( 6062) SS BOND : bond 0.00368 ( 1) SS BOND : angle 0.86235 ( 2) hydrogen bonds : bond 0.05758 ( 273) hydrogen bonds : angle 3.81331 ( 801) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1442.21 seconds wall clock time: 25 minutes 10.53 seconds (1510.53 seconds total)