Starting phenix.real_space_refine on Tue Mar 3 12:51:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r07_53481/03_2026/9r07_53481.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r07_53481/03_2026/9r07_53481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r07_53481/03_2026/9r07_53481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r07_53481/03_2026/9r07_53481.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r07_53481/03_2026/9r07_53481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r07_53481/03_2026/9r07_53481.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.031 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 2901 2.51 5 N 718 2.21 5 O 769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4425 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4349 Classifications: {'peptide': 565} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 531} Chain breaks: 2 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'Y01': 1, 'ZLK': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.20, per 1000 atoms: 0.27 Number of scatterers: 4425 At special positions: 0 Unit cell: (80.704, 99.84, 74.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 769 8.00 N 718 7.00 C 2901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 444 " - pdb=" SG CYS A 494 " distance=2.03 Simple disulfide: pdb=" SG CYS A 450 " - pdb=" SG CYS A 470 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 492 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 594 " 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: 0.43 Conformation dependent library (CDL) restraints added in 282.7 milliseconds 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1048 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 70.4% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 30 through 64 removed outlier: 3.559A pdb=" N PHE A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N THR A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 91 removed outlier: 4.321A pdb=" N ASN A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 96 through 115 Processing helix chain 'A' and resid 116 through 122 removed outlier: 3.551A pdb=" N PHE A 120 " --> pdb=" O THR A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 185 removed outlier: 3.678A pdb=" N VAL A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.500A pdb=" N PHE A 190 " --> pdb=" O PRO A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 217 through 231 removed outlier: 3.714A pdb=" N ARG A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 273 removed outlier: 3.563A pdb=" N GLY A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 277 Processing helix chain 'A' and resid 306 through 323 removed outlier: 3.711A pdb=" N PHE A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 324 through 357 removed outlier: 5.517A pdb=" N ASN A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LYS A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 389 removed outlier: 4.037A pdb=" N LEU A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 394 through 411 removed outlier: 4.354A pdb=" N ARG A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 416 Processing helix chain 'A' and resid 442 through 446 Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 514 through 531 removed outlier: 3.538A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 544 removed outlier: 3.628A pdb=" N VAL A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 564 Processing helix chain 'A' and resid 566 through 578 removed outlier: 4.213A pdb=" N SER A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 635 removed outlier: 3.630A pdb=" N GLN A 610 " --> pdb=" O TYR A 606 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 466 removed outlier: 3.569A pdb=" N CYS A 459 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS A 492 " --> pdb=" O CYS A 474 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N CYS A 474 " --> pdb=" O CYS A 492 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 580 through 585 removed outlier: 4.952A pdb=" N CYS A 580 " --> pdb=" O TYR A 596 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TYR A 596 " --> pdb=" O CYS A 580 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ARG A 582 " --> pdb=" O CYS A 594 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N CYS A 594 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASN A 584 " --> pdb=" O GLY A 592 " (cutoff:3.500A) 288 hydrogen bonds defined for protein. 837 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: 0.66 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 740 1.33 - 1.45: 1221 1.45 - 1.57: 2530 1.57 - 1.69: 1 1.69 - 1.81: 53 Bond restraints: 4545 Sorted by residual: bond pdb=" C20 ZLK A 701 " pdb=" C21 ZLK A 701 " ideal model delta sigma weight residual 1.548 1.486 0.062 2.00e-02 2.50e+03 9.50e+00 bond pdb=" N31 ZLK A 701 " pdb=" S32 ZLK A 701 " ideal model delta sigma weight residual 1.679 1.643 0.036 2.00e-02 2.50e+03 3.28e+00 bond pdb=" N CYS A 23 " pdb=" CA CYS A 23 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" C19 ZLK A 701 " pdb=" C20 ZLK A 701 " ideal model delta sigma weight residual 1.537 1.512 0.025 2.00e-02 2.50e+03 1.57e+00 bond pdb=" C03 ZLK A 701 " pdb=" O02 ZLK A 701 " ideal model delta sigma weight residual 1.341 1.366 -0.025 2.00e-02 2.50e+03 1.56e+00 ... (remaining 4540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 6099 1.85 - 3.71: 68 3.71 - 5.56: 13 5.56 - 7.42: 1 7.42 - 9.27: 2 Bond angle restraints: 6183 Sorted by residual: angle pdb=" C23 ZLK A 701 " pdb=" C13 ZLK A 701 " pdb=" N14 ZLK A 701 " ideal model delta sigma weight residual 115.87 125.14 -9.27 3.00e+00 1.11e-01 9.55e+00 angle pdb=" C12 ZLK A 701 " pdb=" C13 ZLK A 701 " pdb=" N14 ZLK A 701 " ideal model delta sigma weight residual 123.79 114.77 9.02 3.00e+00 1.11e-01 9.03e+00 angle pdb=" C22 ZLK A 701 " pdb=" C18 ZLK A 701 " pdb=" O17 ZLK A 701 " ideal model delta sigma weight residual 110.72 117.00 -6.28 3.00e+00 1.11e-01 4.38e+00 angle pdb=" N GLY A 305 " pdb=" CA GLY A 305 " pdb=" C GLY A 305 " ideal model delta sigma weight residual 113.18 117.97 -4.79 2.37e+00 1.78e-01 4.09e+00 angle pdb=" C PHE A 314 " pdb=" CA PHE A 314 " pdb=" CB PHE A 314 " ideal model delta sigma weight residual 112.38 108.05 4.33 2.17e+00 2.12e-01 3.98e+00 ... (remaining 6178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.87: 2655 33.87 - 67.74: 78 67.74 - 101.61: 7 101.61 - 135.48: 0 135.48 - 169.34: 1 Dihedral angle restraints: 2741 sinusoidal: 1109 harmonic: 1632 Sorted by residual: dihedral pdb=" CB CYS A 459 " pdb=" SG CYS A 459 " pdb=" SG CYS A 507 " pdb=" CB CYS A 507 " ideal model delta sinusoidal sigma weight residual 93.00 166.94 -73.94 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CA CYS A 507 " pdb=" C CYS A 507 " pdb=" N PRO A 508 " pdb=" CA PRO A 508 " ideal model delta harmonic sigma weight residual -180.00 -153.31 -26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" C04 ZLK A 701 " pdb=" C05 ZLK A 701 " pdb=" C06 ZLK A 701 " pdb=" C11 ZLK A 701 " ideal model delta sinusoidal sigma weight residual 67.31 -102.03 169.34 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 2738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 591 0.049 - 0.098: 100 0.098 - 0.146: 11 0.146 - 0.195: 0 0.195 - 0.244: 1 Chirality restraints: 703 Sorted by residual: chirality pdb=" C18 ZLK A 701 " pdb=" C19 ZLK A 701 " pdb=" C22 ZLK A 701 " pdb=" O17 ZLK A 701 " both_signs ideal model delta sigma weight residual False -2.79 -2.55 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA VAL A 424 " pdb=" N VAL A 424 " pdb=" C VAL A 424 " pdb=" CB VAL A 424 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA VAL A 458 " pdb=" N VAL A 458 " pdb=" C VAL A 458 " pdb=" CB VAL A 458 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 700 not shown) Planarity restraints: 763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C03 ZLK A 701 " 0.009 2.00e-02 2.50e+03 2.89e-02 1.88e+01 pdb=" C04 ZLK A 701 " 0.023 2.00e-02 2.50e+03 pdb=" C05 ZLK A 701 " -0.063 2.00e-02 2.50e+03 pdb=" C25 ZLK A 701 " 0.030 2.00e-02 2.50e+03 pdb=" C26 ZLK A 701 " 0.019 2.00e-02 2.50e+03 pdb=" C27 ZLK A 701 " -0.001 2.00e-02 2.50e+03 pdb=" C28 ZLK A 701 " -0.004 2.00e-02 2.50e+03 pdb=" C29 ZLK A 701 " -0.035 2.00e-02 2.50e+03 pdb=" O02 ZLK A 701 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 ZLK A 701 " -0.038 2.00e-02 2.50e+03 1.92e-02 1.10e+01 pdb=" C06 ZLK A 701 " 0.019 2.00e-02 2.50e+03 pdb=" C07 ZLK A 701 " 0.017 2.00e-02 2.50e+03 pdb=" C09 ZLK A 701 " 0.002 2.00e-02 2.50e+03 pdb=" C10 ZLK A 701 " 0.003 2.00e-02 2.50e+03 pdb=" C11 ZLK A 701 " 0.012 2.00e-02 2.50e+03 pdb=" C12 ZLK A 701 " 0.003 2.00e-02 2.50e+03 pdb=" C13 ZLK A 701 " -0.016 2.00e-02 2.50e+03 pdb=" C23 ZLK A 701 " -0.025 2.00e-02 2.50e+03 pdb=" C24 ZLK A 701 " -0.015 2.00e-02 2.50e+03 pdb=" N08 ZLK A 701 " 0.007 2.00e-02 2.50e+03 pdb=" N14 ZLK A 701 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 561 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C ARG A 561 " -0.030 2.00e-02 2.50e+03 pdb=" O ARG A 561 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 562 " 0.010 2.00e-02 2.50e+03 ... (remaining 760 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1243 2.81 - 3.33: 4416 3.33 - 3.86: 7231 3.86 - 4.38: 8221 4.38 - 4.90: 14524 Nonbonded interactions: 35635 Sorted by model distance: nonbonded pdb=" OG1 THR A 421 " pdb=" OD1 ASN A 599 " model vdw 2.290 3.040 nonbonded pdb=" OG SER A 480 " pdb=" OG SER A 484 " model vdw 2.351 3.040 nonbonded pdb=" OG SER A 129 " pdb=" NH2 ARG A 252 " model vdw 2.362 3.120 nonbonded pdb=" OH TYR A 51 " pdb=" O TRP A 257 " model vdw 2.370 3.040 nonbonded pdb=" O ILE A 85 " pdb=" OG SER A 89 " model vdw 2.401 3.040 ... (remaining 35630 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.840 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.003 0.062 4551 Z= 0.143 Angle : 0.545 9.273 6195 Z= 0.260 Chirality : 0.037 0.244 703 Planarity : 0.004 0.030 763 Dihedral : 15.620 169.344 1675 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.88 % Allowed : 12.29 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.36), residues: 559 helix: 2.68 (0.28), residues: 350 sheet: None (None), residues: 0 loop : 0.60 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 316 TYR 0.010 0.001 TYR A 194 PHE 0.010 0.001 PHE A 337 TRP 0.006 0.001 TRP A 253 HIS 0.002 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4545) covalent geometry : angle 0.54394 ( 6183) SS BOND : bond 0.00177 ( 6) SS BOND : angle 0.93983 ( 12) hydrogen bonds : bond 0.13066 ( 288) hydrogen bonds : angle 5.10195 ( 837) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.147 Fit side-chains REVERT: A 173 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6772 (tpp) REVERT: A 282 MET cc_start: 0.7915 (mtt) cc_final: 0.7640 (mtt) REVERT: A 454 PHE cc_start: 0.7931 (m-80) cc_final: 0.7714 (m-80) outliers start: 9 outliers final: 2 residues processed: 92 average time/residue: 0.0632 time to fit residues: 7.6458 Evaluate side-chains 59 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 566 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.114175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.085524 restraints weight = 8434.063| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.05 r_work: 0.3042 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4551 Z= 0.136 Angle : 0.609 7.272 6195 Z= 0.288 Chirality : 0.041 0.248 703 Planarity : 0.005 0.036 763 Dihedral : 9.794 163.723 706 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.75 % Allowed : 12.50 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.36), residues: 559 helix: 2.79 (0.27), residues: 357 sheet: None (None), residues: 0 loop : 0.72 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 590 TYR 0.027 0.002 TYR A 572 PHE 0.020 0.001 PHE A 337 TRP 0.005 0.001 TRP A 170 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 4545) covalent geometry : angle 0.60678 ( 6183) SS BOND : bond 0.00125 ( 6) SS BOND : angle 1.42425 ( 12) hydrogen bonds : bond 0.04091 ( 288) hydrogen bonds : angle 4.01749 ( 837) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 76 LEU cc_start: 0.7853 (mt) cc_final: 0.7438 (tt) REVERT: A 108 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8915 (tt) REVERT: A 117 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8891 (mm) REVERT: A 454 PHE cc_start: 0.7841 (m-80) cc_final: 0.7133 (m-80) outliers start: 18 outliers final: 11 residues processed: 73 average time/residue: 0.0407 time to fit residues: 4.4319 Evaluate side-chains 59 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 566 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN A 394 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.114156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.085567 restraints weight = 8492.876| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.06 r_work: 0.3053 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4551 Z= 0.119 Angle : 0.560 5.544 6195 Z= 0.268 Chirality : 0.042 0.231 703 Planarity : 0.004 0.043 763 Dihedral : 9.680 170.789 701 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.17 % Allowed : 13.54 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.20 (0.36), residues: 559 helix: 2.93 (0.27), residues: 357 sheet: None (None), residues: 0 loop : 0.68 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 316 TYR 0.024 0.002 TYR A 125 PHE 0.016 0.001 PHE A 337 TRP 0.007 0.001 TRP A 170 HIS 0.004 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4545) covalent geometry : angle 0.55885 ( 6183) SS BOND : bond 0.00178 ( 6) SS BOND : angle 0.92955 ( 12) hydrogen bonds : bond 0.03662 ( 288) hydrogen bonds : angle 3.83428 ( 837) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 108 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8996 (tt) REVERT: A 117 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8934 (mm) REVERT: A 125 TYR cc_start: 0.8323 (t80) cc_final: 0.8047 (t80) REVERT: A 335 CYS cc_start: 0.8881 (m) cc_final: 0.8570 (m) REVERT: A 454 PHE cc_start: 0.7853 (m-80) cc_final: 0.7157 (m-80) outliers start: 20 outliers final: 12 residues processed: 75 average time/residue: 0.0461 time to fit residues: 4.9845 Evaluate side-chains 58 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 470 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 32 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.112972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.083737 restraints weight = 8331.747| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.09 r_work: 0.3026 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4551 Z= 0.137 Angle : 0.579 5.919 6195 Z= 0.276 Chirality : 0.042 0.222 703 Planarity : 0.004 0.047 763 Dihedral : 9.610 171.218 699 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.54 % Allowed : 14.79 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.24 (0.36), residues: 559 helix: 2.96 (0.28), residues: 358 sheet: None (None), residues: 0 loop : 0.68 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 231 TYR 0.019 0.001 TYR A 125 PHE 0.017 0.001 PHE A 337 TRP 0.006 0.001 TRP A 170 HIS 0.002 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4545) covalent geometry : angle 0.57652 ( 6183) SS BOND : bond 0.00179 ( 6) SS BOND : angle 1.43263 ( 12) hydrogen bonds : bond 0.03683 ( 288) hydrogen bonds : angle 3.78414 ( 837) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 108 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9033 (tt) REVERT: A 117 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8964 (mm) REVERT: A 335 CYS cc_start: 0.8911 (m) cc_final: 0.8584 (m) REVERT: A 454 PHE cc_start: 0.7912 (m-80) cc_final: 0.7260 (m-80) outliers start: 17 outliers final: 13 residues processed: 58 average time/residue: 0.0401 time to fit residues: 3.5489 Evaluate side-chains 56 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 510 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.112730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.083422 restraints weight = 8433.108| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.11 r_work: 0.3023 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4551 Z= 0.132 Angle : 0.556 6.043 6195 Z= 0.264 Chirality : 0.042 0.220 703 Planarity : 0.004 0.046 763 Dihedral : 9.594 172.348 699 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.54 % Allowed : 15.21 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.27 (0.36), residues: 559 helix: 3.00 (0.28), residues: 359 sheet: None (None), residues: 0 loop : 0.66 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 590 TYR 0.022 0.001 TYR A 125 PHE 0.017 0.001 PHE A 337 TRP 0.007 0.001 TRP A 170 HIS 0.001 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 4545) covalent geometry : angle 0.55366 ( 6183) SS BOND : bond 0.00202 ( 6) SS BOND : angle 1.26307 ( 12) hydrogen bonds : bond 0.03552 ( 288) hydrogen bonds : angle 3.71917 ( 837) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 108 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9112 (tt) REVERT: A 117 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8983 (mm) REVERT: A 125 TYR cc_start: 0.8397 (t80) cc_final: 0.8132 (t80) REVERT: A 335 CYS cc_start: 0.8925 (m) cc_final: 0.8567 (m) REVERT: A 454 PHE cc_start: 0.7987 (m-80) cc_final: 0.7301 (m-80) outliers start: 17 outliers final: 12 residues processed: 59 average time/residue: 0.0458 time to fit residues: 4.0063 Evaluate side-chains 57 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 510 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.110451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.081138 restraints weight = 8670.086| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.13 r_work: 0.2972 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4551 Z= 0.190 Angle : 0.606 6.198 6195 Z= 0.285 Chirality : 0.043 0.228 703 Planarity : 0.004 0.048 763 Dihedral : 9.677 173.197 699 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.75 % Allowed : 15.21 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.24 (0.37), residues: 559 helix: 2.95 (0.27), residues: 358 sheet: None (None), residues: 0 loop : 0.71 (0.46), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 446 TYR 0.022 0.001 TYR A 125 PHE 0.017 0.001 PHE A 337 TRP 0.008 0.001 TRP A 626 HIS 0.002 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 4545) covalent geometry : angle 0.60443 ( 6183) SS BOND : bond 0.00173 ( 6) SS BOND : angle 1.15659 ( 12) hydrogen bonds : bond 0.04062 ( 288) hydrogen bonds : angle 3.85650 ( 837) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 108 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9124 (tt) REVERT: A 117 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9054 (mm) REVERT: A 125 TYR cc_start: 0.8381 (t80) cc_final: 0.8146 (t80) outliers start: 18 outliers final: 13 residues processed: 57 average time/residue: 0.0399 time to fit residues: 3.5447 Evaluate side-chains 56 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 510 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 51 optimal weight: 0.0040 chunk 55 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 overall best weight: 0.3192 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.113989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.085035 restraints weight = 8474.507| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.11 r_work: 0.3058 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4551 Z= 0.102 Angle : 0.537 7.530 6195 Z= 0.254 Chirality : 0.041 0.216 703 Planarity : 0.004 0.049 763 Dihedral : 9.619 172.925 699 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.33 % Allowed : 15.42 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.31 (0.37), residues: 559 helix: 3.03 (0.27), residues: 360 sheet: None (None), residues: 0 loop : 0.65 (0.46), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 446 TYR 0.017 0.001 TYR A 125 PHE 0.017 0.001 PHE A 337 TRP 0.007 0.001 TRP A 170 HIS 0.001 0.000 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 4545) covalent geometry : angle 0.53668 ( 6183) SS BOND : bond 0.00145 ( 6) SS BOND : angle 0.76907 ( 12) hydrogen bonds : bond 0.03288 ( 288) hydrogen bonds : angle 3.62900 ( 837) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 108 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9075 (tt) REVERT: A 117 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9016 (mm) REVERT: A 125 TYR cc_start: 0.8354 (t80) cc_final: 0.8144 (t80) REVERT: A 307 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7710 (tp) REVERT: A 335 CYS cc_start: 0.8901 (m) cc_final: 0.8633 (m) outliers start: 16 outliers final: 10 residues processed: 58 average time/residue: 0.0455 time to fit residues: 3.9374 Evaluate side-chains 54 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 470 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 7 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.113253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.084302 restraints weight = 8458.045| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.11 r_work: 0.3043 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4551 Z= 0.113 Angle : 0.543 7.510 6195 Z= 0.254 Chirality : 0.041 0.226 703 Planarity : 0.004 0.048 763 Dihedral : 9.559 173.572 699 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.75 % Allowed : 15.62 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.34 (0.37), residues: 559 helix: 3.03 (0.27), residues: 361 sheet: None (None), residues: 0 loop : 0.70 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 445 TYR 0.018 0.001 TYR A 125 PHE 0.016 0.001 PHE A 337 TRP 0.007 0.001 TRP A 170 HIS 0.002 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 4545) covalent geometry : angle 0.54222 ( 6183) SS BOND : bond 0.00142 ( 6) SS BOND : angle 0.77042 ( 12) hydrogen bonds : bond 0.03391 ( 288) hydrogen bonds : angle 3.62558 ( 837) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 108 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9110 (tt) REVERT: A 117 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9046 (mm) REVERT: A 307 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7770 (tp) REVERT: A 335 CYS cc_start: 0.8960 (m) cc_final: 0.8629 (m) REVERT: A 454 PHE cc_start: 0.8070 (m-80) cc_final: 0.7448 (m-80) outliers start: 18 outliers final: 13 residues processed: 59 average time/residue: 0.0373 time to fit residues: 3.4005 Evaluate side-chains 60 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 510 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.111304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.081632 restraints weight = 8642.506| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.23 r_work: 0.2988 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4551 Z= 0.119 Angle : 0.551 7.965 6195 Z= 0.257 Chirality : 0.042 0.228 703 Planarity : 0.004 0.048 763 Dihedral : 9.547 173.918 699 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.96 % Allowed : 16.04 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.36 (0.37), residues: 559 helix: 3.07 (0.27), residues: 360 sheet: None (None), residues: 0 loop : 0.68 (0.46), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 446 TYR 0.018 0.001 TYR A 125 PHE 0.018 0.001 PHE A 337 TRP 0.007 0.001 TRP A 170 HIS 0.002 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 4545) covalent geometry : angle 0.55042 ( 6183) SS BOND : bond 0.00158 ( 6) SS BOND : angle 0.73851 ( 12) hydrogen bonds : bond 0.03401 ( 288) hydrogen bonds : angle 3.62856 ( 837) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 76 LEU cc_start: 0.7533 (mt) cc_final: 0.7196 (tt) REVERT: A 108 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9036 (tt) REVERT: A 117 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8910 (mm) REVERT: A 307 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7684 (tp) REVERT: A 335 CYS cc_start: 0.8883 (m) cc_final: 0.8553 (m) REVERT: A 454 PHE cc_start: 0.8017 (m-80) cc_final: 0.7350 (m-80) outliers start: 19 outliers final: 14 residues processed: 58 average time/residue: 0.0456 time to fit residues: 3.8753 Evaluate side-chains 61 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 537 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 23 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.110939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.081216 restraints weight = 8518.477| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.21 r_work: 0.2979 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4551 Z= 0.125 Angle : 0.554 8.540 6195 Z= 0.259 Chirality : 0.042 0.223 703 Planarity : 0.005 0.047 763 Dihedral : 9.551 174.459 699 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.75 % Allowed : 15.83 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.35 (0.37), residues: 559 helix: 3.06 (0.27), residues: 359 sheet: None (None), residues: 0 loop : 0.68 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 99 TYR 0.018 0.001 TYR A 125 PHE 0.019 0.001 PHE A 337 TRP 0.006 0.001 TRP A 170 HIS 0.002 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4545) covalent geometry : angle 0.55331 ( 6183) SS BOND : bond 0.00109 ( 6) SS BOND : angle 0.77212 ( 12) hydrogen bonds : bond 0.03483 ( 288) hydrogen bonds : angle 3.63512 ( 837) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 76 LEU cc_start: 0.7540 (mt) cc_final: 0.7213 (tt) REVERT: A 108 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9054 (tt) REVERT: A 117 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8948 (mm) REVERT: A 307 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7766 (tp) REVERT: A 335 CYS cc_start: 0.8877 (m) cc_final: 0.8532 (m) REVERT: A 454 PHE cc_start: 0.8052 (m-80) cc_final: 0.7392 (m-80) outliers start: 18 outliers final: 14 residues processed: 60 average time/residue: 0.0393 time to fit residues: 3.6206 Evaluate side-chains 60 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 566 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 0.0370 chunk 15 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.112258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.082374 restraints weight = 8563.360| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.25 r_work: 0.3001 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4551 Z= 0.110 Angle : 0.554 8.506 6195 Z= 0.262 Chirality : 0.041 0.221 703 Planarity : 0.004 0.048 763 Dihedral : 9.595 174.571 699 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.33 % Allowed : 16.25 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.37 (0.36), residues: 559 helix: 3.09 (0.27), residues: 360 sheet: None (None), residues: 0 loop : 0.65 (0.46), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 99 TYR 0.019 0.001 TYR A 125 PHE 0.019 0.001 PHE A 337 TRP 0.007 0.001 TRP A 170 HIS 0.002 0.001 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 4545) covalent geometry : angle 0.55119 ( 6183) SS BOND : bond 0.00163 ( 6) SS BOND : angle 1.47366 ( 12) hydrogen bonds : bond 0.03329 ( 288) hydrogen bonds : angle 3.57767 ( 837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1099.33 seconds wall clock time: 19 minutes 31.00 seconds (1171.00 seconds total)