Starting phenix.real_space_refine on Tue Mar 3 19:08:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zgo_14709/03_2026/7zgo_14709.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zgo_14709/03_2026/7zgo_14709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zgo_14709/03_2026/7zgo_14709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zgo_14709/03_2026/7zgo_14709.map" model { file = "/net/cci-nas-00/data/ceres_data/7zgo_14709/03_2026/7zgo_14709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zgo_14709/03_2026/7zgo_14709.cif" } resolution = 2.55 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= 0.008 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: 8 Type Number sf(0) Gaussians K 2 8.98 5 P 7 5.49 5 S 44 5.16 5 Cl 4 4.86 5 Na 2 4.78 5 C 5224 2.51 5 N 1115 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s 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: 7754 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3574 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 15, 'TRANS': 454} Chain: "B" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3574 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 15, 'TRANS': 454} Chain: "A" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 317 Unusual residues: {' K': 1, ' CL': 2, ' NA': 1, 'POV': 4, 'Y01': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 265 Unusual residues: {' K': 1, ' CL': 2, ' NA': 1, 'POV': 3, 'Y01': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 1.87, per 1000 atoms: 0.24 Number of scatterers: 7754 At special positions: 0 Unit cell: (80.106, 114.582, 91.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) K 2 19.00 Cl 4 17.00 S 44 16.00 P 7 15.00 Na 2 11.00 O 1356 8.00 N 1115 7.00 C 5224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 582 " 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: 0.56 Conformation dependent library (CDL) restraints added in 164.1 milliseconds 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 80.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 302 through 307 removed outlier: 3.502A pdb=" N ILE A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 307 " --> pdb=" O MET A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 302 through 307' Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 316 through 343 Processing helix chain 'A' and resid 351 through 360 Processing helix chain 'A' and resid 361 through 398 removed outlier: 3.639A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 427 Processing helix chain 'A' and resid 430 through 454 removed outlier: 4.314A pdb=" N ILE A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 469 through 477 Processing helix chain 'A' and resid 486 through 499 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.993A pdb=" N ILE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 511 Processing helix chain 'A' and resid 513 through 544 Proline residue: A 519 - end of helix Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 574 through 580 removed outlier: 3.871A pdb=" N GLU A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 574 through 580' Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 599 through 632 removed outlier: 3.860A pdb=" N ILE A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 635 through 643 removed outlier: 4.611A pdb=" N MET A 640 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS A 643 " --> pdb=" O MET A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 668 removed outlier: 3.957A pdb=" N ILE A 668 " --> pdb=" O GLY A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 700 Proline residue: A 676 - end of helix Processing helix chain 'A' and resid 712 through 731 Processing helix chain 'A' and resid 731 through 751 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 302 through 307 Processing helix chain 'B' and resid 307 through 315 Processing helix chain 'B' and resid 316 through 344 Processing helix chain 'B' and resid 351 through 360 Processing helix chain 'B' and resid 362 through 398 removed outlier: 3.663A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 Processing helix chain 'B' and resid 429 through 454 removed outlier: 4.533A pdb=" N LYS B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'B' and resid 469 through 477 Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 504 through 511 removed outlier: 3.703A pdb=" N ILE B 507 " --> pdb=" O GLY B 504 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLY B 509 " --> pdb=" O ASN B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 544 Proline residue: B 519 - end of helix Processing helix chain 'B' and resid 565 through 570 Processing helix chain 'B' and resid 574 through 578 Processing helix chain 'B' and resid 591 through 597 Processing helix chain 'B' and resid 599 through 632 removed outlier: 3.626A pdb=" N ILE B 603 " --> pdb=" O PHE B 599 " (cutoff:3.500A) Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 635 through 643 removed outlier: 4.635A pdb=" N MET B 640 " --> pdb=" O ALA B 637 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS B 643 " --> pdb=" O MET B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 668 removed outlier: 3.879A pdb=" N ILE B 668 " --> pdb=" O GLY B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 700 Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 712 through 731 Processing helix chain 'B' and resid 731 through 751 520 hydrogen bonds defined for protein. 1506 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1134 1.31 - 1.44: 2049 1.44 - 1.56: 4632 1.56 - 1.69: 14 1.69 - 1.82: 70 Bond restraints: 7899 Sorted by residual: bond pdb=" CAX Y01 A1311 " pdb=" OAH Y01 A1311 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" CAX Y01 B1308 " pdb=" OAH Y01 B1308 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" CAX Y01 A1310 " pdb=" OAH Y01 A1310 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" CAX Y01 B1309 " pdb=" OAH Y01 B1309 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" CAX Y01 A1309 " pdb=" OAH Y01 A1309 " ideal model delta sigma weight residual 1.248 1.341 -0.093 2.00e-02 2.50e+03 2.18e+01 ... (remaining 7894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 10422 3.62 - 7.24: 222 7.24 - 10.85: 42 10.85 - 14.47: 14 14.47 - 18.09: 7 Bond angle restraints: 10707 Sorted by residual: angle pdb=" C35 POV A1305 " pdb=" C36 POV A1305 " pdb=" C37 POV A1305 " ideal model delta sigma weight residual 113.93 132.02 -18.09 3.00e+00 1.11e-01 3.64e+01 angle pdb=" C35 POV A1306 " pdb=" C36 POV A1306 " pdb=" C37 POV A1306 " ideal model delta sigma weight residual 113.93 131.80 -17.87 3.00e+00 1.11e-01 3.55e+01 angle pdb=" C35 POV B1305 " pdb=" C36 POV B1305 " pdb=" C37 POV B1305 " ideal model delta sigma weight residual 113.93 131.45 -17.52 3.00e+00 1.11e-01 3.41e+01 angle pdb=" C35 POV B1307 " pdb=" C36 POV B1307 " pdb=" C37 POV B1307 " ideal model delta sigma weight residual 113.93 131.38 -17.45 3.00e+00 1.11e-01 3.38e+01 angle pdb=" C35 POV A1308 " pdb=" C36 POV A1308 " pdb=" C37 POV A1308 " ideal model delta sigma weight residual 113.93 131.36 -17.43 3.00e+00 1.11e-01 3.38e+01 ... (remaining 10702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.28: 4683 28.28 - 56.56: 229 56.56 - 84.84: 36 84.84 - 113.12: 12 113.12 - 141.40: 1 Dihedral angle restraints: 4961 sinusoidal: 2275 harmonic: 2686 Sorted by residual: dihedral pdb=" CB CYS A 577 " pdb=" SG CYS A 577 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual -86.00 -171.93 85.93 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS B 577 " pdb=" SG CYS B 577 " pdb=" SG CYS B 582 " pdb=" CB CYS B 582 " ideal model delta sinusoidal sigma weight residual -86.00 -169.56 83.56 1 1.00e+01 1.00e-02 8.52e+01 dihedral pdb=" C3 POV A1306 " pdb=" C31 POV A1306 " pdb=" O31 POV A1306 " pdb=" C32 POV A1306 " ideal model delta sinusoidal sigma weight residual 172.61 -45.99 -141.40 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 4958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1162 0.094 - 0.188: 59 0.188 - 0.282: 14 0.282 - 0.376: 6 0.376 - 0.470: 6 Chirality restraints: 1247 Sorted by residual: chirality pdb=" CBG Y01 A1309 " pdb=" CAQ Y01 A1309 " pdb=" CBD Y01 A1309 " pdb=" CBI Y01 A1309 " both_signs ideal model delta sigma weight residual False -2.33 -2.80 0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" CBG Y01 A1310 " pdb=" CAQ Y01 A1310 " pdb=" CBD Y01 A1310 " pdb=" CBI Y01 A1310 " both_signs ideal model delta sigma weight residual False -2.33 -2.80 0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CBG Y01 B1310 " pdb=" CAQ Y01 B1310 " pdb=" CBD Y01 B1310 " pdb=" CBI Y01 B1310 " both_signs ideal model delta sigma weight residual False -2.33 -2.80 0.47 2.00e-01 2.50e+01 5.42e+00 ... (remaining 1244 not shown) Planarity restraints: 1249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 361 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.95e+00 pdb=" N PRO B 362 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 362 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 362 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 361 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 362 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 580 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO A 581 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 581 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 581 " -0.019 5.00e-02 4.00e+02 ... (remaining 1246 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.76: 1377 2.76 - 3.36: 8988 3.36 - 3.95: 15567 3.95 - 4.55: 22083 4.55 - 5.14: 32006 Nonbonded interactions: 80021 Sorted by model distance: nonbonded pdb=" OE2 GLU A 431 " pdb=" O HOH A1401 " model vdw 2.170 3.040 nonbonded pdb=" OH TYR B 468 " pdb=" OG SER B 539 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR A 468 " pdb=" OG SER A 539 " model vdw 2.227 3.040 nonbonded pdb=" O GLY A 478 " pdb=" NH2 ARG A 546 " model vdw 2.243 3.120 nonbonded pdb=" O LEU A 297 " pdb="NA NA A1301 " model vdw 2.246 2.470 ... (remaining 80016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 284 through 1307 or resid 1309 through 1310)) selection = (chain 'B' and (resid 284 through 1307 or resid 1309 through 1310)) } 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: 1.210 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.500 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:8.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 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 : 0.008 0.094 7903 Z= 0.407 Angle : 1.241 18.089 10715 Z= 0.464 Chirality : 0.063 0.470 1247 Planarity : 0.003 0.043 1249 Dihedral : 16.937 141.402 3233 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.27), residues: 936 helix: 1.80 (0.19), residues: 674 sheet: None (None), residues: 0 loop : -1.56 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.014 0.001 TYR A 354 PHE 0.016 0.002 PHE A 681 TRP 0.010 0.001 TRP A 733 HIS 0.003 0.001 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00830 ( 7899) covalent geometry : angle 1.24123 (10707) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.74224 ( 8) hydrogen bonds : bond 0.11940 ( 520) hydrogen bonds : angle 4.82648 ( 1506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.254 Fit side-chains REVERT: A 294 ARG cc_start: 0.7235 (mtp85) cc_final: 0.6951 (mtp85) REVERT: A 325 MET cc_start: 0.7995 (mmt) cc_final: 0.7780 (mmp) REVERT: A 433 LYS cc_start: 0.6613 (mmmm) cc_final: 0.6213 (mttp) REVERT: A 475 GLU cc_start: 0.7618 (tt0) cc_final: 0.6977 (tt0) REVERT: A 480 ASP cc_start: 0.8135 (t0) cc_final: 0.7790 (t0) REVERT: A 513 ASP cc_start: 0.7392 (t0) cc_final: 0.6879 (t0) REVERT: A 515 GLN cc_start: 0.7795 (mt0) cc_final: 0.7399 (mt0) REVERT: A 625 ILE cc_start: 0.8148 (mt) cc_final: 0.7764 (mt) REVERT: A 727 MET cc_start: 0.8174 (ptm) cc_final: 0.7891 (ptm) REVERT: B 325 MET cc_start: 0.7947 (mmp) cc_final: 0.7733 (mmm) REVERT: B 428 MET cc_start: 0.5128 (mmm) cc_final: 0.4856 (tpt) REVERT: B 433 LYS cc_start: 0.6557 (mmmm) cc_final: 0.6205 (mttp) REVERT: B 475 GLU cc_start: 0.7503 (tt0) cc_final: 0.6848 (tt0) REVERT: B 480 ASP cc_start: 0.8271 (t0) cc_final: 0.7923 (t0) REVERT: B 513 ASP cc_start: 0.7110 (t0) cc_final: 0.6639 (t70) REVERT: B 624 LYS cc_start: 0.7709 (ttpp) cc_final: 0.7170 (mtpt) REVERT: B 688 LEU cc_start: 0.8160 (mm) cc_final: 0.7938 (mt) REVERT: B 713 MET cc_start: 0.8387 (ptm) cc_final: 0.8181 (ptm) REVERT: B 727 MET cc_start: 0.8121 (ptm) cc_final: 0.7775 (ptm) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.4851 time to fit residues: 56.2800 Evaluate side-chains 81 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN A 591 GLN B 435 GLN B 571 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.106678 restraints weight = 8449.122| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.73 r_work: 0.3082 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7903 Z= 0.143 Angle : 0.503 6.242 10715 Z= 0.263 Chirality : 0.040 0.131 1247 Planarity : 0.004 0.045 1249 Dihedral : 16.751 137.240 1715 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.05 % Allowed : 7.22 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.27), residues: 936 helix: 2.14 (0.19), residues: 654 sheet: None (None), residues: 0 loop : -0.91 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 307 TYR 0.010 0.001 TYR A 739 PHE 0.018 0.002 PHE B 681 TRP 0.011 0.002 TRP A 287 HIS 0.003 0.001 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7899) covalent geometry : angle 0.50304 (10707) SS BOND : bond 0.00040 ( 4) SS BOND : angle 0.55125 ( 8) hydrogen bonds : bond 0.04182 ( 520) hydrogen bonds : angle 4.12146 ( 1506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.244 Fit side-chains REVERT: A 294 ARG cc_start: 0.7775 (mtp85) cc_final: 0.7462 (mtp85) REVERT: A 296 MET cc_start: 0.8546 (mtm) cc_final: 0.7980 (mtp) REVERT: A 433 LYS cc_start: 0.6813 (mmmm) cc_final: 0.6467 (mttp) REVERT: A 480 ASP cc_start: 0.8438 (t0) cc_final: 0.8134 (t0) REVERT: A 513 ASP cc_start: 0.7504 (t0) cc_final: 0.7284 (t0) REVERT: A 515 GLN cc_start: 0.7898 (mt0) cc_final: 0.7564 (mt0) REVERT: A 670 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7056 (tt0) REVERT: A 705 ARG cc_start: 0.7026 (mtm110) cc_final: 0.6654 (ttm110) REVERT: A 727 MET cc_start: 0.8657 (ptm) cc_final: 0.8356 (ptm) REVERT: B 296 MET cc_start: 0.8523 (mtm) cc_final: 0.7965 (mtp) REVERT: B 428 MET cc_start: 0.5309 (mmm) cc_final: 0.5047 (tpt) REVERT: B 433 LYS cc_start: 0.6796 (mmmm) cc_final: 0.6432 (mttp) REVERT: B 480 ASP cc_start: 0.8581 (t0) cc_final: 0.8253 (t0) REVERT: B 513 ASP cc_start: 0.7474 (t0) cc_final: 0.6917 (t70) REVERT: B 624 LYS cc_start: 0.8023 (ttpp) cc_final: 0.7514 (mtmm) REVERT: B 705 ARG cc_start: 0.7146 (mtm110) cc_final: 0.6682 (ttm110) REVERT: B 727 MET cc_start: 0.8646 (ptm) cc_final: 0.8375 (ptm) outliers start: 8 outliers final: 3 residues processed: 88 average time/residue: 0.5900 time to fit residues: 54.8255 Evaluate side-chains 83 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 508 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN B 435 GLN B 571 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.105891 restraints weight = 8443.981| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.72 r_work: 0.3067 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7903 Z= 0.177 Angle : 0.539 5.294 10715 Z= 0.282 Chirality : 0.041 0.126 1247 Planarity : 0.004 0.045 1249 Dihedral : 16.674 141.450 1715 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.71 % Allowed : 8.27 % Favored : 90.03 % 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 are not related in a simple way. whole: 1.61 (0.27), residues: 936 helix: 1.78 (0.19), residues: 672 sheet: None (None), residues: 0 loop : -0.78 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 307 TYR 0.013 0.002 TYR A 739 PHE 0.019 0.002 PHE B 681 TRP 0.015 0.002 TRP A 287 HIS 0.002 0.001 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 7899) covalent geometry : angle 0.53854 (10707) SS BOND : bond 0.00111 ( 4) SS BOND : angle 0.51843 ( 8) hydrogen bonds : bond 0.04426 ( 520) hydrogen bonds : angle 4.21024 ( 1506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.192 Fit side-chains REVERT: A 294 ARG cc_start: 0.7856 (mtp85) cc_final: 0.7559 (mtp85) REVERT: A 296 MET cc_start: 0.8567 (mtm) cc_final: 0.8033 (mtp) REVERT: A 428 MET cc_start: 0.5573 (tpt) cc_final: 0.5296 (tpt) REVERT: A 433 LYS cc_start: 0.7028 (mmmm) cc_final: 0.6653 (mttp) REVERT: A 480 ASP cc_start: 0.8429 (t0) cc_final: 0.8100 (t0) REVERT: A 515 GLN cc_start: 0.7724 (mt0) cc_final: 0.7476 (mt0) REVERT: A 631 LYS cc_start: 0.7669 (mmtm) cc_final: 0.6961 (ttmt) REVERT: A 670 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7089 (tt0) REVERT: A 705 ARG cc_start: 0.7052 (mtm110) cc_final: 0.6686 (ttm110) REVERT: A 727 MET cc_start: 0.8675 (ptm) cc_final: 0.8403 (ptm) REVERT: B 296 MET cc_start: 0.8541 (mtm) cc_final: 0.7996 (mtp) REVERT: B 433 LYS cc_start: 0.6874 (mmmm) cc_final: 0.6563 (mttp) REVERT: B 480 ASP cc_start: 0.8572 (t0) cc_final: 0.8264 (t0) REVERT: B 513 ASP cc_start: 0.7525 (t0) cc_final: 0.6980 (t70) REVERT: B 624 LYS cc_start: 0.8052 (ttpp) cc_final: 0.7551 (mtmm) REVERT: B 631 LYS cc_start: 0.7541 (mmtm) cc_final: 0.6819 (ttmt) REVERT: B 667 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7827 (mm) REVERT: B 670 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7090 (tt0) REVERT: B 700 LYS cc_start: 0.7972 (mttp) cc_final: 0.7772 (mttt) REVERT: B 705 ARG cc_start: 0.7224 (mtm110) cc_final: 0.6753 (ttm110) REVERT: B 710 TYR cc_start: 0.8433 (m-80) cc_final: 0.8226 (m-80) outliers start: 13 outliers final: 6 residues processed: 88 average time/residue: 0.5778 time to fit residues: 53.6931 Evaluate side-chains 90 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 667 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 56 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.143531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.108896 restraints weight = 8569.991| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.74 r_work: 0.3109 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7903 Z= 0.113 Angle : 0.444 5.157 10715 Z= 0.237 Chirality : 0.038 0.129 1247 Planarity : 0.004 0.045 1249 Dihedral : 15.888 154.311 1715 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.18 % Allowed : 10.37 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.27), residues: 936 helix: 2.15 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.85 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 307 TYR 0.013 0.001 TYR A 739 PHE 0.016 0.001 PHE A 681 TRP 0.010 0.001 TRP A 287 HIS 0.002 0.001 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 7899) covalent geometry : angle 0.44362 (10707) SS BOND : bond 0.00047 ( 4) SS BOND : angle 0.33885 ( 8) hydrogen bonds : bond 0.03855 ( 520) hydrogen bonds : angle 3.99763 ( 1506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.266 Fit side-chains REVERT: A 294 ARG cc_start: 0.7788 (mtp85) cc_final: 0.7539 (mtp85) REVERT: A 296 MET cc_start: 0.8525 (mtm) cc_final: 0.7997 (mtp) REVERT: A 428 MET cc_start: 0.5672 (tpt) cc_final: 0.5356 (tpt) REVERT: A 433 LYS cc_start: 0.7020 (mmmm) cc_final: 0.6643 (mttp) REVERT: A 480 ASP cc_start: 0.8391 (t0) cc_final: 0.8079 (t0) REVERT: A 515 GLN cc_start: 0.7629 (mt0) cc_final: 0.7386 (mt0) REVERT: A 631 LYS cc_start: 0.7579 (mmtm) cc_final: 0.6895 (ttmt) REVERT: A 667 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7810 (mm) REVERT: A 670 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6998 (tt0) REVERT: A 705 ARG cc_start: 0.7117 (mtm110) cc_final: 0.6718 (ttm110) REVERT: B 296 MET cc_start: 0.8516 (mtm) cc_final: 0.7950 (mtp) REVERT: B 428 MET cc_start: 0.5668 (tpt) cc_final: 0.5443 (tpt) REVERT: B 433 LYS cc_start: 0.6729 (mmmm) cc_final: 0.6383 (mttp) REVERT: B 480 ASP cc_start: 0.8563 (t0) cc_final: 0.8254 (t0) REVERT: B 513 ASP cc_start: 0.7499 (t0) cc_final: 0.6954 (t70) REVERT: B 515 GLN cc_start: 0.8037 (mt0) cc_final: 0.7792 (mt0) REVERT: B 624 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7613 (mtmm) REVERT: B 631 LYS cc_start: 0.7583 (mmtm) cc_final: 0.6812 (ttmt) REVERT: B 670 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6954 (tt0) REVERT: B 705 ARG cc_start: 0.7227 (mtm110) cc_final: 0.6764 (ttm110) outliers start: 9 outliers final: 2 residues processed: 91 average time/residue: 0.5519 time to fit residues: 53.1691 Evaluate side-chains 87 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 506 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 70 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 83 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN A 506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.107664 restraints weight = 8495.059| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.74 r_work: 0.3105 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7903 Z= 0.113 Angle : 0.443 5.132 10715 Z= 0.236 Chirality : 0.038 0.125 1247 Planarity : 0.004 0.042 1249 Dihedral : 15.401 168.369 1715 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.84 % Allowed : 10.89 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.27), residues: 936 helix: 2.25 (0.19), residues: 658 sheet: None (None), residues: 0 loop : -0.73 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 307 TYR 0.012 0.001 TYR A 739 PHE 0.014 0.001 PHE A 681 TRP 0.010 0.001 TRP A 287 HIS 0.002 0.001 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7899) covalent geometry : angle 0.44299 (10707) SS BOND : bond 0.00041 ( 4) SS BOND : angle 0.32476 ( 8) hydrogen bonds : bond 0.03776 ( 520) hydrogen bonds : angle 3.93578 ( 1506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.204 Fit side-chains REVERT: A 294 ARG cc_start: 0.7787 (mtp85) cc_final: 0.7525 (mtp85) REVERT: A 296 MET cc_start: 0.8553 (mtm) cc_final: 0.7999 (mtp) REVERT: A 360 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7209 (pp) REVERT: A 363 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6796 (pm20) REVERT: A 433 LYS cc_start: 0.7038 (mmmm) cc_final: 0.6666 (mttp) REVERT: A 631 LYS cc_start: 0.7576 (mmtm) cc_final: 0.6890 (ttmt) REVERT: A 667 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7823 (mm) REVERT: A 705 ARG cc_start: 0.7103 (mtm110) cc_final: 0.6703 (ttm110) REVERT: B 296 MET cc_start: 0.8534 (mtm) cc_final: 0.7981 (mtp) REVERT: B 319 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7723 (mp) REVERT: B 428 MET cc_start: 0.5606 (tpt) cc_final: 0.5403 (tpt) REVERT: B 433 LYS cc_start: 0.6767 (mmmm) cc_final: 0.6431 (mttp) REVERT: B 480 ASP cc_start: 0.8396 (t0) cc_final: 0.8065 (t0) REVERT: B 513 ASP cc_start: 0.7495 (t0) cc_final: 0.6933 (t70) REVERT: B 515 GLN cc_start: 0.8129 (mt0) cc_final: 0.7903 (mt0) REVERT: B 624 LYS cc_start: 0.8008 (ttpp) cc_final: 0.7581 (mtmm) REVERT: B 631 LYS cc_start: 0.7569 (mmtm) cc_final: 0.6855 (ttmt) REVERT: B 667 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7773 (mm) REVERT: B 670 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6873 (tt0) REVERT: B 705 ARG cc_start: 0.7227 (mtm110) cc_final: 0.6755 (ttm110) outliers start: 14 outliers final: 4 residues processed: 93 average time/residue: 0.5112 time to fit residues: 50.5295 Evaluate side-chains 94 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 667 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN A 506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.141681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.106482 restraints weight = 8507.211| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.75 r_work: 0.3088 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7903 Z= 0.142 Angle : 0.480 5.204 10715 Z= 0.254 Chirality : 0.040 0.124 1247 Planarity : 0.004 0.045 1249 Dihedral : 15.348 158.606 1715 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.23 % Allowed : 11.81 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.27), residues: 936 helix: 2.09 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.84 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 307 TYR 0.014 0.001 TYR A 739 PHE 0.016 0.002 PHE A 681 TRP 0.010 0.002 TRP A 287 HIS 0.002 0.001 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7899) covalent geometry : angle 0.48030 (10707) SS BOND : bond 0.00079 ( 4) SS BOND : angle 0.35633 ( 8) hydrogen bonds : bond 0.04031 ( 520) hydrogen bonds : angle 4.04515 ( 1506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.270 Fit side-chains REVERT: A 294 ARG cc_start: 0.7827 (mtp85) cc_final: 0.7537 (mtp85) REVERT: A 296 MET cc_start: 0.8556 (mtm) cc_final: 0.8009 (mtp) REVERT: A 360 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7223 (pp) REVERT: A 433 LYS cc_start: 0.7001 (mmmm) cc_final: 0.6654 (mttp) REVERT: A 631 LYS cc_start: 0.7574 (mmtm) cc_final: 0.7028 (ttmt) REVERT: A 667 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7809 (mm) REVERT: A 705 ARG cc_start: 0.7123 (mtm110) cc_final: 0.6730 (ttm110) REVERT: B 296 MET cc_start: 0.8554 (mtm) cc_final: 0.8038 (mtp) REVERT: B 319 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7768 (mp) REVERT: B 433 LYS cc_start: 0.6840 (mmmm) cc_final: 0.6517 (mttp) REVERT: B 480 ASP cc_start: 0.8407 (t0) cc_final: 0.8081 (t0) REVERT: B 513 ASP cc_start: 0.7510 (t0) cc_final: 0.6943 (t70) REVERT: B 515 GLN cc_start: 0.8109 (mt0) cc_final: 0.7898 (mt0) REVERT: B 624 LYS cc_start: 0.8082 (ttpp) cc_final: 0.7646 (mtmm) REVERT: B 631 LYS cc_start: 0.7564 (mmtm) cc_final: 0.6937 (ttmt) REVERT: B 667 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7756 (mm) REVERT: B 670 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6968 (tt0) REVERT: B 705 ARG cc_start: 0.7204 (mtm110) cc_final: 0.6751 (ttm110) outliers start: 17 outliers final: 6 residues processed: 93 average time/residue: 0.4807 time to fit residues: 47.5384 Evaluate side-chains 91 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 667 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 13 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.142547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.107453 restraints weight = 8493.461| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.74 r_work: 0.3107 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7903 Z= 0.117 Angle : 0.448 5.153 10715 Z= 0.238 Chirality : 0.038 0.124 1247 Planarity : 0.004 0.043 1249 Dihedral : 14.768 127.178 1715 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.97 % Allowed : 13.12 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.07 (0.27), residues: 936 helix: 2.22 (0.19), residues: 658 sheet: None (None), residues: 0 loop : -0.74 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 307 TYR 0.017 0.001 TYR A 739 PHE 0.014 0.001 PHE A 681 TRP 0.010 0.001 TRP A 733 HIS 0.003 0.001 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7899) covalent geometry : angle 0.44813 (10707) SS BOND : bond 0.00047 ( 4) SS BOND : angle 0.29959 ( 8) hydrogen bonds : bond 0.03787 ( 520) hydrogen bonds : angle 3.94610 ( 1506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.249 Fit side-chains REVERT: A 294 ARG cc_start: 0.7777 (mtp85) cc_final: 0.7499 (mtp85) REVERT: A 296 MET cc_start: 0.8575 (mtm) cc_final: 0.8020 (mtp) REVERT: A 360 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7177 (pp) REVERT: A 433 LYS cc_start: 0.6998 (mmmm) cc_final: 0.6648 (mttp) REVERT: A 631 LYS cc_start: 0.7607 (mmtm) cc_final: 0.7017 (ttmt) REVERT: A 660 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7691 (tp) REVERT: A 667 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7787 (mm) REVERT: A 705 ARG cc_start: 0.7107 (mtm110) cc_final: 0.6719 (ttm110) REVERT: B 296 MET cc_start: 0.8556 (mtm) cc_final: 0.7985 (mtp) REVERT: B 319 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7727 (mp) REVERT: B 433 LYS cc_start: 0.6833 (mmmm) cc_final: 0.6498 (mttp) REVERT: B 480 ASP cc_start: 0.8404 (t0) cc_final: 0.8082 (t0) REVERT: B 513 ASP cc_start: 0.7495 (t0) cc_final: 0.6936 (t70) REVERT: B 624 LYS cc_start: 0.8046 (ttpp) cc_final: 0.7639 (mtpt) REVERT: B 631 LYS cc_start: 0.7555 (mmtm) cc_final: 0.6955 (ttmt) REVERT: B 670 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6842 (tt0) REVERT: B 705 ARG cc_start: 0.7205 (mtm110) cc_final: 0.6733 (ttm110) outliers start: 15 outliers final: 5 residues processed: 93 average time/residue: 0.4833 time to fit residues: 48.0017 Evaluate side-chains 93 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 593 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 77 optimal weight: 0.0670 chunk 45 optimal weight: 0.6980 chunk 64 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.145556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111043 restraints weight = 8562.872| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.74 r_work: 0.3131 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7903 Z= 0.099 Angle : 0.427 5.327 10715 Z= 0.226 Chirality : 0.038 0.121 1247 Planarity : 0.003 0.042 1249 Dihedral : 14.117 124.506 1715 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.97 % Allowed : 13.39 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.27), residues: 936 helix: 2.43 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -0.80 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 294 TYR 0.015 0.001 TYR A 739 PHE 0.013 0.001 PHE B 681 TRP 0.010 0.001 TRP A 733 HIS 0.002 0.001 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 7899) covalent geometry : angle 0.42756 (10707) SS BOND : bond 0.00064 ( 4) SS BOND : angle 0.31667 ( 8) hydrogen bonds : bond 0.03571 ( 520) hydrogen bonds : angle 3.82972 ( 1506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.319 Fit side-chains REVERT: A 294 ARG cc_start: 0.7767 (mtp85) cc_final: 0.7514 (mtp85) REVERT: A 296 MET cc_start: 0.8558 (mtm) cc_final: 0.7988 (mtp) REVERT: A 360 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7227 (pp) REVERT: A 433 LYS cc_start: 0.6994 (mmmm) cc_final: 0.6631 (mttp) REVERT: A 631 LYS cc_start: 0.7562 (mmtm) cc_final: 0.7137 (mtmp) REVERT: A 660 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7736 (tp) REVERT: A 667 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7726 (mm) REVERT: A 705 ARG cc_start: 0.7107 (mtm110) cc_final: 0.6717 (ttm110) REVERT: B 296 MET cc_start: 0.8559 (mtm) cc_final: 0.7996 (mtp) REVERT: B 319 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7691 (mp) REVERT: B 433 LYS cc_start: 0.6859 (mmmm) cc_final: 0.6518 (mttp) REVERT: B 480 ASP cc_start: 0.8405 (t0) cc_final: 0.8093 (t0) REVERT: B 513 ASP cc_start: 0.7370 (t0) cc_final: 0.6824 (t70) REVERT: B 624 LYS cc_start: 0.7988 (ttpp) cc_final: 0.7598 (mtpt) REVERT: B 631 LYS cc_start: 0.7593 (mmtm) cc_final: 0.7129 (mtmp) REVERT: B 705 ARG cc_start: 0.7259 (mtm110) cc_final: 0.6773 (ttm110) outliers start: 15 outliers final: 5 residues processed: 94 average time/residue: 0.4809 time to fit residues: 48.3164 Evaluate side-chains 94 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 609 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 0.0470 chunk 22 optimal weight: 0.6980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN A 591 GLN B 591 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112067 restraints weight = 8450.463| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.75 r_work: 0.3132 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7903 Z= 0.102 Angle : 0.434 5.666 10715 Z= 0.229 Chirality : 0.038 0.120 1247 Planarity : 0.004 0.085 1249 Dihedral : 13.887 124.212 1715 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.10 % Allowed : 13.52 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.27), residues: 936 helix: 2.47 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -0.77 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 294 TYR 0.015 0.001 TYR A 739 PHE 0.013 0.001 PHE A 681 TRP 0.010 0.001 TRP A 733 HIS 0.003 0.001 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 7899) covalent geometry : angle 0.43443 (10707) SS BOND : bond 0.00060 ( 4) SS BOND : angle 0.33001 ( 8) hydrogen bonds : bond 0.03566 ( 520) hydrogen bonds : angle 3.82742 ( 1506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.268 Fit side-chains REVERT: A 294 ARG cc_start: 0.7764 (mtp85) cc_final: 0.7505 (mtp85) REVERT: A 296 MET cc_start: 0.8560 (mtm) cc_final: 0.7989 (mtp) REVERT: A 360 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7263 (pp) REVERT: A 433 LYS cc_start: 0.6990 (mmmm) cc_final: 0.6621 (mttp) REVERT: A 506 ASN cc_start: 0.7083 (m-40) cc_final: 0.6612 (m-40) REVERT: A 631 LYS cc_start: 0.7551 (mmtm) cc_final: 0.7131 (mtmp) REVERT: A 660 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7750 (tp) REVERT: A 667 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7735 (mm) REVERT: A 705 ARG cc_start: 0.7094 (mtm110) cc_final: 0.6697 (ttm110) REVERT: B 296 MET cc_start: 0.8563 (mtm) cc_final: 0.7991 (mtp) REVERT: B 319 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7691 (mp) REVERT: B 433 LYS cc_start: 0.6861 (mmmm) cc_final: 0.6512 (mttp) REVERT: B 480 ASP cc_start: 0.8397 (t0) cc_final: 0.8069 (t0) REVERT: B 513 ASP cc_start: 0.7466 (t0) cc_final: 0.6895 (t70) REVERT: B 515 GLN cc_start: 0.7975 (mt0) cc_final: 0.7420 (mt0) REVERT: B 624 LYS cc_start: 0.7983 (ttpp) cc_final: 0.7567 (mtpt) REVERT: B 631 LYS cc_start: 0.7542 (mmtm) cc_final: 0.7108 (mtmp) REVERT: B 667 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7735 (mm) REVERT: B 705 ARG cc_start: 0.7230 (mtm110) cc_final: 0.6755 (ttm110) outliers start: 16 outliers final: 5 residues processed: 92 average time/residue: 0.4687 time to fit residues: 46.2034 Evaluate side-chains 92 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 667 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 40 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 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 = 0.3717 r_free = 0.3717 target = 0.144637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.109364 restraints weight = 8432.833| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.76 r_work: 0.3131 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7903 Z= 0.105 Angle : 0.442 7.070 10715 Z= 0.231 Chirality : 0.038 0.123 1247 Planarity : 0.004 0.081 1249 Dihedral : 13.745 124.320 1715 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.71 % Allowed : 14.17 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.27), residues: 936 helix: 2.49 (0.19), residues: 652 sheet: None (None), residues: 0 loop : -0.87 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 294 TYR 0.015 0.001 TYR A 739 PHE 0.013 0.001 PHE A 681 TRP 0.010 0.001 TRP A 733 HIS 0.002 0.001 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 7899) covalent geometry : angle 0.44251 (10707) SS BOND : bond 0.00054 ( 4) SS BOND : angle 0.33524 ( 8) hydrogen bonds : bond 0.03602 ( 520) hydrogen bonds : angle 3.84428 ( 1506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.252 Fit side-chains REVERT: A 294 ARG cc_start: 0.7766 (mtp85) cc_final: 0.7497 (mtp85) REVERT: A 296 MET cc_start: 0.8561 (mtm) cc_final: 0.7979 (mtp) REVERT: A 360 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7210 (pp) REVERT: A 433 LYS cc_start: 0.6977 (mmmm) cc_final: 0.6617 (mttp) REVERT: A 506 ASN cc_start: 0.7173 (m-40) cc_final: 0.6705 (m-40) REVERT: A 631 LYS cc_start: 0.7627 (mmtm) cc_final: 0.7165 (mtmp) REVERT: A 660 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7751 (tp) REVERT: A 667 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7711 (mm) REVERT: A 705 ARG cc_start: 0.7103 (mtm110) cc_final: 0.6704 (ttm110) REVERT: B 296 MET cc_start: 0.8566 (mtm) cc_final: 0.7997 (mtp) REVERT: B 319 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7700 (mp) REVERT: B 433 LYS cc_start: 0.6847 (mmmm) cc_final: 0.6505 (mttp) REVERT: B 480 ASP cc_start: 0.8404 (t0) cc_final: 0.8078 (t0) REVERT: B 513 ASP cc_start: 0.7464 (t0) cc_final: 0.6896 (t70) REVERT: B 515 GLN cc_start: 0.7987 (mt0) cc_final: 0.7435 (mt0) REVERT: B 624 LYS cc_start: 0.7987 (ttpp) cc_final: 0.7571 (mtpt) REVERT: B 631 LYS cc_start: 0.7585 (mmtm) cc_final: 0.7125 (mtmp) REVERT: B 667 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7745 (mm) REVERT: B 705 ARG cc_start: 0.7248 (mtm110) cc_final: 0.6760 (ttm110) outliers start: 13 outliers final: 5 residues processed: 90 average time/residue: 0.4450 time to fit residues: 43.0406 Evaluate side-chains 92 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 667 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.142182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.107119 restraints weight = 8424.926| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.73 r_work: 0.3103 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7903 Z= 0.131 Angle : 0.483 7.718 10715 Z= 0.251 Chirality : 0.039 0.136 1247 Planarity : 0.004 0.079 1249 Dihedral : 14.006 126.101 1715 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.57 % Allowed : 14.30 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.27), residues: 936 helix: 2.34 (0.19), residues: 652 sheet: None (None), residues: 0 loop : -0.93 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 307 TYR 0.016 0.002 TYR A 739 PHE 0.015 0.002 PHE A 681 TRP 0.010 0.001 TRP A 733 HIS 0.002 0.001 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7899) covalent geometry : angle 0.48356 (10707) SS BOND : bond 0.00053 ( 4) SS BOND : angle 0.37709 ( 8) hydrogen bonds : bond 0.03878 ( 520) hydrogen bonds : angle 3.95679 ( 1506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2661.18 seconds wall clock time: 46 minutes 2.67 seconds (2762.67 seconds total)