Starting phenix.real_space_refine on Tue Sep 24 14:11:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgo_14709/09_2024/7zgo_14709.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgo_14709/09_2024/7zgo_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgo_14709/09_2024/7zgo_14709.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgo_14709/09_2024/7zgo_14709.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgo_14709/09_2024/7zgo_14709.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgo_14709/09_2024/7zgo_14709.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 5.07, per 1000 atoms: 0.65 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: 2.32 Conformation dependent library (CDL) restraints added in 859.7 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: 0.84 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: 2.26 Time building geometry restraints manager: 2.65 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 753 or resid 1301 through 1307 or resid 1309 t \ hrough 1310)) selection = (chain 'B' and (resid 284 through 753 or resid 1301 through 1307 or resid 1309 t \ hrough 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: 0.700 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.490 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.710 ------------------------------------------------------------------------------- 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 7899 Z= 0.514 Angle : 1.241 18.089 10707 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (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 TRP 0.010 0.001 TRP A 733 HIS 0.003 0.001 HIS B 695 PHE 0.016 0.002 PHE A 681 TYR 0.014 0.001 TYR A 354 ARG 0.003 0.000 ARG A 358 *********************** 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 fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.920 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: 1.1111 time to fit residues: 129.2975 Evaluate side-chains 81 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7899 Z= 0.206 Angle : 0.501 6.026 10707 Z= 0.262 Chirality : 0.040 0.128 1247 Planarity : 0.004 0.045 1249 Dihedral : 16.704 137.543 1715 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.05 % Allowed : 7.35 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.27), residues: 936 helix: 2.14 (0.19), residues: 654 sheet: None (None), residues: 0 loop : -0.89 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 287 HIS 0.003 0.001 HIS B 695 PHE 0.018 0.002 PHE B 681 TYR 0.009 0.001 TYR A 739 ARG 0.003 0.000 ARG A 307 *********************** 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 96 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.799 Fit side-chains REVERT: A 294 ARG cc_start: 0.7302 (mtp85) cc_final: 0.6930 (mtp85) REVERT: A 296 MET cc_start: 0.8263 (mtm) cc_final: 0.7581 (mtp) REVERT: A 325 MET cc_start: 0.7962 (mmt) cc_final: 0.7742 (mmp) REVERT: A 433 LYS cc_start: 0.6673 (mmmm) cc_final: 0.6336 (mttp) REVERT: A 480 ASP cc_start: 0.8170 (t0) cc_final: 0.7819 (t0) REVERT: A 513 ASP cc_start: 0.7261 (t0) cc_final: 0.7059 (t0) REVERT: A 515 GLN cc_start: 0.7723 (mt0) cc_final: 0.7344 (mt0) REVERT: A 727 MET cc_start: 0.8264 (ptm) cc_final: 0.8022 (ptm) REVERT: B 296 MET cc_start: 0.8209 (mtm) cc_final: 0.7590 (mtp) REVERT: B 428 MET cc_start: 0.5097 (mmm) cc_final: 0.4741 (tpt) REVERT: B 433 LYS cc_start: 0.6635 (mmmm) cc_final: 0.6291 (mttp) REVERT: B 480 ASP cc_start: 0.8363 (t0) cc_final: 0.7958 (t0) REVERT: B 513 ASP cc_start: 0.7230 (t0) cc_final: 0.6600 (t70) REVERT: B 624 LYS cc_start: 0.7711 (ttpp) cc_final: 0.7269 (mtmm) REVERT: B 705 ARG cc_start: 0.6736 (mtm110) cc_final: 0.6514 (ttm110) REVERT: B 727 MET cc_start: 0.8232 (ptm) cc_final: 0.7856 (ptm) outliers start: 8 outliers final: 3 residues processed: 89 average time/residue: 1.2044 time to fit residues: 113.8409 Evaluate side-chains 82 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 47 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 0.0000 chunk 85 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 76 optimal weight: 0.3980 chunk 84 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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 506 ASN B 571 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7899 Z= 0.126 Angle : 0.412 5.033 10707 Z= 0.220 Chirality : 0.037 0.129 1247 Planarity : 0.003 0.039 1249 Dihedral : 15.568 129.184 1715 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.05 % Allowed : 9.06 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.27), residues: 936 helix: 2.49 (0.19), residues: 654 sheet: None (None), residues: 0 loop : -0.79 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.002 0.001 HIS B 695 PHE 0.011 0.001 PHE B 681 TYR 0.013 0.001 TYR A 739 ARG 0.002 0.000 ARG B 294 *********************** 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 97 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.842 Fit side-chains REVERT: A 294 ARG cc_start: 0.7173 (mtp85) cc_final: 0.6910 (mtp85) REVERT: A 296 MET cc_start: 0.8261 (mtm) cc_final: 0.7615 (mtp) REVERT: A 325 MET cc_start: 0.7904 (mmt) cc_final: 0.7691 (mmp) REVERT: A 428 MET cc_start: 0.5191 (tpt) cc_final: 0.4983 (tpt) REVERT: A 433 LYS cc_start: 0.6560 (mmmm) cc_final: 0.6220 (mttp) REVERT: A 515 GLN cc_start: 0.7759 (mt0) cc_final: 0.7374 (mt0) REVERT: A 542 SER cc_start: 0.8510 (t) cc_final: 0.8267 (m) REVERT: A 631 LYS cc_start: 0.7393 (mmtm) cc_final: 0.6775 (ttmt) REVERT: B 294 ARG cc_start: 0.7074 (mtp85) cc_final: 0.6799 (ptm160) REVERT: B 296 MET cc_start: 0.8192 (mtm) cc_final: 0.7570 (mtp) REVERT: B 433 LYS cc_start: 0.6618 (mmmm) cc_final: 0.6313 (mttp) REVERT: B 480 ASP cc_start: 0.8273 (t0) cc_final: 0.7931 (t0) REVERT: B 513 ASP cc_start: 0.7241 (t0) cc_final: 0.6550 (t70) REVERT: B 624 LYS cc_start: 0.7568 (ttpp) cc_final: 0.7242 (mtpt) REVERT: B 625 ILE cc_start: 0.8112 (mt) cc_final: 0.7795 (mp) REVERT: B 631 LYS cc_start: 0.7313 (mmtm) cc_final: 0.6645 (ttmt) REVERT: B 667 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7678 (mm) REVERT: B 705 ARG cc_start: 0.6837 (mtm110) cc_final: 0.6577 (ttm110) REVERT: B 739 TYR cc_start: 0.8115 (m-80) cc_final: 0.7904 (m-80) outliers start: 8 outliers final: 1 residues processed: 92 average time/residue: 1.1848 time to fit residues: 115.8118 Evaluate side-chains 86 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU 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 84 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 90 optimal weight: 7.9990 chunk 81 optimal weight: 0.0570 chunk 24 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN B 506 ASN B 571 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7899 Z= 0.133 Angle : 0.415 5.053 10707 Z= 0.221 Chirality : 0.038 0.120 1247 Planarity : 0.004 0.068 1249 Dihedral : 15.183 125.690 1715 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.31 % Allowed : 10.10 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.27), residues: 936 helix: 2.54 (0.19), residues: 654 sheet: None (None), residues: 0 loop : -0.80 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 287 HIS 0.002 0.001 HIS B 695 PHE 0.012 0.001 PHE A 681 TYR 0.011 0.001 TYR A 739 ARG 0.001 0.000 ARG A 358 *********************** 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 fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.751 Fit side-chains REVERT: A 294 ARG cc_start: 0.7202 (mtp85) cc_final: 0.6910 (mtp85) REVERT: A 296 MET cc_start: 0.8233 (mtm) cc_final: 0.7578 (mtp) REVERT: A 325 MET cc_start: 0.7941 (mmt) cc_final: 0.7728 (mmp) REVERT: A 428 MET cc_start: 0.5306 (tpt) cc_final: 0.4970 (tpt) REVERT: A 433 LYS cc_start: 0.6655 (mmmm) cc_final: 0.6338 (mttp) REVERT: A 515 GLN cc_start: 0.7728 (mt0) cc_final: 0.7375 (mt0) REVERT: A 631 LYS cc_start: 0.7312 (mmtm) cc_final: 0.6682 (ttmt) REVERT: A 667 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7777 (mm) REVERT: B 296 MET cc_start: 0.8206 (mtm) cc_final: 0.7566 (mtp) REVERT: B 433 LYS cc_start: 0.6624 (mmmm) cc_final: 0.6313 (mttp) REVERT: B 480 ASP cc_start: 0.8280 (t0) cc_final: 0.7942 (t0) REVERT: B 513 ASP cc_start: 0.7247 (t0) cc_final: 0.6564 (t70) REVERT: B 624 LYS cc_start: 0.7527 (ttpp) cc_final: 0.7238 (mtpt) REVERT: B 631 LYS cc_start: 0.7265 (mmtm) cc_final: 0.6602 (ttmt) REVERT: B 705 ARG cc_start: 0.6810 (mtm110) cc_final: 0.6577 (ttm110) outliers start: 10 outliers final: 3 residues processed: 87 average time/residue: 1.1447 time to fit residues: 106.0067 Evaluate side-chains 88 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 394 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 0 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 30 optimal weight: 0.0980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN B 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7899 Z= 0.156 Angle : 0.433 5.087 10707 Z= 0.230 Chirality : 0.038 0.119 1247 Planarity : 0.004 0.068 1249 Dihedral : 15.007 126.729 1715 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.10 % Allowed : 10.37 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.27), residues: 936 helix: 2.44 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -0.87 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 287 HIS 0.002 0.001 HIS B 695 PHE 0.014 0.001 PHE B 681 TYR 0.011 0.001 TYR A 739 ARG 0.002 0.000 ARG B 307 *********************** 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 102 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.794 Fit side-chains REVERT: A 294 ARG cc_start: 0.7239 (mtp85) cc_final: 0.6950 (mtp85) REVERT: A 296 MET cc_start: 0.8237 (mtm) cc_final: 0.7606 (mtp) REVERT: A 325 MET cc_start: 0.7944 (mmt) cc_final: 0.7728 (mmp) REVERT: A 433 LYS cc_start: 0.6730 (mmmm) cc_final: 0.6372 (mttp) REVERT: A 506 ASN cc_start: 0.7163 (m-40) cc_final: 0.6953 (m-40) REVERT: A 515 GLN cc_start: 0.7597 (mt0) cc_final: 0.7290 (mt0) REVERT: A 631 LYS cc_start: 0.7302 (mmtm) cc_final: 0.6710 (ttmt) REVERT: A 667 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7752 (mm) REVERT: B 296 MET cc_start: 0.8201 (mtm) cc_final: 0.7538 (mtp) REVERT: B 433 LYS cc_start: 0.6572 (mmmm) cc_final: 0.6268 (mttp) REVERT: B 480 ASP cc_start: 0.8156 (t0) cc_final: 0.7789 (t0) REVERT: B 513 ASP cc_start: 0.7189 (t0) cc_final: 0.6566 (t70) REVERT: B 624 LYS cc_start: 0.7663 (ttpp) cc_final: 0.7303 (mtmm) REVERT: B 631 LYS cc_start: 0.7285 (mmtm) cc_final: 0.6662 (ttmt) REVERT: B 667 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7708 (mm) REVERT: B 705 ARG cc_start: 0.6815 (mtm110) cc_final: 0.6559 (ttm110) outliers start: 16 outliers final: 4 residues processed: 94 average time/residue: 1.0812 time to fit residues: 108.5105 Evaluate side-chains 91 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 A residue 667 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 81 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7899 Z= 0.228 Angle : 0.501 5.196 10707 Z= 0.265 Chirality : 0.040 0.125 1247 Planarity : 0.004 0.074 1249 Dihedral : 15.128 132.017 1715 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.97 % Allowed : 11.94 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.27), residues: 936 helix: 2.09 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.79 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 287 HIS 0.003 0.001 HIS B 695 PHE 0.017 0.002 PHE B 681 TYR 0.018 0.002 TYR A 739 ARG 0.002 0.000 ARG B 307 *********************** 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 100 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.869 Fit side-chains REVERT: A 294 ARG cc_start: 0.7314 (mtp85) cc_final: 0.6945 (mtp85) REVERT: A 296 MET cc_start: 0.8271 (mtm) cc_final: 0.7617 (mtp) REVERT: A 325 MET cc_start: 0.7944 (mmt) cc_final: 0.7740 (mmp) REVERT: A 360 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.6970 (pp) REVERT: A 433 LYS cc_start: 0.6834 (mmmm) cc_final: 0.6516 (mttp) REVERT: A 515 GLN cc_start: 0.7531 (mt0) cc_final: 0.7287 (mt0) REVERT: A 631 LYS cc_start: 0.7472 (mmtm) cc_final: 0.6950 (ttmt) REVERT: A 667 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7746 (mm) REVERT: A 710 TYR cc_start: 0.8217 (m-80) cc_final: 0.7945 (m-80) REVERT: B 296 MET cc_start: 0.8225 (mtm) cc_final: 0.7566 (mtp) REVERT: B 319 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7632 (mp) REVERT: B 433 LYS cc_start: 0.6679 (mmmm) cc_final: 0.6425 (mttp) REVERT: B 480 ASP cc_start: 0.8153 (t0) cc_final: 0.7780 (t0) REVERT: B 513 ASP cc_start: 0.7210 (t0) cc_final: 0.6620 (t70) REVERT: B 624 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7306 (mtmm) REVERT: B 631 LYS cc_start: 0.7396 (mmtm) cc_final: 0.6783 (ttmt) REVERT: B 667 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7710 (mm) REVERT: B 705 ARG cc_start: 0.6763 (mtm110) cc_final: 0.6552 (ttm110) REVERT: B 710 TYR cc_start: 0.8206 (m-80) cc_final: 0.7991 (m-80) outliers start: 15 outliers final: 5 residues processed: 92 average time/residue: 1.1843 time to fit residues: 116.5042 Evaluate side-chains 91 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 667 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 0.0970 chunk 54 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7899 Z= 0.135 Angle : 0.422 5.108 10707 Z= 0.225 Chirality : 0.038 0.118 1247 Planarity : 0.004 0.074 1249 Dihedral : 14.432 127.395 1715 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.18 % Allowed : 13.65 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.27), residues: 936 helix: 2.44 (0.19), residues: 652 sheet: None (None), residues: 0 loop : -0.75 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 733 HIS 0.002 0.001 HIS B 695 PHE 0.013 0.001 PHE B 681 TYR 0.018 0.001 TYR A 739 ARG 0.002 0.000 ARG B 294 *********************** 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 95 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.790 Fit side-chains REVERT: A 294 ARG cc_start: 0.7206 (mtp85) cc_final: 0.6882 (mtp85) REVERT: A 296 MET cc_start: 0.8223 (mtm) cc_final: 0.7581 (mtp) REVERT: A 325 MET cc_start: 0.7913 (mmt) cc_final: 0.7691 (mmp) REVERT: A 360 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6865 (pp) REVERT: A 433 LYS cc_start: 0.6845 (mmmm) cc_final: 0.6508 (mttp) REVERT: A 515 GLN cc_start: 0.7588 (mt0) cc_final: 0.7311 (mt0) REVERT: A 631 LYS cc_start: 0.7363 (mmtm) cc_final: 0.6855 (ttmt) REVERT: A 660 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7549 (tp) REVERT: B 296 MET cc_start: 0.8201 (mtm) cc_final: 0.7549 (mtp) REVERT: B 433 LYS cc_start: 0.6605 (mmmm) cc_final: 0.6309 (mttp) REVERT: B 480 ASP cc_start: 0.8169 (t0) cc_final: 0.7805 (t0) REVERT: B 513 ASP cc_start: 0.7243 (t0) cc_final: 0.6542 (t70) REVERT: B 515 GLN cc_start: 0.7765 (mt0) cc_final: 0.7191 (mt0) REVERT: B 624 LYS cc_start: 0.7624 (ttpp) cc_final: 0.7364 (mtpt) REVERT: B 631 LYS cc_start: 0.7406 (mmtm) cc_final: 0.6792 (ttmt) REVERT: B 667 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7744 (mm) REVERT: B 705 ARG cc_start: 0.6777 (mtm110) cc_final: 0.6548 (ttm110) outliers start: 9 outliers final: 2 residues processed: 90 average time/residue: 1.1327 time to fit residues: 108.7862 Evaluate side-chains 90 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU 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 667 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7899 Z= 0.154 Angle : 0.440 5.100 10707 Z= 0.233 Chirality : 0.038 0.118 1247 Planarity : 0.004 0.075 1249 Dihedral : 14.189 126.175 1715 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.31 % Allowed : 13.52 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.27), residues: 936 helix: 2.40 (0.19), residues: 654 sheet: None (None), residues: 0 loop : -0.81 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 733 HIS 0.003 0.001 HIS B 695 PHE 0.013 0.001 PHE A 681 TYR 0.018 0.001 TYR A 739 ARG 0.001 0.000 ARG B 294 *********************** 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 95 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.738 Fit side-chains REVERT: A 294 ARG cc_start: 0.7239 (mtp85) cc_final: 0.6904 (mtp85) REVERT: A 296 MET cc_start: 0.8236 (mtm) cc_final: 0.7590 (mtp) REVERT: A 325 MET cc_start: 0.7949 (mmt) cc_final: 0.7724 (mmp) REVERT: A 360 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6996 (pp) REVERT: A 433 LYS cc_start: 0.6792 (mmmm) cc_final: 0.6473 (mttp) REVERT: A 515 GLN cc_start: 0.7546 (mt0) cc_final: 0.7276 (mt0) REVERT: A 624 LYS cc_start: 0.7288 (mtmm) cc_final: 0.7055 (mtpt) REVERT: A 631 LYS cc_start: 0.7344 (mmtm) cc_final: 0.6844 (ttmt) REVERT: A 660 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7648 (tp) REVERT: A 667 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7773 (mm) REVERT: B 296 MET cc_start: 0.8208 (mtm) cc_final: 0.7576 (mtp) REVERT: B 433 LYS cc_start: 0.6660 (mmmm) cc_final: 0.6383 (mttp) REVERT: B 480 ASP cc_start: 0.8149 (t0) cc_final: 0.7792 (t0) REVERT: B 513 ASP cc_start: 0.7231 (t0) cc_final: 0.6560 (t70) REVERT: B 515 GLN cc_start: 0.7770 (mt0) cc_final: 0.7193 (mt0) REVERT: B 624 LYS cc_start: 0.7624 (ttpp) cc_final: 0.7361 (mtpt) REVERT: B 631 LYS cc_start: 0.7414 (mmtm) cc_final: 0.6822 (ttmt) REVERT: B 667 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7755 (mm) REVERT: B 705 ARG cc_start: 0.6820 (mtm110) cc_final: 0.6562 (ttm110) outliers start: 10 outliers final: 2 residues processed: 89 average time/residue: 1.1373 time to fit residues: 107.7980 Evaluate side-chains 90 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 667 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 36 optimal weight: 0.0270 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 overall best weight: 1.6644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN B 591 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7899 Z= 0.220 Angle : 0.492 5.662 10707 Z= 0.258 Chirality : 0.040 0.125 1247 Planarity : 0.004 0.075 1249 Dihedral : 14.335 129.982 1715 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.71 % Allowed : 13.12 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.27), residues: 936 helix: 2.22 (0.19), residues: 654 sheet: None (None), residues: 0 loop : -0.82 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 287 HIS 0.002 0.001 HIS B 695 PHE 0.016 0.002 PHE A 681 TYR 0.021 0.002 TYR A 739 ARG 0.003 0.001 ARG B 307 *********************** 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 96 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.720 Fit side-chains REVERT: A 294 ARG cc_start: 0.7285 (mtp85) cc_final: 0.6918 (mtp85) REVERT: A 296 MET cc_start: 0.8234 (mtm) cc_final: 0.7624 (mtp) REVERT: A 325 MET cc_start: 0.7969 (mmt) cc_final: 0.7750 (mmp) REVERT: A 360 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6949 (pp) REVERT: A 433 LYS cc_start: 0.6779 (mmmm) cc_final: 0.6485 (mttp) REVERT: A 515 GLN cc_start: 0.7526 (mt0) cc_final: 0.7288 (mt0) REVERT: A 631 LYS cc_start: 0.7372 (mmtm) cc_final: 0.6920 (ttmt) REVERT: A 667 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7742 (mm) REVERT: A 710 TYR cc_start: 0.8201 (m-80) cc_final: 0.7933 (m-80) REVERT: B 296 MET cc_start: 0.8239 (mtm) cc_final: 0.7583 (mtp) REVERT: B 433 LYS cc_start: 0.6671 (mmmm) cc_final: 0.6412 (mttp) REVERT: B 480 ASP cc_start: 0.8156 (t0) cc_final: 0.7790 (t0) REVERT: B 513 ASP cc_start: 0.7248 (t0) cc_final: 0.6647 (t70) REVERT: B 515 GLN cc_start: 0.7795 (mt0) cc_final: 0.7223 (mt0) REVERT: B 624 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7314 (mtmm) REVERT: B 631 LYS cc_start: 0.7384 (mmtm) cc_final: 0.6837 (ttmt) REVERT: B 667 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7691 (mm) REVERT: B 705 ARG cc_start: 0.6774 (mtm110) cc_final: 0.6545 (ttm110) outliers start: 13 outliers final: 6 residues processed: 89 average time/residue: 1.0510 time to fit residues: 99.9766 Evaluate side-chains 91 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 593 MET Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 506 ASN 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 42 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 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 0.023 7899 Z= 0.151 Angle : 0.444 6.190 10707 Z= 0.234 Chirality : 0.038 0.118 1247 Planarity : 0.004 0.076 1249 Dihedral : 13.963 127.124 1715 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.57 % Allowed : 13.39 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.27), residues: 936 helix: 2.37 (0.19), residues: 654 sheet: None (None), residues: 0 loop : -0.84 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 733 HIS 0.002 0.001 HIS B 695 PHE 0.013 0.001 PHE A 681 TYR 0.018 0.001 TYR A 739 ARG 0.002 0.000 ARG B 294 ********************** 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 99 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.819 Fit side-chains REVERT: A 294 ARG cc_start: 0.7239 (mtp85) cc_final: 0.6912 (mtp85) REVERT: A 296 MET cc_start: 0.8239 (mtm) cc_final: 0.7593 (mtp) REVERT: A 325 MET cc_start: 0.7969 (mmt) cc_final: 0.7746 (mmp) REVERT: A 360 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6888 (pp) REVERT: A 433 LYS cc_start: 0.6776 (mmmm) cc_final: 0.6476 (mttp) REVERT: A 515 GLN cc_start: 0.7554 (mt0) cc_final: 0.7293 (mt0) REVERT: A 624 LYS cc_start: 0.7297 (mtmm) cc_final: 0.7058 (mtpt) REVERT: A 631 LYS cc_start: 0.7418 (mmtm) cc_final: 0.6938 (ttmt) REVERT: A 660 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7633 (tp) REVERT: A 667 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7697 (mm) REVERT: B 296 MET cc_start: 0.8214 (mtm) cc_final: 0.7555 (mtp) REVERT: B 319 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7447 (mp) REVERT: B 433 LYS cc_start: 0.6671 (mmmm) cc_final: 0.6382 (mttp) REVERT: B 480 ASP cc_start: 0.8147 (t0) cc_final: 0.7787 (t0) REVERT: B 513 ASP cc_start: 0.7248 (t0) cc_final: 0.6568 (t70) REVERT: B 515 GLN cc_start: 0.7779 (mt0) cc_final: 0.7209 (mt0) REVERT: B 624 LYS cc_start: 0.7632 (ttpp) cc_final: 0.7366 (mtpt) REVERT: B 631 LYS cc_start: 0.7401 (mmtm) cc_final: 0.6856 (ttmt) REVERT: B 667 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7742 (mm) REVERT: B 705 ARG cc_start: 0.6810 (mtm110) cc_final: 0.6562 (ttm110) outliers start: 12 outliers final: 4 residues processed: 92 average time/residue: 1.0562 time to fit residues: 104.0398 Evaluate side-chains 95 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 667 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.0000 chunk 11 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.146928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112544 restraints weight = 8468.711| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.73 r_work: 0.3149 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7899 Z= 0.128 Angle : 0.426 7.312 10707 Z= 0.224 Chirality : 0.037 0.124 1247 Planarity : 0.004 0.073 1249 Dihedral : 13.524 121.986 1715 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.05 % Allowed : 13.78 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.27), residues: 936 helix: 2.59 (0.19), residues: 652 sheet: None (None), residues: 0 loop : -0.77 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 733 HIS 0.002 0.001 HIS B 695 PHE 0.012 0.001 PHE A 681 TYR 0.016 0.001 TYR A 739 ARG 0.002 0.000 ARG B 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2705.37 seconds wall clock time: 48 minutes 17.00 seconds (2897.00 seconds total)