Starting phenix.real_space_refine on Tue Nov 14 05:39:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgo_14709/11_2023/7zgo_14709.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgo_14709/11_2023/7zgo_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_14709/11_2023/7zgo_14709.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgo_14709/11_2023/7zgo_14709.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgo_14709/11_2023/7zgo_14709.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgo_14709/11_2023/7zgo_14709.pdb" } 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 Residue "A GLU 405": "OE1" <-> "OE2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B GLU 670": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 4.65, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 3.18 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.75 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: 2.27 Time building geometry restraints manager: 3.36 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: 98.94 - 105.95: 157 105.95 - 112.96: 4566 112.96 - 119.97: 2523 119.97 - 126.98: 3386 126.98 - 133.99: 75 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: 4338 28.28 - 56.56: 191 56.56 - 84.84: 30 84.84 - 113.12: 11 113.12 - 141.40: 1 Dihedral angle restraints: 4571 sinusoidal: 1885 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 4568 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 2.440 nonbonded pdb=" OH TYR B 468 " pdb=" OG SER B 539 " model vdw 2.223 2.440 nonbonded pdb=" OH TYR A 468 " pdb=" OG SER A 539 " model vdw 2.227 2.440 nonbonded pdb=" O GLY A 478 " pdb=" NH2 ARG A 546 " model vdw 2.243 2.520 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 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: 0.750 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: 3.450 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.350 Find NCS groups from input model: 0.480 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:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.130 ------------------------------------------------------------------------------- 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 : 16.842 141.402 2843 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 *********************** 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 : 0.839 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 1.0443 time to fit residues: 121.7148 Evaluate side-chains 73 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0232 ------------------------------------------------------------------------------- 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: 1.9990 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.7302 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7899 Z= 0.199 Angle : 0.498 8.332 10707 Z= 0.256 Chirality : 0.040 0.142 1247 Planarity : 0.004 0.045 1249 Dihedral : 17.120 137.089 1325 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.18 % Allowed : 8.14 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.27), residues: 936 helix: 2.17 (0.19), residues: 654 sheet: None (None), residues: 0 loop : -0.95 (0.37), residues: 282 *********************** 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 89 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.738 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 82 average time/residue: 1.0972 time to fit residues: 96.1137 Evaluate side-chains 74 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1113 time to fit residues: 1.2052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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: 0.7290 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7899 Z= 0.172 Angle : 0.460 8.357 10707 Z= 0.240 Chirality : 0.038 0.131 1247 Planarity : 0.003 0.043 1249 Dihedral : 16.446 142.416 1325 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.84 % Allowed : 9.71 % 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 (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: 2.00 (0.27), residues: 936 helix: 2.23 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -0.92 (0.38), residues: 280 *********************** 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 84 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.790 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 76 average time/residue: 1.0504 time to fit residues: 85.8763 Evaluate side-chains 76 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.1563 time to fit residues: 1.7868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 3.9990 chunk 64 optimal weight: 0.2980 chunk 44 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1603 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= 0.142 Angle : 0.430 6.633 10707 Z= 0.225 Chirality : 0.038 0.290 1247 Planarity : 0.003 0.041 1249 Dihedral : 15.877 143.513 1325 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.10 % Allowed : 11.02 % Favored : 86.88 % 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: 2.18 (0.27), residues: 936 helix: 2.39 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -0.94 (0.38), residues: 280 *********************** 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 93 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 0.794 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 84 average time/residue: 0.9874 time to fit residues: 89.6768 Evaluate side-chains 75 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.854 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.1330 time to fit residues: 1.8019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 0 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 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 435 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7899 Z= 0.156 Angle : 0.457 8.958 10707 Z= 0.234 Chirality : 0.039 0.276 1247 Planarity : 0.003 0.041 1249 Dihedral : 15.523 137.756 1325 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.71 % Allowed : 12.86 % Favored : 85.43 % 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: 2.42 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -0.89 (0.38), residues: 280 *********************** 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 83 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.823 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 76 average time/residue: 1.0477 time to fit residues: 85.7398 Evaluate side-chains 73 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.716 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.1214 time to fit residues: 1.6267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7899 Z= 0.261 Angle : 0.545 9.339 10707 Z= 0.278 Chirality : 0.042 0.279 1247 Planarity : 0.004 0.044 1249 Dihedral : 15.491 123.575 1325 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.97 % Allowed : 12.73 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.27), residues: 936 helix: 2.06 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.82 (0.39), residues: 270 *********************** 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 85 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.825 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 78 average time/residue: 1.0668 time to fit residues: 89.4199 Evaluate side-chains 72 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.4175 time to fit residues: 2.4683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7899 Z= 0.153 Angle : 0.466 9.279 10707 Z= 0.239 Chirality : 0.039 0.249 1247 Planarity : 0.003 0.043 1249 Dihedral : 14.710 104.702 1325 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.57 % Allowed : 13.25 % 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: 2.06 (0.27), residues: 936 helix: 2.22 (0.19), residues: 668 sheet: None (None), residues: 0 loop : -0.89 (0.39), residues: 268 *********************** 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 81 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.911 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 75 average time/residue: 1.0958 time to fit residues: 88.4890 Evaluate side-chains 73 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.4756 time to fit residues: 2.6856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.0370 chunk 17 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 0.0970 chunk 86 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7899 Z= 0.137 Angle : 0.444 7.856 10707 Z= 0.228 Chirality : 0.038 0.225 1247 Planarity : 0.003 0.042 1249 Dihedral : 13.922 89.283 1325 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.18 % Allowed : 13.52 % Favored : 85.30 % 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: 2.32 (0.27), residues: 936 helix: 2.51 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -0.92 (0.37), residues: 280 *********************** 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 84 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.799 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 82 average time/residue: 1.0390 time to fit residues: 91.6697 Evaluate side-chains 71 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.818 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.1548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.4980 chunk 50 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN B 515 GLN B 591 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7899 Z= 0.153 Angle : 0.459 6.957 10707 Z= 0.236 Chirality : 0.039 0.206 1247 Planarity : 0.004 0.085 1249 Dihedral : 13.827 89.837 1325 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.92 % Allowed : 13.91 % 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: 2.32 (0.27), residues: 936 helix: 2.51 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -0.93 (0.37), residues: 280 *********************** 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 76 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.814 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 73 average time/residue: 1.0119 time to fit residues: 80.0541 Evaluate side-chains 71 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1463 time to fit residues: 1.2850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2076 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= 0.224 Angle : 0.517 6.965 10707 Z= 0.264 Chirality : 0.040 0.228 1247 Planarity : 0.004 0.082 1249 Dihedral : 14.266 88.947 1325 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.79 % Allowed : 13.78 % Favored : 85.43 % 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: 2.03 (0.27), residues: 936 helix: 2.18 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.83 (0.39), residues: 270 ********************** 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 73 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.735 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 70 average time/residue: 1.0835 time to fit residues: 81.4825 Evaluate side-chains 70 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.845 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1291 time to fit residues: 1.3445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.144761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.110640 restraints weight = 8420.636| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.72 r_work: 0.3120 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7899 Z= 0.157 Angle : 0.468 7.150 10707 Z= 0.239 Chirality : 0.039 0.202 1247 Planarity : 0.004 0.078 1249 Dihedral : 13.878 89.767 1325 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.52 % Allowed : 14.30 % 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: 2.18 (0.27), residues: 936 helix: 2.39 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -0.94 (0.37), residues: 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2425.52 seconds wall clock time: 44 minutes 16.78 seconds (2656.78 seconds total)