Starting phenix.real_space_refine on Thu Nov 14 14:56:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf4_39210/11_2024/8yf4_39210.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf4_39210/11_2024/8yf4_39210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf4_39210/11_2024/8yf4_39210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf4_39210/11_2024/8yf4_39210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf4_39210/11_2024/8yf4_39210.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf4_39210/11_2024/8yf4_39210.cif" } resolution = 3.41 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= -0.001 sd= 0.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 4456 2.51 5 N 1048 2.21 5 O 1086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6620 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3275 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 15, 'TRANS': 377} Chain: "B" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3275 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 15, 'TRANS': 377} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.07, per 1000 atoms: 0.61 Number of scatterers: 6620 At special positions: 0 Unit cell: (77, 67.1, 128.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1086 8.00 N 1048 7.00 C 4456 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " distance=2.04 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: 1.77 Conformation dependent library (CDL) restraints added in 932.1 milliseconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 74.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 230 through 258 removed outlier: 3.501A pdb=" N THR A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 295 removed outlier: 5.118A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 337 removed outlier: 3.710A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 removed outlier: 4.307A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 390 through 402 removed outlier: 3.695A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 419 removed outlier: 4.130A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 471 removed outlier: 3.646A pdb=" N VAL A 451 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 476 through 501 removed outlier: 4.260A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 3.828A pdb=" N PHE A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 571 removed outlier: 3.915A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 583 removed outlier: 4.260A pdb=" N ILE A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 579 " --> pdb=" O ILE A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 597 removed outlier: 3.600A pdb=" N ILE A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 619 removed outlier: 4.031A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 258 removed outlier: 3.753A pdb=" N THR B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.521A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 296 " --> pdb=" O TRP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.521A pdb=" N ILE B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 337 removed outlier: 3.833A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 404 through 419 Processing helix chain 'B' and resid 448 through 471 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 473 through 503 removed outlier: 3.745A pdb=" N GLY B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 531 removed outlier: 3.534A pdb=" N TYR B 512 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 513 " --> pdb=" O VAL B 509 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP B 514 " --> pdb=" O PHE B 510 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR B 524 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE B 527 " --> pdb=" O CYS B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 583 removed outlier: 4.313A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 567 " --> pdb=" O ILE B 563 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 619 Proline residue: B 598 - end of helix removed outlier: 4.166A pdb=" N VAL B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N PHE B 602 " --> pdb=" O PRO B 598 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1101 1.33 - 1.45: 2025 1.45 - 1.57: 3678 1.57 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 6846 Sorted by residual: bond pdb=" CG1 ILE A 519 " pdb=" CD1 ILE A 519 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.07e+00 bond pdb=" CB LYS B 258 " pdb=" CG LYS B 258 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.77e+00 bond pdb=" CG1 ILE A 527 " pdb=" CD1 ILE A 527 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.54e+00 bond pdb=" CB GLU B 411 " pdb=" CG GLU B 411 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CB ARG B 468 " pdb=" CG ARG B 468 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.55e-01 ... (remaining 6841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 9110 1.46 - 2.92: 171 2.92 - 4.37: 33 4.37 - 5.83: 14 5.83 - 7.29: 4 Bond angle restraints: 9332 Sorted by residual: angle pdb=" CA LYS B 258 " pdb=" CB LYS B 258 " pdb=" CG LYS B 258 " ideal model delta sigma weight residual 114.10 121.21 -7.11 2.00e+00 2.50e-01 1.26e+01 angle pdb=" CB LYS B 258 " pdb=" CG LYS B 258 " pdb=" CD LYS B 258 " ideal model delta sigma weight residual 111.30 118.59 -7.29 2.30e+00 1.89e-01 1.00e+01 angle pdb=" N ILE A 519 " pdb=" CA ILE A 519 " pdb=" CB ILE A 519 " ideal model delta sigma weight residual 110.54 114.84 -4.30 1.36e+00 5.41e-01 1.00e+01 angle pdb=" CA GLU B 411 " pdb=" CB GLU B 411 " pdb=" CG GLU B 411 " ideal model delta sigma weight residual 114.10 120.31 -6.21 2.00e+00 2.50e-01 9.65e+00 angle pdb=" CA ILE A 519 " pdb=" CB ILE A 519 " pdb=" CG1 ILE A 519 " ideal model delta sigma weight residual 110.40 115.62 -5.22 1.70e+00 3.46e-01 9.44e+00 ... (remaining 9327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 3303 16.10 - 32.20: 476 32.20 - 48.29: 169 48.29 - 64.39: 31 64.39 - 80.49: 9 Dihedral angle restraints: 3988 sinusoidal: 1666 harmonic: 2322 Sorted by residual: dihedral pdb=" CB CYS B 415 " pdb=" SG CYS B 415 " pdb=" SG CYS B 440 " pdb=" CB CYS B 440 " ideal model delta sinusoidal sigma weight residual 93.00 138.60 -45.60 1 1.00e+01 1.00e-02 2.88e+01 dihedral pdb=" CA ILE B 342 " pdb=" C ILE B 342 " pdb=" N PRO B 343 " pdb=" CA PRO B 343 " ideal model delta harmonic sigma weight residual -180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ILE A 342 " pdb=" C ILE A 342 " pdb=" N PRO A 343 " pdb=" CA PRO A 343 " ideal model delta harmonic sigma weight residual 180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 3985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 636 0.028 - 0.057: 229 0.057 - 0.085: 119 0.085 - 0.114: 31 0.114 - 0.142: 9 Chirality restraints: 1024 Sorted by residual: chirality pdb=" CB THR A 261 " pdb=" CA THR A 261 " pdb=" OG1 THR A 261 " pdb=" CG2 THR A 261 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA PRO B 343 " pdb=" N PRO B 343 " pdb=" C PRO B 343 " pdb=" CB PRO B 343 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CB ILE B 342 " pdb=" CA ILE B 342 " pdb=" CG1 ILE B 342 " pdb=" CG2 ILE B 342 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 1021 not shown) Planarity restraints: 1130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 357 " -0.012 2.00e-02 2.50e+03 1.61e-02 4.56e+00 pdb=" CG PHE A 357 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE A 357 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 357 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 357 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 357 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 357 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 286 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C GLY A 286 " -0.028 2.00e-02 2.50e+03 pdb=" O GLY A 286 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 287 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 280 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.42e+00 pdb=" C GLU A 280 " 0.027 2.00e-02 2.50e+03 pdb=" O GLU A 280 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE A 281 " -0.009 2.00e-02 2.50e+03 ... (remaining 1127 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 56 2.63 - 3.20: 6084 3.20 - 3.77: 10179 3.77 - 4.33: 12957 4.33 - 4.90: 21637 Nonbonded interactions: 50913 Sorted by model distance: nonbonded pdb=" O ILE A 575 " pdb=" OG SER A 578 " model vdw 2.064 3.040 nonbonded pdb=" O SER B 578 " pdb=" OG1 THR B 582 " model vdw 2.086 3.040 nonbonded pdb=" O ILE A 271 " pdb=" OH TYR A 352 " model vdw 2.185 3.040 nonbonded pdb=" NH2 ARG A 548 " pdb=" OE1 GLU A 613 " model vdw 2.242 3.120 nonbonded pdb=" N GLU A 501 " pdb=" OE1 GLU A 501 " model vdw 2.260 3.120 ... (remaining 50908 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.690 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6846 Z= 0.178 Angle : 0.546 7.291 9332 Z= 0.302 Chirality : 0.039 0.142 1024 Planarity : 0.004 0.028 1130 Dihedral : 17.002 80.488 2486 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.86 % Allowed : 27.57 % Favored : 71.57 % 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: 0.92 (0.31), residues: 782 helix: 1.63 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -2.06 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 607 HIS 0.003 0.001 HIS A 313 PHE 0.037 0.001 PHE A 357 TYR 0.015 0.001 TYR B 345 ARG 0.005 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.755 Fit side-chains REVERT: B 258 LYS cc_start: 0.5850 (tppt) cc_final: 0.5364 (tptm) outliers start: 6 outliers final: 4 residues processed: 104 average time/residue: 0.1996 time to fit residues: 27.3462 Evaluate side-chains 103 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain B residue 344 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 0.0000 chunk 32 optimal weight: 0.0040 chunk 20 optimal weight: 0.0980 chunk 39 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6846 Z= 0.158 Angle : 0.498 5.440 9332 Z= 0.270 Chirality : 0.038 0.139 1024 Planarity : 0.003 0.035 1130 Dihedral : 6.108 59.370 1015 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.14 % Allowed : 25.14 % Favored : 72.71 % 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: 1.55 (0.31), residues: 782 helix: 2.09 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -2.05 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 528 HIS 0.002 0.000 HIS A 313 PHE 0.026 0.001 PHE A 357 TYR 0.019 0.001 TYR A 496 ARG 0.003 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.794 Fit side-chains REVERT: A 524 TYR cc_start: 0.7189 (t80) cc_final: 0.6793 (t80) REVERT: B 258 LYS cc_start: 0.5564 (tppt) cc_final: 0.5193 (tptm) REVERT: B 452 GLN cc_start: 0.8457 (tp-100) cc_final: 0.7479 (tp-100) REVERT: B 492 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.6470 (t80) outliers start: 15 outliers final: 4 residues processed: 123 average time/residue: 0.1759 time to fit residues: 29.4662 Evaluate side-chains 105 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain B residue 492 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.2980 chunk 21 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 19 optimal weight: 0.0270 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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: 0.7176 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6846 Z= 0.186 Angle : 0.507 5.579 9332 Z= 0.273 Chirality : 0.039 0.174 1024 Planarity : 0.003 0.033 1130 Dihedral : 5.536 58.371 1008 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.43 % Allowed : 23.71 % Favored : 72.86 % 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: 1.56 (0.31), residues: 782 helix: 2.12 (0.21), residues: 565 sheet: None (None), residues: 0 loop : -2.04 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 528 HIS 0.005 0.001 HIS A 313 PHE 0.024 0.001 PHE A 394 TYR 0.017 0.001 TYR B 524 ARG 0.004 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.723 Fit side-chains REVERT: A 283 PHE cc_start: 0.6589 (OUTLIER) cc_final: 0.6190 (t80) REVERT: A 314 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7394 (mm-40) REVERT: A 508 MET cc_start: 0.4735 (pmm) cc_final: 0.4496 (ptt) REVERT: A 524 TYR cc_start: 0.7325 (t80) cc_final: 0.6780 (t80) REVERT: A 617 LEU cc_start: 0.6596 (OUTLIER) cc_final: 0.6222 (mm) REVERT: B 258 LYS cc_start: 0.5540 (tppt) cc_final: 0.5199 (tptm) REVERT: B 331 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.6923 (tp) REVERT: B 394 PHE cc_start: 0.6843 (OUTLIER) cc_final: 0.5159 (p90) REVERT: B 492 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6148 (t80) outliers start: 24 outliers final: 12 residues processed: 123 average time/residue: 0.2004 time to fit residues: 33.2461 Evaluate side-chains 114 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6846 Z= 0.250 Angle : 0.560 6.605 9332 Z= 0.300 Chirality : 0.041 0.161 1024 Planarity : 0.004 0.034 1130 Dihedral : 5.730 57.985 1008 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.63 % Favored : 94.25 % Rotamer: Outliers : 5.43 % Allowed : 21.43 % Favored : 73.14 % 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: 1.23 (0.30), residues: 782 helix: 1.87 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -2.17 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 607 HIS 0.008 0.001 HIS B 299 PHE 0.030 0.002 PHE A 394 TYR 0.018 0.002 TYR B 524 ARG 0.006 0.001 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 0.892 Fit side-chains REVERT: A 283 PHE cc_start: 0.6672 (OUTLIER) cc_final: 0.6118 (t80) REVERT: A 314 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7482 (mm-40) REVERT: A 331 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.6970 (tp) REVERT: A 394 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.6487 (p90) REVERT: A 617 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6595 (mm) REVERT: B 331 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7024 (tp) REVERT: B 394 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.5314 (p90) REVERT: B 452 GLN cc_start: 0.8598 (tp-100) cc_final: 0.7388 (tp-100) REVERT: B 492 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.5897 (t80) outliers start: 38 outliers final: 19 residues processed: 129 average time/residue: 0.1980 time to fit residues: 34.9599 Evaluate side-chains 116 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 19 optimal weight: 0.0030 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN B 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6846 Z= 0.204 Angle : 0.538 6.730 9332 Z= 0.289 Chirality : 0.040 0.164 1024 Planarity : 0.003 0.035 1130 Dihedral : 5.631 58.003 1008 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.50 % Favored : 94.37 % Rotamer: Outliers : 5.00 % Allowed : 22.86 % Favored : 72.14 % 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: 1.36 (0.30), residues: 782 helix: 1.97 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -2.17 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 528 HIS 0.004 0.001 HIS B 299 PHE 0.024 0.001 PHE A 394 TYR 0.012 0.001 TYR A 352 ARG 0.003 0.000 ARG B 548 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.692 Fit side-chains REVERT: A 283 PHE cc_start: 0.6632 (OUTLIER) cc_final: 0.6062 (t80) REVERT: A 314 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7402 (mm-40) REVERT: A 331 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7053 (tp) REVERT: A 617 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6380 (mm) REVERT: B 394 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.5162 (p90) REVERT: B 492 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.5990 (t80) outliers start: 35 outliers final: 21 residues processed: 129 average time/residue: 0.1724 time to fit residues: 30.4644 Evaluate side-chains 118 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 608 ASN B 387 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6846 Z= 0.190 Angle : 0.530 6.553 9332 Z= 0.284 Chirality : 0.040 0.169 1024 Planarity : 0.003 0.036 1130 Dihedral : 5.579 57.425 1008 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.14 % Allowed : 23.57 % Favored : 71.29 % 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: 1.48 (0.30), residues: 782 helix: 2.06 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -2.15 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 528 HIS 0.004 0.001 HIS A 313 PHE 0.022 0.001 PHE A 394 TYR 0.017 0.001 TYR A 496 ARG 0.003 0.000 ARG B 548 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.766 Fit side-chains REVERT: A 314 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7401 (mm-40) REVERT: A 331 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7026 (tp) REVERT: A 394 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6385 (p90) REVERT: A 617 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6400 (mm) REVERT: B 394 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.5132 (p90) REVERT: B 452 GLN cc_start: 0.8540 (tp-100) cc_final: 0.7425 (tp-100) REVERT: B 492 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.5781 (t80) REVERT: B 510 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.6419 (t80) outliers start: 36 outliers final: 24 residues processed: 128 average time/residue: 0.1706 time to fit residues: 29.8595 Evaluate side-chains 121 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 488 PHE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 510 PHE Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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: 0.7216 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6846 Z= 0.188 Angle : 0.527 6.564 9332 Z= 0.283 Chirality : 0.040 0.171 1024 Planarity : 0.003 0.035 1130 Dihedral : 5.540 57.021 1008 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 5.00 % Allowed : 23.57 % Favored : 71.43 % 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: 1.53 (0.31), residues: 782 helix: 2.11 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -2.14 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 528 HIS 0.005 0.001 HIS B 387 PHE 0.020 0.001 PHE A 394 TYR 0.009 0.001 TYR A 412 ARG 0.003 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.723 Fit side-chains REVERT: A 314 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7363 (mm-40) REVERT: A 331 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7118 (tp) REVERT: A 394 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6461 (p90) REVERT: A 524 TYR cc_start: 0.7496 (t80) cc_final: 0.7156 (t80) REVERT: A 617 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6399 (mm) REVERT: B 394 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.5126 (p90) REVERT: B 420 GLU cc_start: 0.5695 (tm-30) cc_final: 0.5328 (tt0) REVERT: B 452 GLN cc_start: 0.8546 (tp-100) cc_final: 0.7449 (tp-100) REVERT: B 492 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.5920 (t80) REVERT: B 510 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.6448 (t80) outliers start: 35 outliers final: 21 residues processed: 123 average time/residue: 0.1635 time to fit residues: 27.3589 Evaluate side-chains 120 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 488 PHE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 510 PHE Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.1980 chunk 47 optimal weight: 0.0170 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 0.0170 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 0.0000 overall best weight: 0.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 6846 Z= 0.165 Angle : 0.504 5.650 9332 Z= 0.273 Chirality : 0.039 0.184 1024 Planarity : 0.003 0.034 1130 Dihedral : 5.388 56.569 1008 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.86 % Allowed : 24.57 % Favored : 71.57 % 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: 1.81 (0.31), residues: 782 helix: 2.32 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -2.05 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 292 HIS 0.002 0.000 HIS A 616 PHE 0.013 0.001 PHE A 394 TYR 0.021 0.001 TYR A 496 ARG 0.002 0.000 ARG B 548 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.706 Fit side-chains REVERT: A 331 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7078 (tp) REVERT: A 394 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.6310 (p90) REVERT: A 617 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6039 (mm) REVERT: B 358 PHE cc_start: 0.8174 (t80) cc_final: 0.7958 (t80) REVERT: B 394 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.4922 (p90) REVERT: B 395 TRP cc_start: 0.7831 (t60) cc_final: 0.7408 (t60) REVERT: B 452 GLN cc_start: 0.8495 (tp-100) cc_final: 0.7479 (tp-100) REVERT: B 492 PHE cc_start: 0.7161 (OUTLIER) cc_final: 0.5871 (t80) REVERT: B 510 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.6449 (t80) outliers start: 27 outliers final: 19 residues processed: 120 average time/residue: 0.1855 time to fit residues: 29.7647 Evaluate side-chains 119 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 488 PHE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 510 PHE Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 590 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.0170 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 69 optimal weight: 0.0980 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6846 Z= 0.180 Angle : 0.524 5.984 9332 Z= 0.284 Chirality : 0.039 0.180 1024 Planarity : 0.003 0.034 1130 Dihedral : 5.414 56.791 1008 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.86 % Allowed : 24.57 % Favored : 71.57 % 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: 1.74 (0.31), residues: 782 helix: 2.27 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -2.06 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 514 HIS 0.003 0.001 HIS A 313 PHE 0.041 0.001 PHE A 357 TYR 0.009 0.001 TYR A 368 ARG 0.005 0.000 ARG B 548 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.781 Fit side-chains REVERT: A 331 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7081 (tp) REVERT: A 394 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6307 (p90) REVERT: A 524 TYR cc_start: 0.7554 (t80) cc_final: 0.7175 (t80) REVERT: A 617 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6309 (mm) REVERT: B 358 PHE cc_start: 0.8196 (t80) cc_final: 0.7983 (t80) REVERT: B 394 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.4961 (p90) REVERT: B 452 GLN cc_start: 0.8557 (tp-100) cc_final: 0.7497 (tp-100) REVERT: B 492 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.5873 (t80) REVERT: B 510 PHE cc_start: 0.6722 (OUTLIER) cc_final: 0.6453 (t80) outliers start: 27 outliers final: 18 residues processed: 115 average time/residue: 0.1821 time to fit residues: 28.5481 Evaluate side-chains 118 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 488 PHE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 510 PHE Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.0000 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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: 0.7208 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6846 Z= 0.207 Angle : 0.557 8.160 9332 Z= 0.302 Chirality : 0.040 0.173 1024 Planarity : 0.003 0.034 1130 Dihedral : 5.480 56.825 1008 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.71 % Allowed : 25.00 % Favored : 71.29 % 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: 1.64 (0.31), residues: 782 helix: 2.16 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -2.01 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 266 HIS 0.004 0.001 HIS B 299 PHE 0.040 0.001 PHE A 357 TYR 0.018 0.001 TYR A 496 ARG 0.005 0.001 ARG A 371 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.778 Fit side-chains REVERT: A 331 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7095 (tp) REVERT: A 394 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6340 (p90) REVERT: A 617 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6453 (mm) REVERT: B 358 PHE cc_start: 0.8237 (t80) cc_final: 0.8012 (t80) REVERT: B 394 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.5042 (p90) REVERT: B 452 GLN cc_start: 0.8561 (tp-100) cc_final: 0.7464 (tp-100) REVERT: B 492 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.5975 (t80) REVERT: B 510 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.6541 (t80) outliers start: 26 outliers final: 19 residues processed: 113 average time/residue: 0.1852 time to fit residues: 28.4136 Evaluate side-chains 115 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 518 TYR Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 488 PHE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 510 PHE Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.0010 chunk 25 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 0.0670 chunk 11 optimal weight: 0.0870 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.219225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.178767 restraints weight = 7834.420| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.80 r_work: 0.3812 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6846 Z= 0.176 Angle : 0.531 8.700 9332 Z= 0.289 Chirality : 0.039 0.176 1024 Planarity : 0.003 0.039 1130 Dihedral : 5.374 56.639 1008 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.86 % Allowed : 25.00 % Favored : 71.14 % 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: 1.78 (0.31), residues: 782 helix: 2.30 (0.22), residues: 565 sheet: None (None), residues: 0 loop : -2.04 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 528 HIS 0.002 0.000 HIS A 313 PHE 0.036 0.001 PHE A 357 TYR 0.009 0.001 TYR A 368 ARG 0.007 0.000 ARG A 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1722.37 seconds wall clock time: 32 minutes 14.39 seconds (1934.39 seconds total)