Starting phenix.real_space_refine on Sun Apr 27 22:11:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yf4_39210/04_2025/8yf4_39210.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yf4_39210/04_2025/8yf4_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/cci-nas-00/data/ceres_data/8yf4_39210/04_2025/8yf4_39210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yf4_39210/04_2025/8yf4_39210.map" model { file = "/net/cci-nas-00/data/ceres_data/8yf4_39210/04_2025/8yf4_39210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yf4_39210/04_2025/8yf4_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-5669/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: 4.68, per 1000 atoms: 0.71 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: 1.75 Conformation dependent library (CDL) restraints added in 915.7 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: 0.55 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: 1.63 Time building geometry restraints manager: 2.08 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: 0.03 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.230 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.920 ------------------------------------------------------------------------------- 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 6848 Z= 0.125 Angle : 0.548 7.291 9336 Z= 0.303 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 Details of bonding type rmsd hydrogen bonds : bond 0.12782 ( 424) hydrogen bonds : angle 5.62876 ( 1272) SS BOND : bond 0.00450 ( 2) SS BOND : angle 2.20639 ( 4) covalent geometry : bond 0.00270 ( 6846) covalent geometry : angle 0.54618 ( 9332) *********************** 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 : 0.642 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: 0.2071 time to fit residues: 28.3925 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 : 0.723 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.220845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.180404 restraints weight = 7726.426| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.20 r_work: 0.3856 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 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 6848 Z= 0.118 Angle : 0.498 5.439 9336 Z= 0.270 Chirality : 0.038 0.139 1024 Planarity : 0.003 0.035 1130 Dihedral : 6.108 59.365 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 Details of bonding type rmsd hydrogen bonds : bond 0.04485 ( 424) hydrogen bonds : angle 4.00016 ( 1272) SS BOND : bond 0.00110 ( 2) SS BOND : angle 0.83803 ( 4) covalent geometry : bond 0.00242 ( 6846) covalent geometry : angle 0.49755 ( 9332) *********************** 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 : 0.715 Fit side-chains REVERT: A 406 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7642 (mt) REVERT: A 524 TYR cc_start: 0.7168 (t80) cc_final: 0.6714 (t80) REVERT: B 258 LYS cc_start: 0.5725 (tppt) cc_final: 0.5279 (tptm) REVERT: B 408 MET cc_start: 0.7179 (mtm) cc_final: 0.6929 (mtm) REVERT: B 452 GLN cc_start: 0.8576 (tp-100) cc_final: 0.7451 (tp-100) REVERT: B 492 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6533 (t80) outliers start: 15 outliers final: 4 residues processed: 123 average time/residue: 0.1683 time to fit residues: 28.2012 Evaluate side-chains 106 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 ILE 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 34 optimal weight: 0.8980 chunk 59 optimal weight: 0.0370 chunk 57 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.217666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.177463 restraints weight = 7837.883| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.51 r_work: 0.3825 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6848 Z= 0.123 Angle : 0.499 5.517 9336 Z= 0.269 Chirality : 0.039 0.178 1024 Planarity : 0.003 0.034 1130 Dihedral : 5.510 58.253 1008 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.14 % Allowed : 24.29 % Favored : 72.57 % 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: 1.60 (0.31), residues: 782 helix: 2.15 (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 0.004 0.001 HIS A 313 PHE 0.022 0.001 PHE A 394 TYR 0.017 0.001 TYR B 524 ARG 0.003 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 424) hydrogen bonds : angle 3.85615 ( 1272) SS BOND : bond 0.00151 ( 2) SS BOND : angle 0.76618 ( 4) covalent geometry : bond 0.00276 ( 6846) covalent geometry : angle 0.49858 ( 9332) *********************** 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 129 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7255 (mm-40) REVERT: A 508 MET cc_start: 0.5743 (pmm) cc_final: 0.5273 (ptt) REVERT: A 524 TYR cc_start: 0.7345 (t80) cc_final: 0.6770 (t80) REVERT: A 617 LEU cc_start: 0.6282 (OUTLIER) cc_final: 0.5819 (mm) REVERT: B 258 LYS cc_start: 0.5751 (tppt) cc_final: 0.5340 (tptm) REVERT: B 331 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.6718 (tp) REVERT: B 394 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.4992 (p90) REVERT: B 452 GLN cc_start: 0.8615 (tp-100) cc_final: 0.7476 (tp-100) REVERT: B 492 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6183 (t80) REVERT: B 531 LYS cc_start: 0.8198 (tptm) cc_final: 0.7955 (tptp) outliers start: 22 outliers final: 10 residues processed: 123 average time/residue: 0.1886 time to fit residues: 31.6694 Evaluate side-chains 112 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 401 ASN 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 71 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 50 optimal weight: 0.0040 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 387 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.218064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.177620 restraints weight = 7867.522| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.54 r_work: 0.3808 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6848 Z= 0.118 Angle : 0.491 5.490 9336 Z= 0.265 Chirality : 0.039 0.165 1024 Planarity : 0.003 0.034 1130 Dihedral : 5.475 58.421 1008 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.86 % Favored : 95.01 % Rotamer: Outliers : 4.29 % Allowed : 22.57 % 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: 1.73 (0.31), residues: 782 helix: 2.24 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -1.98 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 528 HIS 0.004 0.001 HIS A 313 PHE 0.021 0.001 PHE A 394 TYR 0.017 0.001 TYR A 496 ARG 0.003 0.000 ARG B 570 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 424) hydrogen bonds : angle 3.78915 ( 1272) SS BOND : bond 0.00196 ( 2) SS BOND : angle 0.89159 ( 4) covalent geometry : bond 0.00260 ( 6846) covalent geometry : angle 0.49116 ( 9332) *********************** 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 129 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7312 (mm-40) REVERT: A 331 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.6871 (tp) REVERT: A 508 MET cc_start: 0.5857 (pmm) cc_final: 0.5371 (ptt) REVERT: A 617 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6017 (mm) REVERT: B 394 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.5068 (p90) REVERT: B 492 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6049 (t80) REVERT: B 531 LYS cc_start: 0.8198 (tptm) cc_final: 0.7964 (tptp) outliers start: 30 outliers final: 16 residues processed: 123 average time/residue: 0.1662 time to fit residues: 27.9171 Evaluate side-chains 112 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 401 ASN 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 569 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 617 LEU 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 56 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 36 optimal weight: 0.0870 chunk 12 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.218874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.181485 restraints weight = 7634.723| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.18 r_work: 0.3860 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6848 Z= 0.128 Angle : 0.521 8.587 9336 Z= 0.277 Chirality : 0.039 0.176 1024 Planarity : 0.003 0.033 1130 Dihedral : 5.514 58.180 1008 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.86 % Allowed : 22.71 % Favored : 72.43 % 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: 1.63 (0.31), residues: 782 helix: 2.18 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -2.10 (0.41), residues: 214 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 0.023 0.001 PHE A 394 TYR 0.011 0.001 TYR B 524 ARG 0.003 0.000 ARG B 570 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 424) hydrogen bonds : angle 3.83279 ( 1272) SS BOND : bond 0.00179 ( 2) SS BOND : angle 1.10419 ( 4) covalent geometry : bond 0.00295 ( 6846) covalent geometry : angle 0.52053 ( 9332) *********************** 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 132 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7314 (mm-40) REVERT: A 331 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6857 (tp) REVERT: A 508 MET cc_start: 0.5647 (pmm) cc_final: 0.5183 (ttp) REVERT: A 524 TYR cc_start: 0.7408 (t80) cc_final: 0.6886 (t80) REVERT: A 617 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6068 (mm) REVERT: B 394 PHE cc_start: 0.6762 (OUTLIER) cc_final: 0.4981 (p90) REVERT: B 452 GLN cc_start: 0.8486 (tp-100) cc_final: 0.7449 (tp-100) REVERT: B 492 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.5965 (t80) outliers start: 34 outliers final: 22 residues processed: 124 average time/residue: 0.1643 time to fit residues: 27.9475 Evaluate side-chains 117 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 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 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 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 488 PHE Chi-restraints excluded: chain B residue 492 PHE 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 75 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 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 608 ASN B 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.215256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.177297 restraints weight = 7614.528| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.34 r_work: 0.3800 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 6848 Z= 0.149 Angle : 0.553 9.047 9336 Z= 0.294 Chirality : 0.041 0.157 1024 Planarity : 0.004 0.034 1130 Dihedral : 5.618 57.826 1008 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.63 % Favored : 94.25 % Rotamer: Outliers : 5.71 % Allowed : 23.00 % 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: 1.46 (0.30), residues: 782 helix: 2.02 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -2.05 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 607 HIS 0.007 0.001 HIS B 299 PHE 0.027 0.001 PHE A 394 TYR 0.016 0.002 TYR A 496 ARG 0.004 0.001 ARG B 570 Details of bonding type rmsd hydrogen bonds : bond 0.04992 ( 424) hydrogen bonds : angle 3.92073 ( 1272) SS BOND : bond 0.00204 ( 2) SS BOND : angle 1.30529 ( 4) covalent geometry : bond 0.00351 ( 6846) covalent geometry : angle 0.55282 ( 9332) *********************** 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: 40 poor density : 95 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7383 (mm-40) REVERT: A 331 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6765 (tp) REVERT: A 394 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6382 (p90) REVERT: B 394 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.5207 (p90) REVERT: B 452 GLN cc_start: 0.8481 (tp-100) cc_final: 0.7473 (tp-100) REVERT: B 492 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.5953 (t80) outliers start: 40 outliers final: 25 residues processed: 128 average time/residue: 0.1591 time to fit residues: 27.9664 Evaluate side-chains 120 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 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 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 492 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 8 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.0060 chunk 26 optimal weight: 0.8980 chunk 73 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.4397 r_free = 0.4397 target = 0.218369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.180936 restraints weight = 7609.363| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.17 r_work: 0.3857 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 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 : 0.003 0.059 6848 Z= 0.121 Angle : 0.526 9.743 9336 Z= 0.280 Chirality : 0.039 0.183 1024 Planarity : 0.003 0.034 1130 Dihedral : 5.475 57.150 1008 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.29 % Allowed : 24.71 % Favored : 71.00 % 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: 1.65 (0.31), residues: 782 helix: 2.20 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -2.10 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 528 HIS 0.003 0.001 HIS B 387 PHE 0.018 0.001 PHE A 394 TYR 0.011 0.001 TYR A 352 ARG 0.003 0.000 ARG B 548 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 424) hydrogen bonds : angle 3.85422 ( 1272) SS BOND : bond 0.00310 ( 2) SS BOND : angle 1.57788 ( 4) covalent geometry : bond 0.00273 ( 6846) covalent geometry : angle 0.52550 ( 9332) *********************** 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 127 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 331 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6722 (tp) REVERT: A 394 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.6243 (p90) REVERT: A 617 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.5912 (mm) REVERT: B 394 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.4849 (p90) REVERT: B 452 GLN cc_start: 0.8419 (tp-100) cc_final: 0.7566 (tp-100) REVERT: B 492 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.5923 (t80) REVERT: B 510 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6510 (t80) outliers start: 30 outliers final: 20 residues processed: 120 average time/residue: 0.1745 time to fit residues: 28.7162 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 : 0.736 ------------------------------------------------------------------------------- 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 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 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 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 50 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 69 optimal weight: 0.0970 chunk 39 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.216899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.178675 restraints weight = 7675.823| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.39 r_work: 0.3809 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6848 Z= 0.133 Angle : 0.539 5.579 9336 Z= 0.289 Chirality : 0.040 0.183 1024 Planarity : 0.003 0.034 1130 Dihedral : 5.519 57.136 1008 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.00 % Allowed : 23.86 % 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: 1.59 (0.31), residues: 782 helix: 2.13 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -2.08 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 514 HIS 0.004 0.001 HIS B 299 PHE 0.022 0.001 PHE A 394 TYR 0.017 0.001 TYR A 496 ARG 0.003 0.000 ARG B 570 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 424) hydrogen bonds : angle 3.90557 ( 1272) SS BOND : bond 0.00170 ( 2) SS BOND : angle 1.74630 ( 4) covalent geometry : bond 0.00305 ( 6846) covalent geometry : angle 0.53750 ( 9332) *********************** 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 128 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7315 (mm-40) REVERT: A 331 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.6856 (tp) REVERT: A 394 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6311 (p90) REVERT: A 524 TYR cc_start: 0.7569 (t80) cc_final: 0.7191 (t80) REVERT: A 617 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6040 (mm) REVERT: B 394 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.4960 (p90) REVERT: B 452 GLN cc_start: 0.8522 (tp-100) cc_final: 0.7653 (tp-100) REVERT: B 492 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.6032 (t80) REVERT: B 510 PHE cc_start: 0.6884 (OUTLIER) cc_final: 0.6545 (t80) outliers start: 35 outliers final: 25 residues processed: 122 average time/residue: 0.1734 time to fit residues: 29.3749 Evaluate side-chains 119 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 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 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 306 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.0870 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 15 optimal weight: 0.0020 chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 HIS A 608 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.218819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.178935 restraints weight = 7683.693| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.65 r_work: 0.3833 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6848 Z= 0.120 Angle : 0.526 5.355 9336 Z= 0.284 Chirality : 0.039 0.191 1024 Planarity : 0.003 0.034 1130 Dihedral : 5.430 56.898 1008 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.57 % Allowed : 24.14 % 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: 1.71 (0.31), residues: 782 helix: 2.25 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -2.11 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 528 HIS 0.003 0.001 HIS A 313 PHE 0.017 0.001 PHE A 394 TYR 0.011 0.001 TYR A 352 ARG 0.003 0.000 ARG B 548 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 424) hydrogen bonds : angle 3.86077 ( 1272) SS BOND : bond 0.00085 ( 2) SS BOND : angle 1.80720 ( 4) covalent geometry : bond 0.00269 ( 6846) covalent geometry : angle 0.52493 ( 9332) *********************** 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 125 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7228 (mm-40) REVERT: A 331 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6851 (tp) REVERT: A 394 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.6264 (p90) REVERT: A 617 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.6046 (mm) REVERT: B 394 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.4867 (p90) REVERT: B 452 GLN cc_start: 0.8476 (tp-100) cc_final: 0.7545 (tp40) REVERT: B 492 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.5990 (t80) REVERT: B 510 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.6594 (t80) outliers start: 32 outliers final: 22 residues processed: 118 average time/residue: 0.2639 time to fit residues: 43.3655 Evaluate side-chains 118 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 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 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 306 ASN 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 22 optimal weight: 0.0870 chunk 21 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.0010 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.4764 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.216352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.176011 restraints weight = 7948.537| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.68 r_work: 0.3800 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6848 Z= 0.123 Angle : 0.542 7.308 9336 Z= 0.291 Chirality : 0.040 0.196 1024 Planarity : 0.003 0.034 1130 Dihedral : 5.437 56.713 1008 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.29 % Allowed : 24.43 % 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: 1.70 (0.31), residues: 782 helix: 2.24 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -2.10 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 528 HIS 0.003 0.001 HIS A 313 PHE 0.019 0.001 PHE A 394 TYR 0.018 0.001 TYR A 496 ARG 0.006 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 424) hydrogen bonds : angle 3.86522 ( 1272) SS BOND : bond 0.00086 ( 2) SS BOND : angle 1.93403 ( 4) covalent geometry : bond 0.00279 ( 6846) covalent geometry : angle 0.54094 ( 9332) ********************** 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 126 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 1.423 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7218 (mm-40) REVERT: A 331 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.6855 (tp) REVERT: A 394 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.6305 (p90) REVERT: A 458 LEU cc_start: 0.7240 (mt) cc_final: 0.7024 (mt) REVERT: A 617 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.6035 (mm) REVERT: B 258 LYS cc_start: 0.5547 (tppt) cc_final: 0.4985 (tptm) REVERT: B 388 LYS cc_start: 0.6636 (tttm) cc_final: 0.6153 (tptp) REVERT: B 394 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.4844 (p90) REVERT: B 452 GLN cc_start: 0.8479 (tp-100) cc_final: 0.7558 (tp40) REVERT: B 492 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.6045 (t80) REVERT: B 510 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.6584 (t80) outliers start: 30 outliers final: 22 residues processed: 119 average time/residue: 0.2316 time to fit residues: 38.7615 Evaluate side-chains 121 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 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 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 306 ASN 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 50 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 42 optimal weight: 0.0020 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.4373 r_free = 0.4373 target = 0.215915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.175768 restraints weight = 7962.959| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.64 r_work: 0.3790 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6848 Z= 0.129 Angle : 0.551 7.089 9336 Z= 0.298 Chirality : 0.040 0.199 1024 Planarity : 0.003 0.034 1130 Dihedral : 5.469 56.709 1008 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.43 % Allowed : 24.57 % Favored : 71.00 % 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: 1.65 (0.31), residues: 782 helix: 2.19 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -2.09 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 607 HIS 0.004 0.001 HIS B 299 PHE 0.041 0.001 PHE B 511 TYR 0.011 0.001 TYR A 352 ARG 0.005 0.000 ARG B 548 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 424) hydrogen bonds : angle 3.88151 ( 1272) SS BOND : bond 0.00339 ( 2) SS BOND : angle 1.92027 ( 4) covalent geometry : bond 0.00294 ( 6846) covalent geometry : angle 0.54919 ( 9332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3650.64 seconds wall clock time: 64 minutes 55.45 seconds (3895.45 seconds total)