Starting phenix.real_space_refine on Wed Sep 17 07:18:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yf4_39210/09_2025/8yf4_39210.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yf4_39210/09_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_39210/09_2025/8yf4_39210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yf4_39210/09_2025/8yf4_39210.map" model { file = "/net/cci-nas-00/data/ceres_data/8yf4_39210/09_2025/8yf4_39210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yf4_39210/09_2025/8yf4_39210.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.70, per 1000 atoms: 0.26 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: 0.49 Conformation dependent library (CDL) restraints added in 384.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.18 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: 0.95 Time building geometry restraints manager: 0.66 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: 0.01 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: 1.510 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.380 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.640 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG A 371 TYR 0.015 0.001 TYR B 345 PHE 0.037 0.001 PHE A 357 TRP 0.010 0.001 TRP A 607 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6846) covalent geometry : angle 0.54618 ( 9332) SS BOND : bond 0.00450 ( 2) SS BOND : angle 2.20639 ( 4) hydrogen bonds : bond 0.12782 ( 424) hydrogen bonds : angle 5.62876 ( 1272) *********************** 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 : 0.221 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: 0.0874 time to fit residues: 11.9739 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 : 0.231 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4374 r_free = 0.4374 target = 0.215556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.175272 restraints weight = 7849.492| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.42 r_work: 0.3809 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6848 Z= 0.145 Angle : 0.534 6.411 9336 Z= 0.289 Chirality : 0.040 0.135 1024 Planarity : 0.004 0.035 1130 Dihedral : 6.230 58.654 1015 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.14 % Allowed : 23.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.30), residues: 782 helix: 1.90 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -2.04 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 548 TYR 0.017 0.002 TYR A 496 PHE 0.028 0.001 PHE A 357 TRP 0.012 0.001 TRP A 607 HIS 0.005 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6846) covalent geometry : angle 0.53405 ( 9332) SS BOND : bond 0.00068 ( 2) SS BOND : angle 0.88629 ( 4) hydrogen bonds : bond 0.05283 ( 424) hydrogen bonds : angle 4.19034 ( 1272) *********************** 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 129 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.244 Fit side-chains REVERT: A 314 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7302 (mm-40) REVERT: A 406 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7698 (mt) REVERT: B 258 LYS cc_start: 0.5872 (tppt) cc_final: 0.5456 (tptm) REVERT: B 394 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.5065 (p90) REVERT: B 408 MET cc_start: 0.7367 (mtm) cc_final: 0.7052 (mtm) REVERT: B 452 GLN cc_start: 0.8641 (tp-100) cc_final: 0.7345 (tp-100) REVERT: B 492 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.6672 (t80) outliers start: 22 outliers final: 9 residues processed: 122 average time/residue: 0.0722 time to fit residues: 11.9916 Evaluate side-chains 107 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 406 ILE 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 601 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 567 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 0.0020 chunk 40 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- 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 = 0.4358 r_free = 0.4358 target = 0.214151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.176111 restraints weight = 7814.369| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.18 r_work: 0.3808 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6848 Z= 0.137 Angle : 0.519 6.313 9336 Z= 0.279 Chirality : 0.040 0.133 1024 Planarity : 0.004 0.035 1130 Dihedral : 5.637 58.318 1008 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.37 % Favored : 94.50 % Rotamer: Outliers : 4.71 % Allowed : 22.29 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.30), residues: 782 helix: 1.93 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -2.15 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 548 TYR 0.015 0.001 TYR B 345 PHE 0.025 0.001 PHE A 394 TRP 0.010 0.001 TRP B 528 HIS 0.005 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6846) covalent geometry : angle 0.51907 ( 9332) SS BOND : bond 0.00301 ( 2) SS BOND : angle 0.72875 ( 4) hydrogen bonds : bond 0.04982 ( 424) hydrogen bonds : angle 3.96989 ( 1272) *********************** 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 140 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7266 (mm-40) REVERT: A 331 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6782 (tp) REVERT: A 508 MET cc_start: 0.5625 (pmm) cc_final: 0.5152 (ptt) REVERT: A 617 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6228 (mm) REVERT: B 258 LYS cc_start: 0.5706 (tppt) cc_final: 0.5389 (tptm) REVERT: B 331 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.6765 (tp) REVERT: B 394 PHE cc_start: 0.6696 (OUTLIER) cc_final: 0.4997 (p90) REVERT: B 492 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6147 (t80) outliers start: 33 outliers final: 17 residues processed: 136 average time/residue: 0.0723 time to fit residues: 13.3719 Evaluate side-chains 112 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 346 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 401 ASN 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 492 PHE Chi-restraints excluded: chain B residue 526 LEU 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 51 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.213454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.174981 restraints weight = 7943.776| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.44 r_work: 0.3759 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6848 Z= 0.140 Angle : 0.538 9.971 9336 Z= 0.285 Chirality : 0.040 0.133 1024 Planarity : 0.003 0.036 1130 Dihedral : 5.650 57.957 1008 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.75 % Favored : 94.12 % Rotamer: Outliers : 5.00 % Allowed : 24.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.30), residues: 782 helix: 1.96 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -2.18 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 548 TYR 0.017 0.002 TYR B 524 PHE 0.026 0.001 PHE A 394 TRP 0.010 0.001 TRP B 528 HIS 0.005 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6846) covalent geometry : angle 0.53750 ( 9332) SS BOND : bond 0.00268 ( 2) SS BOND : angle 0.97879 ( 4) hydrogen bonds : bond 0.04961 ( 424) hydrogen bonds : angle 3.94946 ( 1272) *********************** 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: 35 poor density : 100 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7268 (mm-40) REVERT: A 331 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6778 (tp) REVERT: A 394 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.6387 (p90) REVERT: B 331 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.6792 (tp) REVERT: B 394 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.5112 (p90) REVERT: B 452 GLN cc_start: 0.8529 (tp-100) cc_final: 0.7405 (tp-100) REVERT: B 492 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.5942 (t80) outliers start: 35 outliers final: 20 residues processed: 128 average time/residue: 0.0666 time to fit residues: 11.8740 Evaluate side-chains 117 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 394 PHE Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 419 LEU 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 61 optimal weight: 0.0050 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.216304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.178521 restraints weight = 7700.348| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.25 r_work: 0.3820 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 6848 Z= 0.131 Angle : 0.534 9.495 9336 Z= 0.284 Chirality : 0.039 0.133 1024 Planarity : 0.003 0.035 1130 Dihedral : 5.591 57.544 1008 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.57 % Allowed : 23.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.30), residues: 782 helix: 2.05 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -2.14 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 570 TYR 0.015 0.001 TYR B 345 PHE 0.022 0.001 PHE A 394 TRP 0.009 0.001 TRP B 528 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6846) covalent geometry : angle 0.53379 ( 9332) SS BOND : bond 0.00370 ( 2) SS BOND : angle 1.18928 ( 4) hydrogen bonds : bond 0.04701 ( 424) hydrogen bonds : angle 3.94544 ( 1272) *********************** 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 140 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7256 (mm-40) REVERT: A 331 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6848 (tp) REVERT: A 394 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6257 (p90) REVERT: A 524 TYR cc_start: 0.7502 (t80) cc_final: 0.7015 (t80) REVERT: A 617 LEU cc_start: 0.6136 (OUTLIER) cc_final: 0.5804 (mm) REVERT: B 331 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.6777 (tp) REVERT: B 394 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.4993 (p90) REVERT: B 452 GLN cc_start: 0.8456 (tp-100) cc_final: 0.7446 (tp-100) REVERT: B 492 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.5913 (t80) outliers start: 39 outliers final: 21 residues processed: 134 average time/residue: 0.0653 time to fit residues: 12.2809 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 : 0.230 ------------------------------------------------------------------------------- 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 394 PHE Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 419 LEU 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 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 486 THR Chi-restraints excluded: chain B residue 488 PHE 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 37 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 74 optimal weight: 0.0010 chunk 67 optimal weight: 4.9990 chunk 8 optimal weight: 0.0030 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.4393 r_free = 0.4393 target = 0.217843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.179386 restraints weight = 7720.887| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.41 r_work: 0.3823 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6848 Z= 0.121 Angle : 0.527 8.636 9336 Z= 0.281 Chirality : 0.039 0.146 1024 Planarity : 0.003 0.036 1130 Dihedral : 5.525 57.168 1008 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.29 % Allowed : 24.29 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.30), residues: 782 helix: 2.13 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -2.10 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 371 TYR 0.018 0.001 TYR A 496 PHE 0.019 0.001 PHE A 394 TRP 0.009 0.001 TRP B 528 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6846) covalent geometry : angle 0.52664 ( 9332) SS BOND : bond 0.00135 ( 2) SS BOND : angle 1.30416 ( 4) hydrogen bonds : bond 0.04360 ( 424) hydrogen bonds : angle 3.90364 ( 1272) *********************** 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 139 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7201 (mm-40) REVERT: A 331 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6855 (tp) REVERT: A 394 PHE cc_start: 0.7003 (OUTLIER) cc_final: 0.6193 (p90) REVERT: B 258 LYS cc_start: 0.5110 (tppt) cc_final: 0.4815 (tppt) REVERT: B 331 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.6766 (tp) REVERT: B 394 PHE cc_start: 0.6735 (OUTLIER) cc_final: 0.4943 (p90) REVERT: B 452 GLN cc_start: 0.8440 (tp-100) cc_final: 0.7540 (tp-100) REVERT: B 492 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.5878 (t80) REVERT: B 510 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.6582 (t80) outliers start: 37 outliers final: 23 residues processed: 131 average time/residue: 0.0694 time to fit residues: 12.7144 Evaluate side-chains 122 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 344 THR 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 20 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 44 optimal weight: 0.1980 chunk 55 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.4406 r_free = 0.4406 target = 0.218963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.181899 restraints weight = 7631.649| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.16 r_work: 0.3856 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6848 Z= 0.121 Angle : 0.526 8.035 9336 Z= 0.282 Chirality : 0.039 0.143 1024 Planarity : 0.003 0.035 1130 Dihedral : 5.480 56.936 1008 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.57 % Allowed : 23.71 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.31), residues: 782 helix: 2.15 (0.21), residues: 569 sheet: None (None), residues: 0 loop : -2.14 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 371 TYR 0.015 0.001 TYR B 345 PHE 0.019 0.001 PHE A 394 TRP 0.009 0.001 TRP B 528 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6846) covalent geometry : angle 0.52542 ( 9332) SS BOND : bond 0.00342 ( 2) SS BOND : angle 1.57713 ( 4) hydrogen bonds : bond 0.04260 ( 424) hydrogen bonds : angle 3.93321 ( 1272) *********************** 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 136 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7242 (mm-40) REVERT: A 331 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6843 (tp) REVERT: A 394 PHE cc_start: 0.6980 (OUTLIER) cc_final: 0.6188 (p90) REVERT: A 458 LEU cc_start: 0.7283 (mt) cc_final: 0.7059 (mt) REVERT: A 524 TYR cc_start: 0.7411 (t80) cc_final: 0.6914 (t80) REVERT: B 331 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.6791 (tp) REVERT: B 394 PHE cc_start: 0.6635 (OUTLIER) cc_final: 0.4800 (p90) REVERT: B 452 GLN cc_start: 0.8427 (tp-100) cc_final: 0.7596 (tp-100) REVERT: B 492 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.5965 (t80) REVERT: B 510 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6525 (t80) outliers start: 39 outliers final: 22 residues processed: 128 average time/residue: 0.0664 time to fit residues: 11.7055 Evaluate side-chains 120 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 394 PHE Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 419 LEU 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 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 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 Chi-restraints excluded: chain B residue 600 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 0.0670 chunk 12 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 72 optimal weight: 0.1980 chunk 63 optimal weight: 0.0670 chunk 27 optimal weight: 9.9990 chunk 17 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.1974 ------------------------------------------------------------------------------- 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 = 0.4432 r_free = 0.4432 target = 0.222138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.182856 restraints weight = 7650.927| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.38 r_work: 0.3875 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6848 Z= 0.117 Angle : 0.525 7.516 9336 Z= 0.282 Chirality : 0.040 0.223 1024 Planarity : 0.003 0.035 1130 Dihedral : 5.386 56.603 1008 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.57 % Allowed : 25.57 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.31), residues: 782 helix: 2.26 (0.21), residues: 569 sheet: None (None), residues: 0 loop : -2.11 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 371 TYR 0.020 0.001 TYR A 496 PHE 0.014 0.001 PHE A 394 TRP 0.009 0.001 TRP B 528 HIS 0.002 0.000 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6846) covalent geometry : angle 0.52400 ( 9332) SS BOND : bond 0.00027 ( 2) SS BOND : angle 1.60057 ( 4) hydrogen bonds : bond 0.03955 ( 424) hydrogen bonds : angle 3.85906 ( 1272) *********************** 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 127 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 331 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6851 (tp) REVERT: A 394 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6276 (p90) REVERT: A 524 TYR cc_start: 0.7367 (t80) cc_final: 0.6892 (t80) REVERT: A 549 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7368 (mm-30) REVERT: B 358 PHE cc_start: 0.8243 (t80) cc_final: 0.8002 (t80) REVERT: B 394 PHE cc_start: 0.6408 (OUTLIER) cc_final: 0.4596 (p90) REVERT: B 452 GLN cc_start: 0.8465 (tp-100) cc_final: 0.7675 (tp-100) REVERT: B 492 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.5914 (t80) REVERT: B 510 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6527 (t80) outliers start: 25 outliers final: 15 residues processed: 122 average time/residue: 0.0716 time to fit residues: 12.1048 Evaluate side-chains 116 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 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 B residue 335 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 463 CYS 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 44 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.216153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.178324 restraints weight = 7660.293| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.29 r_work: 0.3799 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6848 Z= 0.149 Angle : 0.575 7.204 9336 Z= 0.309 Chirality : 0.042 0.176 1024 Planarity : 0.004 0.034 1130 Dihedral : 5.566 56.382 1008 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.99 % Favored : 94.88 % Rotamer: Outliers : 4.57 % Allowed : 24.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.31), residues: 782 helix: 2.01 (0.21), residues: 570 sheet: None (None), residues: 0 loop : -2.07 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 548 TYR 0.013 0.001 TYR A 352 PHE 0.027 0.001 PHE A 394 TRP 0.012 0.001 TRP B 266 HIS 0.005 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6846) covalent geometry : angle 0.57348 ( 9332) SS BOND : bond 0.00261 ( 2) SS BOND : angle 1.86998 ( 4) hydrogen bonds : bond 0.04846 ( 424) hydrogen bonds : angle 4.03118 ( 1272) *********************** 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 129 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.178 Fit side-chains REVERT: A 331 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6802 (tp) REVERT: A 394 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.6378 (p90) REVERT: B 394 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.5048 (p90) REVERT: B 420 GLU cc_start: 0.6312 (tm-30) cc_final: 0.5746 (tt0) REVERT: B 452 GLN cc_start: 0.8558 (tp-100) cc_final: 0.7704 (tp-100) REVERT: B 492 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.6019 (t80) REVERT: B 510 PHE cc_start: 0.6914 (OUTLIER) cc_final: 0.6636 (t80) outliers start: 32 outliers final: 22 residues processed: 124 average time/residue: 0.0673 time to fit residues: 11.6210 Evaluate side-chains 122 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 331 LEU Chi-restraints excluded: chain A residue 339 ILE 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 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 B residue 335 PHE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 378 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.215443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.174413 restraints weight = 7847.962| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.76 r_work: 0.3788 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1960 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= 0.133 Angle : 0.570 7.943 9336 Z= 0.307 Chirality : 0.041 0.180 1024 Planarity : 0.003 0.034 1130 Dihedral : 5.493 56.910 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 : 4.00 % Allowed : 24.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.31), residues: 782 helix: 2.06 (0.21), residues: 570 sheet: None (None), residues: 0 loop : -2.09 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 548 TYR 0.018 0.001 TYR A 496 PHE 0.020 0.001 PHE A 394 TRP 0.009 0.001 TRP B 266 HIS 0.004 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6846) covalent geometry : angle 0.56836 ( 9332) SS BOND : bond 0.00344 ( 2) SS BOND : angle 2.01194 ( 4) hydrogen bonds : bond 0.04552 ( 424) hydrogen bonds : angle 3.99081 ( 1272) ********************** 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 124 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 272 TYR cc_start: 0.8346 (m-80) cc_final: 0.8043 (m-80) REVERT: A 331 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6895 (tp) REVERT: A 394 PHE cc_start: 0.7224 (OUTLIER) cc_final: 0.6273 (p90) REVERT: A 458 LEU cc_start: 0.7272 (mt) cc_final: 0.7054 (mt) REVERT: B 394 PHE cc_start: 0.6664 (OUTLIER) cc_final: 0.4839 (p90) REVERT: B 420 GLU cc_start: 0.6126 (tm-30) cc_final: 0.5634 (tt0) REVERT: B 452 GLN cc_start: 0.8483 (tp-100) cc_final: 0.7679 (tp-100) REVERT: B 492 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.6063 (t80) REVERT: B 510 PHE cc_start: 0.6970 (OUTLIER) cc_final: 0.6629 (t80) outliers start: 28 outliers final: 22 residues processed: 119 average time/residue: 0.0711 time to fit residues: 11.7420 Evaluate side-chains 122 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 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 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 B residue 335 PHE Chi-restraints excluded: chain B residue 378 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 0.0980 chunk 43 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 0.0010 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.217947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.180470 restraints weight = 7880.383| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.22 r_work: 0.3829 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6848 Z= 0.123 Angle : 0.555 8.966 9336 Z= 0.300 Chirality : 0.040 0.185 1024 Planarity : 0.003 0.034 1130 Dihedral : 5.411 56.528 1008 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.31), residues: 782 helix: 2.23 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -2.12 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 548 TYR 0.010 0.001 TYR A 352 PHE 0.017 0.001 PHE A 394 TRP 0.010 0.001 TRP B 528 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6846) covalent geometry : angle 0.55351 ( 9332) SS BOND : bond 0.00150 ( 2) SS BOND : angle 1.94715 ( 4) hydrogen bonds : bond 0.04181 ( 424) hydrogen bonds : angle 3.92572 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1534.47 seconds wall clock time: 27 minutes 0.48 seconds (1620.48 seconds total)